From ca1325504dd747ff895e54758518dd832dc056cb Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Fri, 28 Jul 2023 11:59:48 +0200 Subject: [PATCH 01/18] Fix `path` wrongly converted to lower case --- chemex/configuration/base.py | 4 +--- chemex/configuration/experiment.py | 7 ++++++- chemex/configuration/methods.py | 3 ++- 3 files changed, 9 insertions(+), 5 deletions(-) diff --git a/chemex/configuration/base.py b/chemex/configuration/base.py index f9b9c58f..784fb488 100644 --- a/chemex/configuration/base.py +++ b/chemex/configuration/base.py @@ -2,7 +2,7 @@ from typing import Any -from pydantic import BaseModel, ConfigDict, model_validator +from pydantic import BaseModel, model_validator def ensure_list(variable: Any | list[Any] | None) -> list[Any]: @@ -20,8 +20,6 @@ def to_lower(string: Any) -> Any: class BaseModelLowerCase(BaseModel): - model_config = ConfigDict(str_to_lower=True) - @model_validator(mode="before") def key_to_lower(cls, model: dict[str, Any]) -> dict[str, Any]: return {to_lower(k): v for k, v in model.items()} diff --git a/chemex/configuration/experiment.py b/chemex/configuration/experiment.py index 01c74b81..f96e8e23 100644 --- a/chemex/configuration/experiment.py +++ b/chemex/configuration/experiment.py @@ -4,7 +4,7 @@ from typing import Generic, TypeVar import numpy as np -from pydantic import BaseModel +from pydantic import BaseModel, ConfigDict from chemex.configuration.base import BaseModelLowerCase from chemex.configuration.conditions import ConditionsFromFile @@ -17,14 +17,17 @@ class ToBeFitted: class ExperimentNameSettings(BaseModelLowerCase): + model_config = ConfigDict(str_to_lower=True) name: str class RelaxationSettings(BaseModelLowerCase): + model_config = ConfigDict(str_to_lower=True) name: str class CpmgSettings(BaseModelLowerCase): + model_config = ConfigDict(str_to_lower=True) name: str even_ncycs: bool = False @@ -34,11 +37,13 @@ class CpmgSettingsEvenNcycs(CpmgSettings): class CestSettings(BaseModelLowerCase): + model_config = ConfigDict(str_to_lower=True) name: str sw: float = np.inf class ShiftSettings(BaseModelLowerCase): + model_config = ConfigDict(str_to_lower=True) name: str diff --git a/chemex/configuration/methods.py b/chemex/configuration/methods.py index 9ed10c6f..5bd35d48 100644 --- a/chemex/configuration/methods.py +++ b/chemex/configuration/methods.py @@ -4,7 +4,7 @@ from dataclasses import dataclass from typing import TYPE_CHECKING, Annotated, Literal -from pydantic import BeforeValidator, Field, ValidationError +from pydantic import BeforeValidator, ConfigDict, Field, ValidationError from pydantic.types import PositiveInt from chemex.configuration.base import BaseModelLowerCase @@ -35,6 +35,7 @@ class Selection: class Method(BaseModelLowerCase): + model_config = ConfigDict(str_to_lower=True) fitmethod: str = "leastsq" include: SelectionType = None exclude: SelectionType = None From 8c887379e04f0384d6702c510385f90ec42bac9e Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Fri, 28 Jul 2023 12:00:09 +0200 Subject: [PATCH 02/18] Bump package versions --- pdm.lock | 235 +++++++++++++++++++++++++++++++++---------------- pyproject.toml | 22 ++--- 2 files changed, 170 insertions(+), 87 deletions(-) diff --git a/pdm.lock b/pdm.lock index d6669005..e2863194 100644 --- a/pdm.lock +++ b/pdm.lock @@ -2,11 +2,11 @@ # It is not intended for manual editing. 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"Pygments is a syntax highlighting package written in Python." files = [ - {file = "Pygments-2.15.1-py3-none-any.whl", hash = "sha256:db2db3deb4b4179f399a09054b023b6a586b76499d36965813c71aa8ed7b5fd1"}, - {file = "Pygments-2.15.1.tar.gz", hash = "sha256:8ace4d3c1dd481894b2005f560ead0f9f19ee64fe983366be1a21e171d12775c"}, + {file = "Pygments-2.16.1-py3-none-any.whl", hash = "sha256:13fc09fa63bc8d8671a6d247e1eb303c4b343eaee81d861f3404db2935653692"}, + {file = "Pygments-2.16.1.tar.gz", hash = "sha256:1daff0494820c69bc8941e407aa20f577374ee88364ee10a98fdbe0aece96e29"}, ] [[package]] @@ -527,6 +590,24 @@ files = [ {file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"}, ] +[[package]] +name = "pytest" +version = "7.4.0" +requires_python = ">=3.7" +summary = "pytest: simple powerful testing with Python" +dependencies = [ + "colorama; sys_platform == \"win32\"", + "exceptiongroup>=1.0.0rc8; python_version < \"3.11\"", + "iniconfig", + "packaging", + "pluggy<2.0,>=0.12", + "tomli>=1.0.0; python_version < \"3.11\"", +] +files = [ + {file = "pytest-7.4.0-py3-none-any.whl", hash = "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32"}, + {file = "pytest-7.4.0.tar.gz", hash = "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"}, +] + [[package]] name = "python-dateutil" version = "2.8.2" diff --git a/pyproject.toml b/pyproject.toml index ba7f45bd..e550fbfe 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,15 +7,16 @@ description = "An analysis program for chemical exchange detected by NMR" authors = [ { name = "Guillaume Bouvignies", email = "guillaume.bouvignies@ens.psl.eu" } ] dependencies = [ - "numpy>=1.25.0", - "scipy>=1.9.3", - "matplotlib>=3.7.1", - "lmfit>=1.2.1", - "pydantic>=2.0.1", - "cachetools>=5.3.1", - "rich>=13.4.2", - "tomli>=2.0.1", - "rapidfuzz>=3.1.1", + "numpy>=1.25.0", + "scipy>=1.9.3", + "matplotlib>=3.7.1", + "lmfit>=1.2.1", + "pydantic>=2.0.1", + "cachetools>=5.3.1", + "rich>=13.4.2", + "tomli>=2.0.1", + "rapidfuzz>=3.1.1", + "emcee>=3.1.4", ] requires-python = ">=3.10" readme = "README.md" @@ -35,7 +36,8 @@ source = "scm" [tool.pdm.dev-dependencies] - linting = [ "black>=23.3.0", "ruff>=0.0.277" ] + test = [ "pytest>=7.4.0" ] + lint = [ "black>=23.7.0", "ruff>=0.0.278" ] [tool.black] target-version = [ "py310" ] From d6de214869181e645d80268a3f5d4bf209448e52 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Fri, 28 Jul 2023 13:34:14 +0200 Subject: [PATCH 03/18] Add the "4st_binding_partner_2st" model --- chemex/models/kinetic/settings_2st_binding.py | 48 ++-- .../settings_4st_binding_2st_partner.py | 208 ++++++++++++++++++ 2 files changed, 243 insertions(+), 13 deletions(-) create mode 100644 chemex/models/kinetic/settings_4st_binding_2st_partner.py diff --git a/chemex/models/kinetic/settings_2st_binding.py b/chemex/models/kinetic/settings_2st_binding.py index a649c4e6..cdf43b76 100644 --- a/chemex/models/kinetic/settings_2st_binding.py +++ b/chemex/models/kinetic/settings_2st_binding.py @@ -4,26 +4,43 @@ from typing import TYPE_CHECKING import numpy as np +from scipy.optimize import root -from chemex.models.constraints import pop_2st from chemex.models.factory import model_factory from chemex.parameters.setting import NameSetting, ParamLocalSetting from chemex.parameters.userfunctions import user_function_registry if TYPE_CHECKING: from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat NAME = "2st_binding" TPL = ("temperature", "p_total", "l_total") +def calculate_residuals( + concentrations: ArrayFloat, p_total: float, l_total: float, kd: float +) -> ArrayFloat: + p_free, l_free, pl = concentrations + return np.array( + [ + l_total - l_free - pl, + p_total - p_free - pl, + kd * pl - p_free * l_free, + ] + ) + + @lru_cache(maxsize=100) -def calculate_l_free_2st_binding(kd: float, p_total: float, l_total: float) -> float: - coefficients = (p_total * l_total, -(l_total + p_total + kd), 1.0) - polynomial = np.polynomial.polynomial.Polynomial(coefficients) - p_bound = min(polynomial.roots()) - return l_total - p_bound +def calculate_concentrations( + p_total: float, l_total: float, kd: float +) -> dict[str, float]: + concentrations_start = (p_total, l_total, 0.0) + results = root( + calculate_residuals, concentrations_start, args=(p_total, l_total, kd) + ) + return dict(zip(("p_free", "l_free", "pl"), results["x"], strict=True)) def make_settings_2st_binding(conditions: Conditions) -> dict[str, ParamLocalSetting]: @@ -49,9 +66,17 @@ def make_settings_2st_binding(conditions: Conditions) -> dict[str, ParamLocalSet name_setting=NameSetting("kon", "", ("temperature",)), expr="{koff} / max({kd}, 1e-100)", ), + "p_free": ParamLocalSetting( + name_setting=NameSetting("p_free", "", TPL), + expr=f"calc_conc({p_total}, {l_total}, {{kd}})['p_free']", + ), "l_free": ParamLocalSetting( name_setting=NameSetting("l_free", "", TPL), - expr=f"l_free_2st({{kd}}, {p_total}, {l_total})", + expr=f"calc_conc({p_total}, {l_total}, {{kd}})['l_free']", + ), + "pl": ParamLocalSetting( + name_setting=NameSetting("pl", "", TPL), + expr=f"calc_conc({p_total}, {l_total}, {{kd}})['pl']", ), "kab": ParamLocalSetting( name_setting=NameSetting("kab", "", TPL), @@ -63,19 +88,16 @@ def make_settings_2st_binding(conditions: Conditions) -> dict[str, ParamLocalSet ), "pa": ParamLocalSetting( name_setting=NameSetting("pa", "", TPL), - expr="pop_2st({kab}, {kba})['pa']", + expr=f"{{p_free}} / {p_total}", ), "pb": ParamLocalSetting( name_setting=NameSetting("pb", "", TPL), - expr="pop_2st({kab}, {kba})['pb']", + expr=f"{{pl}} / {p_total}", ), } def register() -> None: model_factory.register(name=NAME, setting_maker=make_settings_2st_binding) - user_functions = { - "l_free_2st": calculate_l_free_2st_binding, - "pop_2st": pop_2st, - } + user_functions = {"calc_conc": calculate_concentrations} user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_4st_binding_2st_partner.py b/chemex/models/kinetic/settings_4st_binding_2st_partner.py new file mode 100644 index 00000000..f617aafe --- /dev/null +++ b/chemex/models/kinetic/settings_4st_binding_2st_partner.py @@ -0,0 +1,208 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat + + +NAME = "4st_binding_partner_2st" + +TPL = ("temperature", "p_total", "l_total") + + +def calculate_residuals( + concentrations: ArrayFloat, + p_total: float, + l_total: float, + kd1: float, + kd2: float, + keq_l: float, + keq_pl: float, +) -> ArrayFloat: + p, l1, l2, pl1, pl2, pl3 = concentrations + return np.array( + [ + l_total - (l1 + l2 + pl1 + pl2 + pl3), + p_total - (p + pl1 + pl2 + pl3), + kd1 * pl1 - p * l1, + kd2 * pl2 - p * l2, + keq_l * l1 - l2, + keq_pl * pl2 - pl3, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_concentrations( + p_total: float, l_total: float, kd1: float, kd2: float, keq_l: float, keq_pl: float +) -> dict[str, float]: + concentrations_start = (p_total, l_total / 2, l_total / 2, 0.0, 0.0, 0.0) + results = root( + calculate_residuals, + concentrations_start, + args=(p_total, l_total, kd1, kd2, keq_l, keq_pl), + ) + return dict(zip(("p", "l1", "l2", "pl1", "pl2", "pl3"), results["x"], strict=True)) + + +def make_settings_4st_binding_partner_2st( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p_total = conditions.p_total + l_total = conditions.l_total + if p_total is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + if l_total is None: + msg = f"'l_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "koff_ab": ParamLocalSetting( + name_setting=NameSetting("koff_ab", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kd_ab": ParamLocalSetting( + name_setting=NameSetting("kd_ab", "", ("temperature",)), + value=1e-3, + min=0.0, + vary=True, + ), + "koff_ac": ParamLocalSetting( + name_setting=NameSetting("koff_ac", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kd_ac": ParamLocalSetting( + name_setting=NameSetting("kd_ac", "", ("temperature",)), + value=1e-3, + min=0.0, + vary=True, + ), + "keq_l": ParamLocalSetting( + name_setting=NameSetting("keq_l", "", ("temperature",)), + value=1.0, + min=0.0, + vary=True, + ), + "keq_pl": ParamLocalSetting( + name_setting=NameSetting("keq_pl", "", ("temperature",)), + value=1.0, + min=0.0, + vary=True, + ), + "kex_bc": ParamLocalSetting( + name_setting=NameSetting("kex_bc", "", ("temperature",)), + value=1e3, + min=0.0, + vary=True, + ), + "kex_cd": ParamLocalSetting( + name_setting=NameSetting("kex_cd", "", ("temperature",)), + value=1e3, + min=0.0, + vary=True, + ), + "kon_ab": ParamLocalSetting( + name_setting=NameSetting("kon_ab", "", ("temperature",)), + expr="{koff_ab} / max({kd_ab}, 1e-100)", + ), + "kon_ac": ParamLocalSetting( + name_setting=NameSetting("kon_ac", "", ("temperature",)), + expr="{koff_ac} / max({kd_ac}, 1e-100)", + ), + "p_free": ParamLocalSetting( + name_setting=NameSetting("p_free", "", TPL), + expr=f"calc_conc({p_total},{l_total},{{kd_ab}},{{kd_ac}},{{keq_l}},{{keq_pl}})['p']", + ), + "l1_free": ParamLocalSetting( + name_setting=NameSetting("l1_free", "", TPL), + expr=f"calc_conc({p_total},{l_total},{{kd_ab}},{{kd_ac}},{{keq_l}},{{keq_pl}})['l1']", + ), + "l2_free": ParamLocalSetting( + name_setting=NameSetting("l1_free", "", TPL), + expr=f"calc_conc({p_total},{l_total},{{kd_ab}},{{kd_ac}},{{keq_l}},{{keq_pl}})['l2']", + ), + "pl1": ParamLocalSetting( + name_setting=NameSetting("pl1", "", TPL), + expr=f"calc_conc({p_total},{l_total},{{kd_ab}},{{kd_ac}},{{keq_l}},{{keq_pl}})['pl1']", + ), + "pl2": ParamLocalSetting( + name_setting=NameSetting("pl2", "", TPL), + expr=f"calc_conc({p_total},{l_total},{{kd_ab}},{{kd_ac}},{{keq_l}},{{keq_pl}})['pl2']", + ), + "pl3": ParamLocalSetting( + name_setting=NameSetting("pl3", "", TPL), + expr=f"calc_conc({p_total},{l_total},{{kd_ab}},{{kd_ac}},{{keq_l}},{{keq_pl}})['pl3']", + ), + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", TPL), + expr="{kon_ab} * {l1_free}", + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", TPL), + expr="{koff_ab}", + ), + "kac": ParamLocalSetting( + name_setting=NameSetting("kac", "", TPL), + expr="{kon_ac} * {l2_free}", + ), + "kca": ParamLocalSetting( + name_setting=NameSetting("kca", "", TPL), + expr="{koff_ac}", + ), + "kbc": ParamLocalSetting( + name_setting=NameSetting("kbc", "", TPL), + expr="{kex_bc} * {pl2} / max({pl1} + {pl2}, 1e-100)", + ), + "kcb": ParamLocalSetting( + name_setting=NameSetting("kcb", "", TPL), + expr="{kex_bc} * {pl1} / max({pl1} + {pl2}, 1e-100)", + ), + "kcd": ParamLocalSetting( + name_setting=NameSetting("kcd", "", TPL), + expr="{kex_cd} * {pl3} / max({pl2} + {pl3}, 1e-100)", + ), + "kdc": ParamLocalSetting( + name_setting=NameSetting("kdc", "", TPL), + expr="{kex_cd} * {pl2} / max({pl2} + {pl3}, 1e-100)", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TPL), + expr=f"{{p_free}} / {p_total}", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TPL), + expr=f"{{pl1}} / {p_total}", + ), + "pc": ParamLocalSetting( + name_setting=NameSetting("pc", "", TPL), + expr=f"{{pl2}} / {p_total}", + ), + "pd": ParamLocalSetting( + name_setting=NameSetting("pc", "", TPL), + expr=f"{{pl3}} / {p_total}", + ), + } + + +def register() -> None: + model_factory.register( + name=NAME, setting_maker=make_settings_4st_binding_partner_2st + ) + user_functions = { + "calc_conc": calculate_concentrations, + } + user_function_registry.register(name=NAME, user_functions=user_functions) From 2aa49628ac991229160c0a74a823e0366ab18c63 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Sat, 5 Aug 2023 01:30:27 +0200 Subject: [PATCH 04/18] Add 3st_binding_offpathway model --- .../settings_3st_binding_offpathway.py | 130 ++++++++++++++++++ 1 file changed, 130 insertions(+) create mode 100644 chemex/models/kinetic/settings_3st_binding_offpathway.py diff --git a/chemex/models/kinetic/settings_3st_binding_offpathway.py b/chemex/models/kinetic/settings_3st_binding_offpathway.py new file mode 100644 index 00000000..3600fb14 --- /dev/null +++ b/chemex/models/kinetic/settings_3st_binding_offpathway.py @@ -0,0 +1,130 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.constraints import pop_3st +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + +NAME = "3st_binding_offpathway" + +TPL = ("temperature", "p_total", "l_total") + + +def calculate_residuals( + populations: np.ndarray, + p_total: float, + l_total: float, + kd_ab: float, + kac: float, + kca: float, +) -> np.ndarray: + pfree_a, pfree_c, pl_b = populations + lfree = l_total - pl_b + return np.array( + [ + pfree_a + pfree_c + pl_b - p_total, + lfree * pfree_a - kd_ab * pl_b, + kac * pfree_a - kca * pfree_c, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_lfree( + p_total: float, l_total: float, kd_ab: float, kac: float, kca: float +) -> float: + concentrations_start = (p_total, 0.0, 0.0) + results = root( + calculate_residuals, + concentrations_start, + args=(p_total, l_total, kd_ab, kac, kca), + ) + _pfree_a, _pfree_c, pl_b = results["x"] + return l_total - pl_b + + +def make_settings_3st_binding_offpathway( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p_total = conditions.p_total + l_total = conditions.l_total + if p_total is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + if l_total is None: + msg = f"'l_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "koff_ab": ParamLocalSetting( + name_setting=NameSetting("koff_ab", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kd_ab": ParamLocalSetting( + name_setting=NameSetting("kd_ab", "", ("temperature",)), + value=1e-3, + min=0.0, + vary=True, + ), + "kac": ParamLocalSetting( + name_setting=NameSetting("kac", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kca": ParamLocalSetting( + name_setting=NameSetting("kca", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kon_ab": ParamLocalSetting( + name_setting=NameSetting("kon_ab", "", ("temperature",)), + expr="{koff_ab} / max({kd_ab}, 1e-100)", + ), + "l_free": ParamLocalSetting( + name_setting=NameSetting("l_free", "", TPL), + expr=f"calculate_lfree({p_total}, {l_total}, {{kd_ab}}, {{kac}}, {{kca}})", + ), + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", TPL), + expr="{kon_ab} * {l_free}", + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", TPL), + expr="{koff_ab}", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TPL), + expr="pop_3st({kab}, {kba}, {kac}, {kca}, 0.0, 0.0)['pa']", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TPL), + expr="pop_3st({kab}, {kba}, {kac}, {kca}, 0.0, 0.0)['pb']", + ), + "pc": ParamLocalSetting( + name_setting=NameSetting("pc", "", TPL), + expr="pop_3st({kab}, {kba}, {kac}, {kca}, 0.0, 0.0)['pc']", + ), + } + + +def register() -> None: + model_factory.register( + name=NAME, setting_maker=make_settings_3st_binding_offpathway + ) + user_functions = { + "calculate_lfree": calculate_lfree, + "pop_3st": pop_3st, + } + user_function_registry.register(name=NAME, user_functions=user_functions) From efbf312799e95fc3c5dd2e02497eda6bc2feb0da Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Sat, 5 Aug 2023 01:45:08 +0200 Subject: [PATCH 05/18] WIP --- chemex/containers/data.py | 2 + chemex/models/constraints.py | 38 ++++++--- chemex/models/kinetic/settings_2st_binding.py | 3 +- chemex/models/kinetic/settings_3st_eyring.py | 4 +- chemex/optimize/fitting.py | 8 +- chemex/optimize/grouping.py | 55 +++++++++++- chemex/optimize/minimizer.py | 84 ++++++++++++++++--- 7 files changed, 166 insertions(+), 28 deletions(-) diff --git a/chemex/containers/data.py b/chemex/containers/data.py index 7226d203..fe4a2f30 100644 --- a/chemex/containers/data.py +++ b/chemex/containers/data.py @@ -15,6 +15,8 @@ def get_scale(exp: ArrayFloat, err: ArrayFloat, calc: ArrayFloat) -> float: + if (calc == 0).all(): + return 1.0 try: calc_err2 = calc / err**2 return sum(exp * calc_err2) / sum(calc * calc_err2) diff --git a/chemex/models/constraints.py b/chemex/models/constraints.py index 0182f1d2..3a9f5745 100644 --- a/chemex/models/constraints.py +++ b/chemex/models/constraints.py @@ -8,10 +8,20 @@ @lru_cache(maxsize=100) def pop_2st(kab: float = 0.0, kba: float = 0.0) -> dict[str, float]: + if np.isclose(kab, 0.0): + return {"pa": 1.0, "pb": 0.0} + + if np.isclose(kba, 0.0): + return {"pa": 0.0, "pb": 1.0} + mat = np.array([[kab, -kba], [1.0, 1.0]]) + + if np.isclose(np.linalg.det(mat), 0.0): + return {"pa": 1.0, "pb": 0.0} + vec = np.array([0.0, 1.0]) res = linalg.solve(mat, vec) - return dict(zip(("pa", "pb"), res, strict=True)) + return {"pa": res[0], "pb": res[1]} @lru_cache(maxsize=100) @@ -23,15 +33,15 @@ def pop_3st( kbc: float = 0.0, kcb: float = 0.0, ) -> dict[str, float]: - if all(np.isclose([kab + kba, kac + kca], [0.0, 0.0])): + if np.isclose(kab + kba + kac + kca, 0.0): pb, pc = pop_2st(kbc, kcb).values() return {"pa": 0.0, "pb": pb, "pc": pc} - if all(np.isclose([kab + kba, kbc + kcb], [0.0, 0.0])): + if np.isclose(kab + kba + kbc + kcb, 0.0): pa, pc = pop_2st(kac, kca).values() return {"pa": pa, "pb": 0.0, "pc": pc} - if all(np.isclose([kac + kca, kbc + kcb], [0.0, 0.0])): + if np.isclose(kac + kca + kbc + kcb, 0.0): pa, pb = pop_2st(kab, kba).values() return {"pa": pa, "pb": pb, "pc": 0.0} @@ -42,10 +52,14 @@ def pop_3st( [1.0, 1.0, 1.0], ] ) + + if np.isclose(np.linalg.det(mat), 0.0): + return {"pa": 1.0, "pb": 0.0, "pc": 0.0} + vec = np.array([0.0, 0.0, 1.0]) res = linalg.solve(mat, vec) - return dict(zip(("pa", "pb", "pc"), res, strict=True)) + return {"pa": res[0], "pb": res[1], "pc": res[2]} @lru_cache(maxsize=100) @@ -63,19 +77,19 @@ def pop_4st( kcd: float = 0.0, kdc: float = 0.0, ) -> dict[str, float]: - if all(np.isclose([kab + kba, kac + kca, kad + kda], [0.0, 0.0, 0.0])): + if np.isclose(kab + kba + kac + kca + kad + kda, 0.0): pb, pc, pd = pop_3st(kbc, kcb, kbd, kdb, kcd, kdc).values() return {"pa": 0.0, "pb": pb, "pc": pc, "pd": pd} - if all(np.isclose([kab + kba, kbc + kcb, kbd + kdb], [0.0, 0.0, 0.0])): + if np.isclose(kab + kba + kbc + kcb + kbd + kdb, 0.0): pa, pc, pd = pop_3st(kac, kca, kad, kda, kcd, kdc).values() return {"pa": pa, "pb": 0.0, "pc": pc, "pd": pd} - if all(np.isclose([kac + kca, kbc + kcb, kcd + kdc], [0.0, 0.0, 0.0])): + if np.isclose(kac + kca + kbc + kcb + kcd + kdc, 0.0): pa, pb, pd = pop_3st(kab, kba, kad, kda, kbd, kdb).values() return {"pa": pa, "pb": pb, "pc": 0.0, "pd": pd} - if all(np.isclose([kad + kda, kbd + kdb, kcd + kdc], [0.0, 0.0, 0.0])): + if np.isclose(kad + kda + kbd + kdb + kcd + kdc, 0.0): pa, pb, pc = pop_3st(kab, kba, kac, kca, kbc, kcb).values() return {"pa": pa, "pb": pb, "pc": pc, "pd": 0.0} @@ -87,7 +101,11 @@ def pop_4st( [1.0, 1.0, 1.0, 1.0], ] ) + + if np.isclose(np.linalg.det(mat), 0.0): + return {"pa": 1.0, "pb": 0.0, "pc": 0.0, "pd": 0.0} + vec = np.array([0.0, 0.0, 0.0, 1.0]) res = linalg.solve(mat, vec) - return dict(zip(("pa", "pb", "pc", "pd"), res, strict=True)) + return {"pa": res[0], "pb": res[1], "pc": res[2], "pd": res[3]} diff --git a/chemex/models/kinetic/settings_2st_binding.py b/chemex/models/kinetic/settings_2st_binding.py index cdf43b76..fc94fda2 100644 --- a/chemex/models/kinetic/settings_2st_binding.py +++ b/chemex/models/kinetic/settings_2st_binding.py @@ -40,7 +40,8 @@ def calculate_concentrations( results = root( calculate_residuals, concentrations_start, args=(p_total, l_total, kd) ) - return dict(zip(("p_free", "l_free", "pl"), results["x"], strict=True)) + p_free, l_free, pl = results["x"] + return {"p_free": p_free, "l_free": l_free, "pl": pl} def make_settings_2st_binding(conditions: Conditions) -> dict[str, ParamLocalSetting]: diff --git a/chemex/models/kinetic/settings_3st_eyring.py b/chemex/models/kinetic/settings_3st_eyring.py index e99bee2d..eef2278e 100644 --- a/chemex/models/kinetic/settings_3st_eyring.py +++ b/chemex/models/kinetic/settings_3st_eyring.py @@ -11,6 +11,7 @@ from chemex.models.factory import model_factory from chemex.parameters.setting import NameSetting, ParamLocalSetting from chemex.parameters.userfunctions import user_function_registry +from chemex.typing import ArrayFloat if TYPE_CHECKING: from chemex.configuration.conditions import Conditions @@ -49,7 +50,8 @@ def calculate_kij_3st_eyring( dh_bc - dh_c - kelvin * (ds_bc - ds_c), ) ) - kij_values = kbt_h * np.exp(-ddg_ij / rt) + kij_values: ArrayFloat = kbt_h * np.exp(-ddg_ij / rt) + kij_values = np.clip(kij_values, 0.0, 1e16) kij_names = (f"k{i}{j}" for i, j in permutations("abc", 2)) return dict(zip(kij_names, kij_values, strict=True)) diff --git a/chemex/optimize/fitting.py b/chemex/optimize/fitting.py index 0ce61123..27ad6873 100644 --- a/chemex/optimize/fitting.py +++ b/chemex/optimize/fitting.py @@ -26,7 +26,10 @@ print_header, print_values_stat, ) -from chemex.optimize.minimizer import minimize, minimize_with_report +from chemex.optimize.minimizer import ( + minimize, + minimize_with_report, +) from chemex.parameters import database if TYPE_CHECKING: @@ -103,6 +106,9 @@ def _fit_groups( best_lmfit_params = minimize_with_report( group.experiments, group_lmfit_params, fitmethod ) + # best_lmfit_params = minimize_hierarchical( + # group.experiments, group_lmfit_params, fitmethod + # ) database.update_from_parameters(best_lmfit_params) execute_post_fit(group.experiments, group_path, plot_flg) diff --git a/chemex/optimize/grouping.py b/chemex/optimize/grouping.py index 5566609c..2a7af9ab 100644 --- a/chemex/optimize/grouping.py +++ b/chemex/optimize/grouping.py @@ -8,10 +8,11 @@ from typing import TYPE_CHECKING from chemex.parameters import database +from chemex.parameters.name import ParamName +from chemex.parameters.setting import Parameters if TYPE_CHECKING: from chemex.containers.experiments import Experiments - from chemex.parameters.name import ParamName @dataclass @@ -22,13 +23,18 @@ class Group: def ids_to_param_name(param_ids: set[str]) -> ParamName: + if not param_ids: + return ParamName() parameters = database.get_parameters(param_ids) param_names = (parameter.param_name for parameter in parameters.values()) return reduce(and_, param_names) -def group_ids(experiments: Experiments) -> list[tuple[ParamName, set[str]]]: - parameters = database.get_parameters(experiments.param_ids) +def group_ids( + experiments: Experiments, parameters: Parameters | None = None +) -> list[tuple[ParamName, set[str]]]: + if parameters is None: + parameters = database.get_parameters(experiments.param_ids) ids_vary: set[str] = { param_id @@ -93,3 +99,46 @@ def create_groups(experiments: Experiments) -> list[Group]: groups.append(Group(group_path, group_message, group_experiments)) return groups + + +@dataclass +class ParamTree: + ids_to_fit: set[str] + experiments: Experiments + branches: list[ParamTree] + + +def create_group_tree( + experiments: Experiments, parameters: Parameters | None = None +) -> ParamTree: + if parameters is None: + parameters = database.get_parameters(experiments.param_ids) + + ids_vary: set[str] = { + param_id + for param_id, param in parameters.items() + if param.vary and not param.expr + } + + ids_global = { + param_id + for param_id in ids_vary + if len(experiments.get_relevant_subset({param_id})) == len(experiments) + } + + for param_id in ids_global: + parameters[param_id].vary = False + + id_groups = group_ids(experiments, parameters) + + branches: list[ParamTree] = [] + + if len(id_groups) > 1: + for _, ids in id_groups: + sub_experiments = experiments.get_relevant_subset(ids) + branches.append(create_group_tree(sub_experiments)) + + for param_id in ids_global: + parameters[param_id].vary = True + + return ParamTree(ids_to_fit=ids_global, experiments=experiments, branches=branches) diff --git a/chemex/optimize/minimizer.py b/chemex/optimize/minimizer.py index e19d2426..960100ca 100644 --- a/chemex/optimize/minimizer.py +++ b/chemex/optimize/minimizer.py @@ -4,6 +4,8 @@ from dataclasses import dataclass from typing import TYPE_CHECKING +import lmfit +import numpy as np from lmfit import Minimizer, Parameters from chemex.messages import ( @@ -13,6 +15,7 @@ print_chi2_table_line, print_value_error, ) +from chemex.optimize.grouping import ParamTree, create_group_tree if TYPE_CHECKING: from chemex.containers.experiments import Experiments @@ -25,7 +28,12 @@ class Reporter: threshold: float = -1.0e-3 def iter_cb( - self, params: Parameters, iteration: int, residuals: ArrayFloat + self, + params: Parameters, + iteration: int, + residuals: ArrayFloat, + *_args, + **_kwargs, ) -> None: chisqr = (residuals**2).sum() change = (chisqr - self.last_chisqr) / self.last_chisqr @@ -54,11 +62,8 @@ def print_footer(self, iteration: int, chisqr: float, redchi: float) -> None: def minimize( - experiments: Experiments, params: Parameters, fitmethod: str | None = None + experiments: Experiments, params: Parameters, fitmethod: str ) -> Parameters: - if fitmethod is None: - fitmethod = "leastsq" - kws = { "brute": {"keep": "all"}, "basinhopping": {"niter_success": 10}, @@ -70,14 +75,13 @@ def minimize( def minimize_with_report( - experiments: Experiments, params: Parameters, fitmethod: str | None = None + experiments: Experiments, params: Parameters, fitmethod: str ) -> Parameters: - if fitmethod is None: - fitmethod = "leastsq" - kws = { "brute": {"keep": "all"}, "basinhopping": {"niter_success": 10}, + "differential_evolution": {"polish": True, "disp": True, "init": "sobol"}, + "ampgo": {"disp": True}, } reporter = Reporter() @@ -87,10 +91,66 @@ def minimize_with_report( reporter.print_header() try: - minimizer.minimize(method=fitmethod, **(kws.get(fitmethod, {}))) - reporter.print_footer( - minimizer.result.nfev, minimizer.result.chisqr, minimizer.result.redchi + result = minimizer.minimize(method=fitmethod, **(kws.get(fitmethod, {}))) + reporter.print_footer(result.nfev, result.chisqr, result.redchi) + except KeyboardInterrupt: + print_calculation_stopped_error() + except ValueError: + print_value_error() + + return deepcopy(minimizer.result.params) + + +def residuals_hierarchical(params: Parameters, param_tree: ParamTree) -> ArrayFloat: + # print(param_tree.ids_to_fit) + if not param_tree.branches: + return param_tree.experiments.residuals(params) + + for param_id in param_tree.ids_to_fit: + params[param_id].vary = False + + residuals_list: list[ArrayFloat] = [] + + for branch in param_tree.branches: + branch_results = lmfit.minimize( + residuals_hierarchical, params, args=(branch,), method="leastsq" ) + residuals_list.append(branch_results.residual) + + residuals = np.concatenate(residuals_list, axis=0) + + for param_id in param_tree.ids_to_fit: + params[param_id].vary = True + + return residuals + + +def minimize_hierarchical(experiments: Experiments, params: Parameters, fitmethod: str): + kws = { + "brute": {"keep": "all"}, + "basinhopping": {"niter_success": 10}, + "differential_evolution": {"polish": True, "disp": True, "init": "sobol"}, + "ampgo": {"disp": True}, + } + + reporter = Reporter() + + param_tree = create_group_tree(experiments) + + new_params = params.copy() + for param in new_params.values(): + if param.name not in param_tree.ids_to_fit: + param.vary = False + + minimizer = Minimizer( + residuals_hierarchical, params, fcn_args=(param_tree,), iter_cb=reporter.iter_cb + ) + + reporter.print_header() + + try: + result = minimizer.minimize(method=fitmethod, **(kws.get(fitmethod, {}))) + reporter.print_footer(result.nfev, result.chisqr, result.redchi) except KeyboardInterrupt: print_calculation_stopped_error() except ValueError: From 25250731ba688ac4598463357832310e2800abd5 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Mon, 30 Oct 2023 18:35:34 +0100 Subject: [PATCH 06/18] Update packages --- .pre-commit-config.yaml | 6 +- pdm.lock | 492 +++++++++++++++++++++------------------- pyproject.toml | 2 +- 3 files changed, 263 insertions(+), 237 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7015013f..1eebebab 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v4.5.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer @@ -17,13 +17,13 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.0.286 + rev: v0.1.3 hooks: - id: ruff args: [--fix, --exit-non-zero-on-fix] - repo: https://github.com/psf/black - rev: 23.7.0 # Replace by any tag/version: https://github.com/psf/black/tags + rev: 23.10.1 # Replace by any tag/version: https://github.com/psf/black/tags hooks: - id: black language_version: python3.10 diff --git a/pdm.lock b/pdm.lock index e2863194..e9a52b30 100644 --- a/pdm.lock +++ b/pdm.lock 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license = { text = "GPL-3.0-or-later" } dynamic = [ "version" ] From ee7e5df159513c6b388a13d3ec35b9faab893615 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Mon, 30 Oct 2023 18:39:16 +0100 Subject: [PATCH 07/18] Update the calculation of propagators This is to match the way stacked matrices are dealt with in SciPy. When there is only one delay to compute, the function `scipy.linalg.expm` is used instead of the diagonalization approach. --- chemex/nmr/spectrometer.py | 73 +++++++++++++++++++++++++++++--------- 1 file changed, 57 insertions(+), 16 deletions(-) diff --git a/chemex/nmr/spectrometer.py b/chemex/nmr/spectrometer.py index 24929a98..6db0957e 100644 --- a/chemex/nmr/spectrometer.py +++ b/chemex/nmr/spectrometer.py @@ -1,14 +1,16 @@ from __future__ import annotations from functools import reduce +from itertools import product from typing import TYPE_CHECKING import numpy as np from cachetools import cached from cachetools.keys import hashkey -from scipy.linalg import eig, eigvals, expm, inv +from scipy.linalg import expm if TYPE_CHECKING: + # Imports related to type checking and annotations from collections.abc import Iterable, Sequence from chemex.nmr.constants import Distribution @@ -17,28 +19,67 @@ DictArrayFloat = dict[str, ArrayFloat] - +# A small value used for numerical stability SMALL_VALUE = 1e-6 def calculate_propagators( liouv: ArrayFloat, delays: float | Iterable[float], dephasing: bool = False ) -> ArrayFloat: - delays_ = np.asarray(delays).reshape(-1) - shape = liouv.shape - propagator_list = [] - for a_liouvillian in liouv.reshape(-1, *shape[-2:]): - s, vr = eig(a_liouvillian) - vri = inv(vr) - if dephasing: - indexes = np.where(abs(s.imag) < SMALL_VALUE)[0] - vr, s, vri = vr[:, indexes], s[indexes], vri[indexes, :] - d = np.asarray([np.diag(np.exp(s * t)) for t in delays_]) - propagator_list.append((vr @ d @ vri).real) - propagators = np.asarray(propagator_list).swapaxes(0, 1).reshape(-1, *shape) + """ + Calculate the propagators for the given delays. + + Parameters + ---------- + liouv : ArrayFloat + The Liouvillians of the system + delays : float | Iterable[float] + The delays to calculate the propagators for + dephasing : bool, optional + Whether to apply dephasing, by default False + + Returns + ------- + ArrayFloat + The propagators + """ + + # Ensure delays is a 1D NumPy array + delays = np.asarray(delays).flatten() + + if delays.size == 1 and not dephasing: + # If there's only one delay and no dephasing, calculate the propagator directly + # using scipy expm function + return expm(liouv * delays[0]) + + # Calculate eigenvalues and eigenvectors of the Liouvillian matrices + eigenvalues, eigenvectors = np.linalg.eig(liouv) + + if dephasing: + # If dephasing is requested, adjust eigenvalues + eigenvalues = np.where( + abs(eigenvalues.imag) < SMALL_VALUE, eigenvalues, eigenvalues * 1e9 + ) + + # Calculate the exponentiated eigenvalues for each delay + evt = np.exp(np.multiply.outer(delays, eigenvalues)) + + # Create an empty array for diagonal matrices + diag = np.empty((*delays.shape, *liouv.shape), dtype=np.complex128) + + # Calculate diagonal matrices for each delay + for index in product(*(range(x) for x in evt.shape[:-1])): + diag[index] = np.diag(evt[index]) + + # Calculate the propagators using matrix multiplication + propagators = eigenvectors @ diag @ np.linalg.inv(eigenvectors) + if propagators.shape[0] == 1: + # If there's only one propagator, return it with no extra time dimension propagators = propagators[0] - return propagators + + # Return the real part of the propagators + return propagators.real def _get_key(liouvillian: LiouvillianIS, *args, **kwargs): @@ -386,7 +427,7 @@ def calculate_shifts(self) -> ArrayFloat: liouv = self.liouvillian.l_free.reshape( (self.liouvillian.size, self.liouvillian.size) ) - return eigvals(liouv).imag + return np.linalg.eigvals(liouv).imag def offsets_to_ppms(self, offsets: ArrayFloat) -> ArrayFloat: return self.liouvillian.offsets_to_ppms(offsets) From fffbee7a6f0929c27a86e1f832d8518830973d29 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Mon, 30 Oct 2023 18:41:21 +0100 Subject: [PATCH 08/18] Use `NonNegativeFloat` instead of `PositiveFloat` This corrects a bug where `0.0` was not an acceptable value for `h_larmor_frq`, `p_total`, and `l_total`. --- chemex/configuration/conditions.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/chemex/configuration/conditions.py b/chemex/configuration/conditions.py index 142900d5..374a0f64 100644 --- a/chemex/configuration/conditions.py +++ b/chemex/configuration/conditions.py @@ -7,7 +7,7 @@ BaseModel, BeforeValidator, Field, - PositiveFloat, + NonNegativeFloat, ValidationError, field_validator, model_validator, @@ -24,10 +24,10 @@ @total_ordering class Conditions(BaseModel, frozen=True): - h_larmor_frq: PositiveFloat | None = None + h_larmor_frq: NonNegativeFloat | None = None temperature: float | None = None - p_total: PositiveFloat | None = None - l_total: PositiveFloat | None = None + p_total: NonNegativeFloat | None = None + l_total: NonNegativeFloat | None = None d2o: float | None = Field(gt=0.0, lt=1.0, default=None) label: tuple[LabelType, ...] = () From 6b84a6e5e3d61be1eb304614d94613b86b0c7f61 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Mon, 30 Oct 2023 18:42:00 +0100 Subject: [PATCH 09/18] Add new and update old kinetic models --- chemex/models/constraints.py | 17 +- chemex/models/kinetic/settings_2st_a_a2.py | 95 --------- chemex/models/kinetic/settings_2st_a_a3.py | 96 --------- chemex/models/kinetic/settings_2st_a_a4.py | 95 --------- .../kinetic/settings_2st_monomer_dimer.py | 100 +++++++++ .../kinetic/settings_2st_monomer_tetramer.py | 100 +++++++++ .../kinetic/settings_2st_monomer_trimer.py | 100 +++++++++ chemex/models/kinetic/settings_3st_a_a2_a3.py | 136 ------------ chemex/models/kinetic/settings_3st_a_a2_a4.py | 131 ------------ .../models/kinetic/settings_3st_binding_cs.py | 141 +++++++++++++ ...uced_fit.py => settings_3st_binding_if.py} | 0 .../settings_3st_binding_offpathway.py | 130 ------------ .../settings_3st_monomer_dimer_tetramer.py | 141 +++++++++++++ .../settings_3st_monomer_dimer_trimer.py | 150 ++++++++++++++ .../settings_4st_binding_3_bound_states.py | 193 ++++++++++++++++++ 15 files changed, 931 insertions(+), 694 deletions(-) delete mode 100644 chemex/models/kinetic/settings_2st_a_a2.py delete mode 100644 chemex/models/kinetic/settings_2st_a_a3.py delete mode 100644 chemex/models/kinetic/settings_2st_a_a4.py create mode 100644 chemex/models/kinetic/settings_2st_monomer_dimer.py create mode 100644 chemex/models/kinetic/settings_2st_monomer_tetramer.py create mode 100644 chemex/models/kinetic/settings_2st_monomer_trimer.py delete mode 100644 chemex/models/kinetic/settings_3st_a_a2_a3.py delete mode 100644 chemex/models/kinetic/settings_3st_a_a2_a4.py create mode 100644 chemex/models/kinetic/settings_3st_binding_cs.py rename chemex/models/kinetic/{settings_3st_induced_fit.py => settings_3st_binding_if.py} (100%) delete mode 100644 chemex/models/kinetic/settings_3st_binding_offpathway.py create mode 100644 chemex/models/kinetic/settings_3st_monomer_dimer_tetramer.py create mode 100644 chemex/models/kinetic/settings_3st_monomer_dimer_trimer.py create mode 100644 chemex/models/kinetic/settings_4st_binding_3_bound_states.py diff --git a/chemex/models/constraints.py b/chemex/models/constraints.py index 3a9f5745..6f1e411e 100644 --- a/chemex/models/constraints.py +++ b/chemex/models/constraints.py @@ -14,14 +14,9 @@ def pop_2st(kab: float = 0.0, kba: float = 0.0) -> dict[str, float]: if np.isclose(kba, 0.0): return {"pa": 0.0, "pb": 1.0} - mat = np.array([[kab, -kba], [1.0, 1.0]]) + kex = kab + kba - if np.isclose(np.linalg.det(mat), 0.0): - return {"pa": 1.0, "pb": 0.0} - - vec = np.array([0.0, 1.0]) - res = linalg.solve(mat, vec) - return {"pa": res[0], "pb": res[1]} + return {"pa": kba / kex, "pb": kab / kex} @lru_cache(maxsize=100) @@ -57,9 +52,9 @@ def pop_3st( return {"pa": 1.0, "pb": 0.0, "pc": 0.0} vec = np.array([0.0, 0.0, 1.0]) - res = linalg.solve(mat, vec) + pa, pb, pc = linalg.solve(mat, vec) - return {"pa": res[0], "pb": res[1], "pc": res[2]} + return {"pa": pa, "pb": pb, "pc": pc} @lru_cache(maxsize=100) @@ -106,6 +101,6 @@ def pop_4st( return {"pa": 1.0, "pb": 0.0, "pc": 0.0, "pd": 0.0} vec = np.array([0.0, 0.0, 0.0, 1.0]) - res = linalg.solve(mat, vec) + pa, pb, pc, pd = linalg.solve(mat, vec) - return {"pa": res[0], "pb": res[1], "pc": res[2], "pd": res[3]} + return {"pa": pa, "pb": pb, "pc": pc, "pd": pd} diff --git a/chemex/models/kinetic/settings_2st_a_a2.py b/chemex/models/kinetic/settings_2st_a_a2.py deleted file mode 100644 index 3c2cdc77..00000000 --- a/chemex/models/kinetic/settings_2st_a_a2.py +++ /dev/null @@ -1,95 +0,0 @@ -from __future__ import annotations - -from functools import lru_cache -from typing import TYPE_CHECKING - -import numpy as np -from scipy.optimize import root - -from chemex.models.constraints import pop_2st -from chemex.models.factory import model_factory -from chemex.parameters.setting import NameSetting, ParamLocalSetting -from chemex.parameters.userfunctions import user_function_registry - -if TYPE_CHECKING: - from chemex.configuration.conditions import Conditions - from chemex.typing import ArrayFloat - -NAME = "2st_a_a2" - -TPL = ("temperature", "p_total", "l_total") - - -def calculate_concentrations( - concentrations: ArrayFloat, p_total: float, k1: float -) -> ArrayFloat: - p_monomer, p_dimer = concentrations - return np.array( - [ - p_monomer + 2.0 * p_dimer - p_total, - k1 * p_monomer**2 - p_dimer, - ] - ) - - -@lru_cache(maxsize=100) -def calculate_monomer_concentration(p_total: float, k1: float) -> float: - concentrations_start = (p_total, 0.0) - results = root(calculate_concentrations, concentrations_start, args=(p_total, k1)) - p_monomer, _p_dimer = results["x"] - return p_monomer - - -def make_settings_2st_binding(conditions: Conditions) -> dict[str, ParamLocalSetting]: - p_total = conditions.p_total - if p_total is None: - msg = "'p_total' must be specified to use the '2st_a_a2' model" - raise ValueError(msg) - return { - "k_a2_a": ParamLocalSetting( - name_setting=NameSetting("k_a2_a", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "k1": ParamLocalSetting( - name_setting=NameSetting("k1", "", ("temperature",)), - value=2.0, - min=0.0, - vary=True, - ), - "k_a_a2": ParamLocalSetting( - name_setting=NameSetting("k_a_a2", "", ("temperature",)), - min=0.0, - expr="{k_a2_a} * {k1}", - ), - "p_monomer": ParamLocalSetting( - name_setting=NameSetting("p_monomer", "", TPL), - expr=f"calc_p_monomer({p_total}, {{k1}})", - ), - "kab": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="2.0 * {k_a_a2} * {p_monomer}", - ), - "kba": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="{k_a2_a}", - ), - "pa": ParamLocalSetting( - name_setting=NameSetting("pa", "", TPL), - expr="pop_2st({kab}, {kba})['pa']", - ), - "pb": ParamLocalSetting( - name_setting=NameSetting("pb", "", TPL), - expr="pop_2st({kab}, {kba})['pb']", - ), - } - - -def register() -> None: - model_factory.register(name=NAME, setting_maker=make_settings_2st_binding) - user_functions = { - "calc_p_monomer": calculate_monomer_concentration, - "pop_2st": pop_2st, - } - user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_2st_a_a3.py b/chemex/models/kinetic/settings_2st_a_a3.py deleted file mode 100644 index e4e63906..00000000 --- a/chemex/models/kinetic/settings_2st_a_a3.py +++ /dev/null @@ -1,96 +0,0 @@ -from __future__ import annotations - -from functools import lru_cache -from typing import TYPE_CHECKING - -import numpy as np -from scipy.optimize import root - -from chemex.models.constraints import pop_2st -from chemex.models.factory import model_factory -from chemex.parameters.setting import NameSetting, ParamLocalSetting -from chemex.parameters.userfunctions import user_function_registry - -if TYPE_CHECKING: - from chemex.configuration.conditions import Conditions - from chemex.typing import ArrayFloat - -NAME = "2st_a_a3" - -TPL = ("temperature", "p_total", "l_total") - - -def calculate_concentrations( - concentrations: ArrayFloat, p_total: float, k1: float -) -> ArrayFloat: - """Calculate the concentrations of monomer and trimer.""" - p_monomer, p_trimer = concentrations - return np.array( - [ - p_monomer + 3.0 * p_trimer - p_total, - k1 * p_monomer**3 - p_trimer, - ] - ) - - -@lru_cache(maxsize=100) -def calculate_monomer_concentration(p_total: float, k1: float) -> float: - concentrations_start = (p_total, 0.0) - results = root(calculate_concentrations, concentrations_start, args=(p_total, k1)) - p_monomer, _p_trimer = results["x"] - return p_monomer - - -def make_settings_2st_binding(conditions: Conditions) -> dict[str, ParamLocalSetting]: - p_total = conditions.p_total - if p_total is None: - msg = "'p_total' must be specified to use the '2st_a_a2' model" - raise ValueError(msg) - return { - "k1": ParamLocalSetting( - name_setting=NameSetting("k1", "", ("temperature",)), - value=2.0, - min=0.0, - vary=True, - ), - "k_a3_a": ParamLocalSetting( - name_setting=NameSetting("k_a3_a", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "k_a_a3": ParamLocalSetting( - name_setting=NameSetting("k_a_a3", "", ("temperature",)), - min=0.0, - expr="{k_a3_a} * {k1}", - ), - "p_monomer": ParamLocalSetting( - name_setting=NameSetting("p_monomer", "", TPL), - expr=f"calc_p_monomer({p_total}, {{k1}})", - ), - "kab": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="3.0 * {k_a_a3} * {p_monomer}", - ), - "kba": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="{k_a3_a}", - ), - "pa": ParamLocalSetting( - name_setting=NameSetting("pa", "", TPL), - expr="pop_2st({kab}, {kba})['pa']", - ), - "pb": ParamLocalSetting( - name_setting=NameSetting("pb", "", TPL), - expr="pop_2st({kab}, {kba})['pb']", - ), - } - - -def register() -> None: - model_factory.register(name=NAME, setting_maker=make_settings_2st_binding) - user_functions = { - "calc_p_monomer": calculate_monomer_concentration, - "pop_2st": pop_2st, - } - user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_2st_a_a4.py b/chemex/models/kinetic/settings_2st_a_a4.py deleted file mode 100644 index ee639efc..00000000 --- a/chemex/models/kinetic/settings_2st_a_a4.py +++ /dev/null @@ -1,95 +0,0 @@ -from __future__ import annotations - -from functools import lru_cache -from typing import TYPE_CHECKING - -import numpy as np -from scipy.optimize import root - -from chemex.models.constraints import pop_2st -from chemex.models.factory import model_factory -from chemex.parameters.setting import NameSetting, ParamLocalSetting -from chemex.parameters.userfunctions import user_function_registry - -if TYPE_CHECKING: - from chemex.configuration.conditions import Conditions - from chemex.typing import ArrayFloat - -NAME = "2st_a_a4" - -TPL = ("temperature", "p_total", "l_total") - - -def calculate_concentrations( - concentrations: ArrayFloat, p_total: float, k1: float -) -> ArrayFloat: - p_monomer, p_tetramer = concentrations - return np.array( - [ - p_monomer + 4.0 * p_tetramer - p_total, - k1 * p_monomer**4 - p_tetramer, - ] - ) - - -@lru_cache(maxsize=100) -def calculate_monomer_concentration(p_total: float, k1: float) -> float: - concentrations_start = (p_total, 0.0) - results = root(calculate_concentrations, concentrations_start, args=(p_total, k1)) - p_monomer, _p_tetramer = results["x"] - return p_monomer - - -def make_settings_2st_binding(conditions: Conditions) -> dict[str, ParamLocalSetting]: - p_total = conditions.p_total - if p_total is None: - msg = "'p_total' must be specified to use the '2st_a_a2' model" - raise ValueError(msg) - return { - "k_a4_a": ParamLocalSetting( - name_setting=NameSetting("k_a4_a", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "k1": ParamLocalSetting( - name_setting=NameSetting("k1", "", ("temperature",)), - value=2.0, - min=0.0, - vary=True, - ), - "k_a_a4": ParamLocalSetting( - name_setting=NameSetting("k_a_a4", "", ("temperature",)), - min=0.0, - expr="{k_a4_a} * {k1}", - ), - "p_monomer": ParamLocalSetting( - name_setting=NameSetting("p_monomer", "", TPL), - expr=f"calc_p_monomer({p_total}, {{k1}})", - ), - "kab": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="4.0 * {k_a_a4} * {p_monomer}", - ), - "kba": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="{k_a4_a}", - ), - "pa": ParamLocalSetting( - name_setting=NameSetting("pa", "", TPL), - expr="pop_2st({kab}, {kba})['pa']", - ), - "pb": ParamLocalSetting( - name_setting=NameSetting("pb", "", TPL), - expr="pop_2st({kab}, {kba})['pb']", - ), - } - - -def register() -> None: - model_factory.register(name=NAME, setting_maker=make_settings_2st_binding) - user_functions = { - "calc_p_monomer": calculate_monomer_concentration, - "pop_2st": pop_2st, - } - user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_2st_monomer_dimer.py b/chemex/models/kinetic/settings_2st_monomer_dimer.py new file mode 100644 index 00000000..35d2d635 --- /dev/null +++ b/chemex/models/kinetic/settings_2st_monomer_dimer.py @@ -0,0 +1,100 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.constraints import pop_2st +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat + +NAME = "2st_monomer_dimer" + +TP = ("temperature", "p_total") + + +def calculate_residuals( + concentrations: ArrayFloat, p_total: float, kd: float +) -> ArrayFloat: + monomer, dimer = concentrations + return np.array( + [ + monomer + 2.0 * dimer - p_total, + kd * dimer - monomer**2, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_concentrations(p_total: float, kd: float) -> dict[str, float]: + concentrations_start = (p_total, 0.0) + results = root(calculate_residuals, concentrations_start, args=(p_total, kd)) + return {"monomer": results["x"][0], "dimer": results["x"][1]} + + +def make_settings_2st_monomer_dimer( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p_total = conditions.p_total + if p_total is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "koff": ParamLocalSetting( + name_setting=NameSetting("koff", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kd": ParamLocalSetting( + name_setting=NameSetting("kd", "", ("temperature",)), + value=1e-6, + min=0.0, + vary=True, + ), + "kon": ParamLocalSetting( + name_setting=NameSetting("kon", "", ("temperature",)), + min=0.0, + expr="{koff} / max({kd}, 1e-32)", + ), + "c_monomer": ParamLocalSetting( + name_setting=NameSetting("c_monomer", "", TP), + expr=f"concentrations({p_total}, {{kd}})['monomer']", + ), + "c_dimer": ParamLocalSetting( + name_setting=NameSetting("c_dimer", "", TP), + expr=f"concentrations({p_total}, {{kd}})['dimer']", + ), + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", TP), + expr="2.0 * {kon} * {c_monomer}", + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", TP), + expr="{koff}", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TP), + expr="pop_2st({kab}, {kba})['pa']", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TP), + expr="pop_2st({kab}, {kba})['pb']", + ), + } + + +def register() -> None: + model_factory.register(name=NAME, setting_maker=make_settings_2st_monomer_dimer) + user_functions = { + "concentrations": calculate_concentrations, + "pop_2st": pop_2st, + } + user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_2st_monomer_tetramer.py b/chemex/models/kinetic/settings_2st_monomer_tetramer.py new file mode 100644 index 00000000..98bd3197 --- /dev/null +++ b/chemex/models/kinetic/settings_2st_monomer_tetramer.py @@ -0,0 +1,100 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.constraints import pop_2st +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat + +NAME = "2st_monomer_tetramer" + +TP = ("temperature", "p_total") + + +def calculate_residuals( + concentrations: ArrayFloat, p_total: float, kd: float +) -> ArrayFloat: + monomer, tetramer = concentrations + return np.array( + [ + monomer + 4.0 * tetramer - p_total, + kd * tetramer - monomer**4, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_concentrations(p_total: float, kd: float) -> dict[str, float]: + concentrations_start = (p_total, 0.0) + results = root(calculate_residuals, concentrations_start, args=(p_total, kd)) + return {"monomer": results["x"][0], "tetramer": results["x"][1]} + + +def make_settings_2st_monomer_tetramer( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p_total = conditions.p_total + if p_total is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "koff": ParamLocalSetting( + name_setting=NameSetting("koff", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kd": ParamLocalSetting( + name_setting=NameSetting("kd", "", ("temperature",)), + value=1e-6, + min=0.0, + vary=True, + ), + "kon": ParamLocalSetting( + name_setting=NameSetting("kon", "", ("temperature",)), + min=0.0, + expr="{koff} / max({kd}, 1e-32)", + ), + "c_monomer": ParamLocalSetting( + name_setting=NameSetting("c_monomer", "", TP), + expr=f"concentrations({p_total}, {{kd}})['monomer']", + ), + "c_tetramer": ParamLocalSetting( + name_setting=NameSetting("c_tetramer", "", TP), + expr=f"concentrations({p_total}, {{kd}})['tetramer']", + ), + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", TP), + expr="4.0 * {kon} * {c_monomer}", + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", TP), + expr="{koff}", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TP), + expr="pop_2st({kab}, {kba})['pa']", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TP), + expr="pop_2st({kab}, {kba})['pb']", + ), + } + + +def register() -> None: + model_factory.register(name=NAME, setting_maker=make_settings_2st_monomer_tetramer) + user_functions = { + "concentrations": calculate_concentrations, + "pop_2st": pop_2st, + } + user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_2st_monomer_trimer.py b/chemex/models/kinetic/settings_2st_monomer_trimer.py new file mode 100644 index 00000000..b6593a4d --- /dev/null +++ b/chemex/models/kinetic/settings_2st_monomer_trimer.py @@ -0,0 +1,100 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.constraints import pop_2st +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat + +NAME = "2st_monomer_trimer" + +TP = ("temperature", "p_total") + + +def calculate_residuals( + concentrations: ArrayFloat, p_total: float, kd: float +) -> ArrayFloat: + monomer, trimer = concentrations + return np.array( + [ + monomer + 3.0 * trimer - p_total, + kd * trimer - monomer**3, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_concentrations(p_total: float, kd: float) -> dict[str, float]: + concentrations_start = (p_total, 0.0) + results = root(calculate_residuals, concentrations_start, args=(p_total, kd)) + return {"monomer": results["x"][0], "trimer": results["x"][1]} + + +def make_settings_2st_monomer_trimer( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p_total = conditions.p_total + if p_total is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "koff": ParamLocalSetting( + name_setting=NameSetting("koff", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kd": ParamLocalSetting( + name_setting=NameSetting("kd", "", ("temperature",)), + value=1e-6, + min=0.0, + vary=True, + ), + "kon": ParamLocalSetting( + name_setting=NameSetting("kon", "", ("temperature",)), + min=0.0, + expr="{koff} / max({kd}, 1e-32)", + ), + "c_monomer": ParamLocalSetting( + name_setting=NameSetting("c_monomer", "", TP), + expr=f"concentrations({p_total}, {{kd}})['monomer']", + ), + "c_trimer": ParamLocalSetting( + name_setting=NameSetting("c_trimer", "", TP), + expr=f"concentrations({p_total}, {{kd}})['trimer']", + ), + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", TP), + expr="3.0 * {kon} * {c_monomer}", + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", TP), + expr="{koff}", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TP), + expr="pop_2st({kab}, {kba})['pa']", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TP), + expr="pop_2st({kab}, {kba})['pb']", + ), + } + + +def register() -> None: + model_factory.register(name=NAME, setting_maker=make_settings_2st_monomer_trimer) + user_functions = { + "concentrations": calculate_concentrations, + "pop_2st": pop_2st, + } + user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_3st_a_a2_a3.py b/chemex/models/kinetic/settings_3st_a_a2_a3.py deleted file mode 100644 index 40738a2f..00000000 --- a/chemex/models/kinetic/settings_3st_a_a2_a3.py +++ /dev/null @@ -1,136 +0,0 @@ -from __future__ import annotations - -from functools import lru_cache -from typing import TYPE_CHECKING - -import numpy as np -from scipy.optimize import root - -from chemex.models.constraints import pop_3st -from chemex.models.factory import model_factory -from chemex.parameters.setting import NameSetting, ParamLocalSetting -from chemex.parameters.userfunctions import user_function_registry - -if TYPE_CHECKING: - from chemex.configuration.conditions import Conditions - from chemex.typing import ArrayFloat - -NAME = "3st_a_a2_a3" - -TPL = ("temperature", "p_total", "l_total") - - -def calculate_residuals( - concentrations: ArrayFloat, p_total: float, k1: float, k2: float -) -> ArrayFloat: - p_monomer, p_dimer, p_trimer = concentrations - return np.array( - [ - p_monomer + 2.0 * p_dimer + 3.0 * p_trimer - p_total, - k1 * p_monomer**2 - p_dimer, - k2 * p_monomer * p_dimer - p_trimer, - ] - ) - - -@lru_cache(maxsize=100) -def calculate_concentrations(p_total: float, k1: float, k2: float) -> dict[str, float]: - concentrations_start = (p_total, 0.0, 0.0) - results = root(calculate_residuals, concentrations_start, args=(p_total, k1, k2)) - return dict(zip(("p_monomer", "p_dimer", "p_trimer"), results["x"], strict=True)) - - -def make_settings_3st_a_a2_a3(conditions: Conditions) -> dict[str, ParamLocalSetting]: - p_total = conditions.p_total - if p_total is None: - msg = f"'p_total' must be specified to use the '{NAME}' model" - raise ValueError(msg) - return { - "k1": ParamLocalSetting( - name_setting=NameSetting("k1", "", ("temperature",)), - value=2.0, - min=0.0, - vary=True, - ), - "k2": ParamLocalSetting( - name_setting=NameSetting("k2", "", ("temperature",)), - value=2.0, - min=0.0, - vary=True, - ), - "k_a2_a": ParamLocalSetting( - name_setting=NameSetting("k_a2_a", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "k_a3_aa2": ParamLocalSetting( - name_setting=NameSetting("k_a3_aa2", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "k_a_a2": ParamLocalSetting( - name_setting=NameSetting("k_a_a4", "", ("temperature",)), - min=0.0, - expr="{k_a2_a} * {k1}", - ), - "k_aa2_a3": ParamLocalSetting( - name_setting=NameSetting("k_a_a4", "", ("temperature",)), - min=0.0, - expr="{k_a3_aa2} * {k2}", - ), - "p_monomer": ParamLocalSetting( - name_setting=NameSetting("p_monomer", "", TPL), - expr=f"calc_conc({p_total}, {{k1}}, {{k2}})['p_monomer']", - ), - "p_dimer": ParamLocalSetting( - name_setting=NameSetting("p_dimer", "", TPL), - expr=f"calc_conc({p_total}, {{k1}}, {{k2}})['p_dimer']", - ), - "kab": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="2.0 * {k_a_a2} * {p_monomer}", - ), - "kba": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="{k_a2_a}", - ), - "kac": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="{k_aa2_a3} * {p_dimer}", - ), - "kca": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="{k_a3_aa2} / 3.0", - ), - "kbc": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="{k_aa2_a3} * {p_monomer}", - ), - "kcb": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="2.0 * {k_a3_aa2} / 3.0", - ), - "pa": ParamLocalSetting( - name_setting=NameSetting("pa", "", TPL), - expr="pop_3st({kab}, {kba}, {kac}, {kca}, {kbc}, {kcb})['pa']", - ), - "pb": ParamLocalSetting( - name_setting=NameSetting("pb", "", TPL), - expr="pop_3st({kab}, {kba}, {kac}, {kca}, {kbc}, {kcb})['pb']", - ), - "pc": ParamLocalSetting( - name_setting=NameSetting("pc", "", TPL), - expr="pop_3st({kab}, {kba}, {kac}, {kca}, {kbc}, {kcb})['pc']", - ), - } - - -def register() -> None: - model_factory.register(name=NAME, setting_maker=make_settings_3st_a_a2_a3) - user_functions = { - "calc_conc": calculate_concentrations, - "pop_3st": pop_3st, - } - user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_3st_a_a2_a4.py b/chemex/models/kinetic/settings_3st_a_a2_a4.py deleted file mode 100644 index 66d3d1c1..00000000 --- a/chemex/models/kinetic/settings_3st_a_a2_a4.py +++ /dev/null @@ -1,131 +0,0 @@ -from __future__ import annotations - -from functools import lru_cache -from typing import TYPE_CHECKING - -import numpy as np -from scipy.optimize import root - -from chemex.models.constraints import pop_3st -from chemex.models.factory import model_factory -from chemex.parameters.setting import NameSetting, ParamLocalSetting -from chemex.parameters.userfunctions import user_function_registry - -if TYPE_CHECKING: - from chemex.configuration.conditions import Conditions - from chemex.typing import ArrayFloat - -NAME = "3st_a_a2_a4" - -TPL = ("temperature", "p_total", "l_total") - - -def calculate_residuals( - concentrations: ArrayFloat, - p_total: float, - k1: float, - k2: float, -) -> ArrayFloat: - p_monomer, p_dimer, p_tetramer = concentrations - return np.array( - [ - p_monomer + 2.0 * p_dimer + 4.0 * p_tetramer - p_total, - k1 * p_monomer**2 - p_dimer, - k2 * p_dimer**2 - p_tetramer, - ] - ) - - -@lru_cache(maxsize=100) -def calculate_concentrations(p_total: float, k1: float, k2: float) -> dict[str, float]: - concentrations_start = (p_total, 0.0, 0.0) - results = root(calculate_residuals, concentrations_start, args=(p_total, k1, k2)) - return dict(zip(("p_monomer", "p_dimer", "p_tetramer"), results["x"], strict=True)) - - -def make_settings_3st_a_a2_a4(conditions: Conditions) -> dict[str, ParamLocalSetting]: - p_total = conditions.p_total - if p_total is None: - msg = f"'p_total' must be specified to use the '{NAME}' model" - raise ValueError(msg) - return { - "k1": ParamLocalSetting( - name_setting=NameSetting("k1", "", ("temperature",)), - value=2.0, - min=0.0, - vary=True, - ), - "k2": ParamLocalSetting( - name_setting=NameSetting("k2", "", ("temperature",)), - value=2.0, - min=0.0, - vary=True, - ), - "k_a2_a": ParamLocalSetting( - name_setting=NameSetting("k_a2_a", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "k_a4_a2": ParamLocalSetting( - name_setting=NameSetting("k_a4_a2", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "k_a_a2": ParamLocalSetting( - name_setting=NameSetting("k_a_a4", "", ("temperature",)), - min=0.0, - expr="{k_a2_a} * {k1}", - ), - "k_a2_a4": ParamLocalSetting( - name_setting=NameSetting("k_a_a4", "", ("temperature",)), - min=0.0, - expr="{k_a4_a2} * {k2}", - ), - "p_monomer": ParamLocalSetting( - name_setting=NameSetting("p_monomer", "", TPL), - expr=f"calc_conc({p_total}, {{k1}}, {{k2}})['p_monomer']", - ), - "p_dimer": ParamLocalSetting( - name_setting=NameSetting("p_dimer", "", TPL), - expr=f"calc_conc({p_total}, {{k1}}, {{k2}})['p_dimer']", - ), - "kab": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="2.0 * {k_a_a2} * {p_monomer}", - ), - "kba": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="{k_a2_a}", - ), - "kbc": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="2.0 * {k_a2_a4} * {p_dimer}", - ), - "kcb": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="{k_a4_a2}", - ), - "pa": ParamLocalSetting( - name_setting=NameSetting("pa", "", TPL), - expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pa']", - ), - "pb": ParamLocalSetting( - name_setting=NameSetting("pb", "", TPL), - expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pb']", - ), - "pc": ParamLocalSetting( - name_setting=NameSetting("pc", "", TPL), - expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pc']", - ), - } - - -def register() -> None: - model_factory.register(name=NAME, setting_maker=make_settings_3st_a_a2_a4) - user_functions = { - "calc_conc": calculate_concentrations, - "pop_3st": pop_3st, - } - user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_3st_binding_cs.py b/chemex/models/kinetic/settings_3st_binding_cs.py new file mode 100644 index 00000000..2fb5440c --- /dev/null +++ b/chemex/models/kinetic/settings_3st_binding_cs.py @@ -0,0 +1,141 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.constraints import pop_3st +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry +from chemex.typing import ArrayFloat + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + +NAME = "3st_binding_cs" + +TPL = ("temperature", "p_total", "l_total") + + +def calculate_residuals( + concentrations: ArrayFloat, + p_total: float, + l_total: float, + kab: float, + kba: float, + kd: float, +) -> ArrayFloat: + p1, p2, pl, l_ = concentrations + return np.array( + [ + p_total - p1 - p2 - pl, + l_total - l_ - pl, + kab * p1 - kba * p2, + kd * pl - p2 * l_, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_concentrations( + p_total: float, l_total: float, kd: float, kab: float, kba: float +) -> dict[str, float]: + concentrations_start = (p_total, 0.0, 0.0, l_total) + results = root( + calculate_residuals, + concentrations_start, + args=(p_total, l_total, kab, kba, kd), + ) + p1, p2, pl, l_ = results["x"] + return {"p1": p1, "p2": p2, "pl": pl, "l": l_} + + +def make_settings_3st_binding_cs( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p0 = conditions.p_total + l0 = conditions.l_total + if p0 is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + if l0 is None: + msg = f"'l_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "koff": ParamLocalSetting( + name_setting=NameSetting("koff", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kd": ParamLocalSetting( + name_setting=NameSetting("kd", "", ("temperature",)), + value=1e-3, + min=0.0, + vary=True, + ), + "kon": ParamLocalSetting( + name_setting=NameSetting("kon", "", ("temperature",)), + expr="{koff} / max({kd}, 1e-100)", + ), + "c_l": ParamLocalSetting( + name_setting=NameSetting("c_l", "", TPL), + expr=f"concentrations({p0}, {l0}, {{kab}}, {{kba}}, {{kd}})['l']", + ), + "c_p1": ParamLocalSetting( + name_setting=NameSetting("c_p1", "", TPL), + expr=f"concentrations({p0}, {l0}, {{kab}}, {{kba}}, {{kd}})['p1']", + ), + "c_p2": ParamLocalSetting( + name_setting=NameSetting("c_p2", "", TPL), + expr=f"concentrations({p0}, {l0}, {{kab}}, {{kba}}, {{kd}})['p2']", + ), + "c_pl": ParamLocalSetting( + name_setting=NameSetting("c_pl", "", TPL), + expr=f"concentrations({p0}, {l0}, {{kab}}, {{kba}}, {{kd}})['pl']", + ), + "kbc": ParamLocalSetting( + name_setting=NameSetting("kbc", "", TPL), + expr="{kon} * {c_l}", + ), + "kcb": ParamLocalSetting( + name_setting=NameSetting("kcb", "", TPL), + expr="{koff}", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TPL), + expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pa']", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TPL), + expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pb']", + ), + "pc": ParamLocalSetting( + name_setting=NameSetting("pc", "", TPL), + expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pc']", + ), + } + + +def register() -> None: + model_factory.register(name=NAME, setting_maker=make_settings_3st_binding_cs) + user_functions = { + "concentrations": calculate_concentrations, + "pop_3st": pop_3st, + } + user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_3st_induced_fit.py b/chemex/models/kinetic/settings_3st_binding_if.py similarity index 100% rename from chemex/models/kinetic/settings_3st_induced_fit.py rename to chemex/models/kinetic/settings_3st_binding_if.py diff --git a/chemex/models/kinetic/settings_3st_binding_offpathway.py b/chemex/models/kinetic/settings_3st_binding_offpathway.py deleted file mode 100644 index 3600fb14..00000000 --- a/chemex/models/kinetic/settings_3st_binding_offpathway.py +++ /dev/null @@ -1,130 +0,0 @@ -from __future__ import annotations - -from functools import lru_cache -from typing import TYPE_CHECKING - -import numpy as np -from scipy.optimize import root - -from chemex.models.constraints import pop_3st -from chemex.models.factory import model_factory -from chemex.parameters.setting import NameSetting, ParamLocalSetting -from chemex.parameters.userfunctions import user_function_registry - -if TYPE_CHECKING: - from chemex.configuration.conditions import Conditions - -NAME = "3st_binding_offpathway" - -TPL = ("temperature", "p_total", "l_total") - - -def calculate_residuals( - populations: np.ndarray, - p_total: float, - l_total: float, - kd_ab: float, - kac: float, - kca: float, -) -> np.ndarray: - pfree_a, pfree_c, pl_b = populations - lfree = l_total - pl_b - return np.array( - [ - pfree_a + pfree_c + pl_b - p_total, - lfree * pfree_a - kd_ab * pl_b, - kac * pfree_a - kca * pfree_c, - ] - ) - - -@lru_cache(maxsize=100) -def calculate_lfree( - p_total: float, l_total: float, kd_ab: float, kac: float, kca: float -) -> float: - concentrations_start = (p_total, 0.0, 0.0) - results = root( - calculate_residuals, - concentrations_start, - args=(p_total, l_total, kd_ab, kac, kca), - ) - _pfree_a, _pfree_c, pl_b = results["x"] - return l_total - pl_b - - -def make_settings_3st_binding_offpathway( - conditions: Conditions, -) -> dict[str, ParamLocalSetting]: - p_total = conditions.p_total - l_total = conditions.l_total - if p_total is None: - msg = f"'p_total' must be specified to use the '{NAME}' model" - raise ValueError(msg) - if l_total is None: - msg = f"'l_total' must be specified to use the '{NAME}' model" - raise ValueError(msg) - return { - "koff_ab": ParamLocalSetting( - name_setting=NameSetting("koff_ab", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "kd_ab": ParamLocalSetting( - name_setting=NameSetting("kd_ab", "", ("temperature",)), - value=1e-3, - min=0.0, - vary=True, - ), - "kac": ParamLocalSetting( - name_setting=NameSetting("kac", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "kca": ParamLocalSetting( - name_setting=NameSetting("kca", "", ("temperature",)), - value=100.0, - min=0.0, - vary=True, - ), - "kon_ab": ParamLocalSetting( - name_setting=NameSetting("kon_ab", "", ("temperature",)), - expr="{koff_ab} / max({kd_ab}, 1e-100)", - ), - "l_free": ParamLocalSetting( - name_setting=NameSetting("l_free", "", TPL), - expr=f"calculate_lfree({p_total}, {l_total}, {{kd_ab}}, {{kac}}, {{kca}})", - ), - "kab": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), - expr="{kon_ab} * {l_free}", - ), - "kba": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), - expr="{koff_ab}", - ), - "pa": ParamLocalSetting( - name_setting=NameSetting("pa", "", TPL), - expr="pop_3st({kab}, {kba}, {kac}, {kca}, 0.0, 0.0)['pa']", - ), - "pb": ParamLocalSetting( - name_setting=NameSetting("pb", "", TPL), - expr="pop_3st({kab}, {kba}, {kac}, {kca}, 0.0, 0.0)['pb']", - ), - "pc": ParamLocalSetting( - name_setting=NameSetting("pc", "", TPL), - expr="pop_3st({kab}, {kba}, {kac}, {kca}, 0.0, 0.0)['pc']", - ), - } - - -def register() -> None: - model_factory.register( - name=NAME, setting_maker=make_settings_3st_binding_offpathway - ) - user_functions = { - "calculate_lfree": calculate_lfree, - "pop_3st": pop_3st, - } - user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_3st_monomer_dimer_tetramer.py b/chemex/models/kinetic/settings_3st_monomer_dimer_tetramer.py new file mode 100644 index 00000000..10b01cbb --- /dev/null +++ b/chemex/models/kinetic/settings_3st_monomer_dimer_tetramer.py @@ -0,0 +1,141 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.constraints import pop_3st +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat + +NAME = "3st_monomer_dimer_tetramer" + +TP = ("temperature", "p_total") + + +def calculate_residuals( + concentrations: ArrayFloat, + p_total: float, + kd1: float, + kd2: float, +) -> ArrayFloat: + monomer, dimer, tetramer = concentrations + return np.array( + [ + monomer + 2.0 * dimer + 4.0 * tetramer - p_total, + kd1 * dimer - monomer**2, + kd2 * tetramer - dimer**2, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_concentrations( + p_total: float, kd1: float, kd2: float +) -> dict[str, float]: + concentrations_start = (p_total, 0.0, 0.0) + results = root(calculate_residuals, concentrations_start, args=(p_total, kd1, kd2)) + return { + "monomer": results["x"][0], + "dimer": results["x"][1], + "tetramer": results["x"][2], + } + + +def make_settings_3st_monomer_dimer_tetramer( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p_total = conditions.p_total + if p_total is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "kd1": ParamLocalSetting( + name_setting=NameSetting("kd1", "", ("temperature",)), + value=1e-6, + min=0.0, + vary=True, + ), + "kd2": ParamLocalSetting( + name_setting=NameSetting("kd2", "", ("temperature",)), + value=1e-6, + min=0.0, + vary=True, + ), + "koff1": ParamLocalSetting( + name_setting=NameSetting("koff1", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "koff2": ParamLocalSetting( + name_setting=NameSetting("koff2", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kon1": ParamLocalSetting( + name_setting=NameSetting("kon1", "", ("temperature",)), + min=0.0, + expr="{koff1} / max({kd1}, 1e-32)", + ), + "kon2": ParamLocalSetting( + name_setting=NameSetting("kon2", "", ("temperature",)), + min=0.0, + expr="{koff2} / max({kd2}, 1e-32)", + ), + "c_monomer": ParamLocalSetting( + name_setting=NameSetting("monomer", "", TP), + expr=f"concentrations({p_total}, {{kd1}}, {{kd2}})['monomer']", + ), + "c_dimer": ParamLocalSetting( + name_setting=NameSetting("dimer", "", TP), + expr=f"concentrations({p_total}, {{kd1}}, {{kd2}})['dimer']", + ), + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", TP), + expr="2.0 * {kon1} * {monomer}", + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", TP), + expr="{koff1}", + ), + "kbc": ParamLocalSetting( + name_setting=NameSetting("kab", "", TP), + expr="2.0 * {kon2} * {dimer}", + ), + "kcb": ParamLocalSetting( + name_setting=NameSetting("kba", "", TP), + expr="{koff2}", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TP), + expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pa']", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TP), + expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pb']", + ), + "pc": ParamLocalSetting( + name_setting=NameSetting("pc", "", TP), + expr="pop_3st({kab}, {kba}, 0.0, 0.0, {kbc}, {kcb})['pc']", + ), + } + + +def register() -> None: + model_factory.register( + name=NAME, setting_maker=make_settings_3st_monomer_dimer_tetramer + ) + user_functions = { + "concentrations": calculate_concentrations, + "pop_3st": pop_3st, + } + user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_3st_monomer_dimer_trimer.py b/chemex/models/kinetic/settings_3st_monomer_dimer_trimer.py new file mode 100644 index 00000000..90a49988 --- /dev/null +++ b/chemex/models/kinetic/settings_3st_monomer_dimer_trimer.py @@ -0,0 +1,150 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.constraints import pop_3st +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat + +NAME = "3st_monomer_dimer_trimer" + +TP = ("temperature", "p_total") + + +def calculate_residuals( + concentrations: ArrayFloat, p_total: float, kd1: float, kd2: float +) -> ArrayFloat: + monomer, dimer, trimer = concentrations + return np.array( + [ + monomer + 2.0 * dimer + 3.0 * trimer - p_total, + kd1 * dimer - monomer**2, + kd2 * trimer - monomer * dimer, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_concentrations( + p_total: float, kd1: float, kd2: float +) -> dict[str, float]: + concentrations_start = (p_total, 0.0, 0.0) + results = root(calculate_residuals, concentrations_start, args=(p_total, kd1, kd2)) + return { + "monomer": results["x"][0], + "dimer": results["x"][1], + "trimer": results["x"][2], + } + + +def make_settings_3st_monomer_dimer_trimer( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p_total = conditions.p_total + if p_total is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "kd1": ParamLocalSetting( + name_setting=NameSetting("kd1", "", ("temperature",)), + value=1e-6, + min=0.0, + vary=True, + ), + "kd2": ParamLocalSetting( + name_setting=NameSetting("kd2", "", ("temperature",)), + value=1e-6, + min=0.0, + vary=True, + ), + "koff1": ParamLocalSetting( + name_setting=NameSetting("koff1", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "koff2": ParamLocalSetting( + name_setting=NameSetting("koff2", "", ("temperature",)), + value=100.0, + min=0.0, + vary=True, + ), + "kon1": ParamLocalSetting( + name_setting=NameSetting("kon1", "", ("temperature",)), + min=0.0, + expr="{koff1} / max({kd1}, 1e-32)", + ), + "kon2": ParamLocalSetting( + name_setting=NameSetting("kon2", "", ("temperature",)), + min=0.0, + expr="{koff2} / max({kd2}, 1e-32)", + ), + "c_monomer": ParamLocalSetting( + name_setting=NameSetting("c_monomer", "", TP), + expr=f"concetrations({p_total}, {{kd1}}, {{kd2}})['monomer']", + ), + "c_dimer": ParamLocalSetting( + name_setting=NameSetting("c_dimer", "", TP), + expr=f"concetrations({p_total}, {{kd1}}, {{kd2}})['dimer']", + ), + "c_trimer": ParamLocalSetting( + name_setting=NameSetting("c_trimer", "", TP), + expr=f"concetrations({p_total}, {{kd1}}, {{kd2}})['trimer']", + ), + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", TP), + expr="2.0 * {kon1} * {c_monomer}", + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", TP), + expr="{koff1}", + ), + "kac": ParamLocalSetting( + name_setting=NameSetting("kac", "", TP), + expr="{kon2} * {c_dimer}", + ), + "kca": ParamLocalSetting( + name_setting=NameSetting("kca", "", TP), + expr="{koff2} / 3.0", + ), + "kbc": ParamLocalSetting( + name_setting=NameSetting("kbc", "", TP), + expr="{kon2} * {c_monomer}", + ), + "kcb": ParamLocalSetting( + name_setting=NameSetting("kcb", "", TP), + expr="2.0 * {koff2} / 3.0", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TP), + expr="pop_3st({kab}, {kba}, {kac}, {kca}, {kbc}, {kcb})['pa']", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TP), + expr="pop_3st({kab}, {kba}, {kac}, {kca}, {kbc}, {kcb})['pb']", + ), + "pc": ParamLocalSetting( + name_setting=NameSetting("pc", "", TP), + expr="pop_3st({kab}, {kba}, {kac}, {kca}, {kbc}, {kcb})['pc']", + ), + } + + +def register() -> None: + model_factory.register( + name=NAME, setting_maker=make_settings_3st_monomer_dimer_trimer + ) + user_functions = { + "concetrations": calculate_concentrations, + "pop_3st": pop_3st, + } + user_function_registry.register(name=NAME, user_functions=user_functions) diff --git a/chemex/models/kinetic/settings_4st_binding_3_bound_states.py b/chemex/models/kinetic/settings_4st_binding_3_bound_states.py new file mode 100644 index 00000000..f7c19af3 --- /dev/null +++ b/chemex/models/kinetic/settings_4st_binding_3_bound_states.py @@ -0,0 +1,193 @@ +from __future__ import annotations + +from functools import lru_cache +from typing import TYPE_CHECKING + +import numpy as np +from scipy.optimize import root + +from chemex.models.factory import model_factory +from chemex.parameters.setting import NameSetting, ParamLocalSetting +from chemex.parameters.userfunctions import user_function_registry + +if TYPE_CHECKING: + from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat + + +NAME = "4st_binding_3_bound_states" + +TPL = ("temperature", "p_total", "l_total") + + +def calculate_residuals( + concentrations: ArrayFloat, + p_total: float, + l_total: float, + kd_ab: float, + keq_bc: float, + keq_cd: float, +) -> ArrayFloat: + p_, l_, pl1, pl2, pl3 = concentrations + return np.array( + [ + l_total - (l_ + pl1 + pl2 + pl3), + p_total - (p_ + pl1 + pl2 + pl3), + kd_ab * pl1 - p_ * l_, + keq_bc * pl1 - pl2, + keq_cd * pl2 - pl3, + ] + ) + + +@lru_cache(maxsize=100) +def calculate_concentrations( + p_total: float, l_total: float, kd_ab: float, keq_bc: float, keq_cd: float +) -> dict[str, float]: + concentrations_start = (p_total, l_total, 0.0, 0.0, 0.0) + results = root( + calculate_residuals, + concentrations_start, + args=(p_total, l_total, kd_ab, keq_bc, keq_cd), + ) + p_, l_, pl1, pl2, pl3 = results["x"] + return {"p": p_, "l": l_, "pl1": pl1, "pl2": pl2, "pl3": pl3} + + +def make_settings_4st_binding_3_bound_states( + conditions: Conditions, +) -> dict[str, ParamLocalSetting]: + p_total = conditions.p_total + l_total = conditions.l_total + if p_total is None: + msg = f"'p_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + if l_total is None: + msg = f"'l_total' must be specified to use the '{NAME}' model" + raise ValueError(msg) + return { + "koff_ab": ParamLocalSetting( + name_setting=NameSetting("koff_ab", "", ("temperature",)), + value=100.0, + min=0.0, + max=1e6, + vary=True, + ), + "kd_ab": ParamLocalSetting( + name_setting=NameSetting("kd_ab", "", ("temperature",)), + value=1e-6, + min=0.0, + max=1.0, + vary=True, + ), + "kex_bc": ParamLocalSetting( + name_setting=NameSetting("kex_bc", "", ("temperature",)), + value=1000.0, + min=0.0, + max=1e6, + vary=True, + ), + "keq_bc": ParamLocalSetting( + name_setting=NameSetting("keq_bc", "", ("temperature",)), + value=1.0, + min=0.0, + max=100.0, + vary=True, + ), + "kex_cd": ParamLocalSetting( + name_setting=NameSetting("kex_cd", "", ("temperature",)), + value=1000.0, + min=0.0, + max=1e6, + vary=True, + ), + "keq_cd": ParamLocalSetting( + name_setting=NameSetting("keq_cd", "", ("temperature",)), + value=1.0, + min=0.0, + max=100.0, + vary=True, + ), + "kon_ab": ParamLocalSetting( + name_setting=NameSetting("kon_ab", "", ("temperature",)), + expr="{koff_ab} / max({kd_ab}, 1e-32)", + ), + "c_p": ParamLocalSetting( + name_setting=NameSetting("c_p", "", TPL), + expr=f"concentrations({p_total},{l_total},{{kd_ab}},{{keq_bc}},{{keq_cd}})['p']", + ), + "c_l": ParamLocalSetting( + name_setting=NameSetting("c_l", "", TPL), + expr=f"concentrations({p_total},{l_total},{{kd_ab}},{{keq_bc}},{{keq_cd}})['l']", + ), + "c_pl1": ParamLocalSetting( + name_setting=NameSetting("c_pl1", "", TPL), + expr=f"concentrations({p_total},{l_total},{{kd_ab}},{{keq_bc}},{{keq_cd}})['pl1']", + ), + "c_pl2": ParamLocalSetting( + name_setting=NameSetting("c_pl2", "", TPL), + expr=f"concentrations({p_total},{l_total},{{kd_ab}},{{keq_bc}},{{keq_cd}})['pl2']", + ), + "c_pl3": ParamLocalSetting( + name_setting=NameSetting("c_pl3", "", TPL), + expr=f"concentrations({p_total},{l_total},{{kd_ab}},{{keq_bc}},{{keq_cd}})['pl3']", + ), + "c_pl": ParamLocalSetting( + name_setting=NameSetting("c_pl", "", TPL), + expr="{c_pl1}+{c_pl2}+{c_pl3}", + ), + "kd_eff": ParamLocalSetting( + name_setting=NameSetting("kd_eff", "", TPL), + expr="({c_p}+{c_l}) / max({c_pl}, 1e-32)", + ), + "kab": ParamLocalSetting( + name_setting=NameSetting("kab", "", TPL), + expr="{kon_ab} * {c_l}", + ), + "kba": ParamLocalSetting( + name_setting=NameSetting("kba", "", TPL), + expr="{koff_ab}", + ), + "kbc": ParamLocalSetting( + name_setting=NameSetting("kbc", "", TPL), + expr="{keq_bc}*{kex_bc}/(1.0+{keq_bc})", + ), + "kcb": ParamLocalSetting( + name_setting=NameSetting("kcb", "", TPL), + expr="{kex_bc}/(1.0+{keq_bc})", + ), + "kcd": ParamLocalSetting( + name_setting=NameSetting("kcd", "", TPL), + expr="{keq_cd}*{kex_cd}/(1.0+{keq_cd})", + ), + "kdc": ParamLocalSetting( + name_setting=NameSetting("kdc", "", TPL), + expr="{kex_cd}/(1.0+{keq_cd})", + ), + "pa": ParamLocalSetting( + name_setting=NameSetting("pa", "", TPL), + expr=f"{{c_p}} / {p_total}", + ), + "pb": ParamLocalSetting( + name_setting=NameSetting("pb", "", TPL), + expr=f"{{c_pl1}} / {p_total}", + ), + "pc": ParamLocalSetting( + name_setting=NameSetting("pc", "", TPL), + expr=f"{{c_pl2}} / {p_total}", + ), + "pd": ParamLocalSetting( + name_setting=NameSetting("pc", "", TPL), + expr=f"{{c_pl3}} / {p_total}", + ), + } + + +def register() -> None: + model_factory.register( + name=NAME, setting_maker=make_settings_4st_binding_3_bound_states + ) + user_functions = { + "concentrations": calculate_concentrations, + } + user_function_registry.register(name=NAME, user_functions=user_functions) From ea1684da4276192b607f62fc3093ac3a2f8be906 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Mon, 30 Oct 2023 19:23:43 +0100 Subject: [PATCH 10/18] Bump packages versions to the latest --- pdm.lock | 2 +- pyproject.toml | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/pdm.lock b/pdm.lock index e9a52b30..dca8bac6 100644 --- a/pdm.lock +++ b/pdm.lock @@ -5,7 +5,7 @@ groups = ["default", "test", "lint"] strategy = ["cross_platform"] lock_version = "4.4" -content_hash = "sha256:115ec515ec87887eabb2fd1943163f5958d405349df937c954136f42cd035715" +content_hash = "sha256:16cf8e14f5f89b3c7c0a0d9f76b765c2db56400a4b8d3f62866d47d3028298c2" [[package]] name = "annotated-types" diff --git a/pyproject.toml b/pyproject.toml index f6c87dab..1217a34c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,15 +7,15 @@ description = "An analysis program for chemical exchange detected by NMR" authors = [ { name = "Guillaume Bouvignies", email = "guillaume.bouvignies@ens.psl.eu" } ] dependencies = [ - "numpy>=1.25.0", - "scipy>=1.9.3", - "matplotlib>=3.7.1", - "lmfit>=1.2.1", - "pydantic>=2.0.1", - "cachetools>=5.3.1", - "rich>=13.4.2", + "numpy>=1.26.1", + "scipy>=1.11.3", + "matplotlib>=3.8.0", + "lmfit>=1.2.2", + "pydantic>=2.4.2", + "cachetools>=5.3.2", + "rich>=13.6.0", "tomli>=2.0.1", - "rapidfuzz>=3.1.1", + "rapidfuzz>=3.4.0", "emcee>=3.1.4", ] requires-python = ">=3.10,<3.13" From 10a2aaf9dd5aba43075244d29af965908e3a31cf Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Fri, 24 Nov 2023 17:34:02 +0100 Subject: [PATCH 11/18] Remove pre-commit --- .pre-commit-config.yaml | 29 ----------------------------- 1 file changed, 29 deletions(-) delete mode 100644 .pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index 1eebebab..00000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,29 +0,0 @@ -repos: - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.5.0 - hooks: - - id: trailing-whitespace - - id: end-of-file-fixer - - id: check-case-conflict # Check for files that would conflict in case-insensitive filesystems - - id: check-merge-conflict # Check for files that contain merge conflict strings. - - id: check-toml # Check toml files for parseable syntax. - - id: debug-statements # Check for debugger imports and py37+ `breakpoint()` calls in python source. - - id: forbid-new-submodules # Check for git submodules - - - repo: https://github.com/bwhmather/ssort - rev: v0.11.6 - hooks: - - id: ssort - - - repo: https://github.com/astral-sh/ruff-pre-commit - # Ruff version. - rev: v0.1.3 - hooks: - - id: ruff - args: [--fix, --exit-non-zero-on-fix] - - - repo: 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"emcee>=3.1.4", + "numpy>=1.26.1", + "scipy>=1.11.3", + "matplotlib>=3.8.0", + "lmfit>=1.2.2", + "pydantic>=2.4.2", + "cachetools>=5.3.2", + "rich>=13.6.0", + "tomli>=2.0.1", + "rapidfuzz>=3.4.0", + "emcee>=3.1.4", ] requires-python = ">=3.10,<3.13" readme = "README.md" @@ -36,43 +36,12 @@ source = "scm" [tool.pdm.dev-dependencies] - test = [ "pytest>=7.4.0" ] - lint = [ "black>=23.7.0", "ruff>=0.0.278" ] - -[tool.black] - target-version = [ "py310" ] + test = [ "pytest>=7.4.3" ] + lint = [ "ruff>=0.1.3" ] [tool.ruff] - select = [ - "E", - "F", - "W", # flake8 - "B", # flake8-bugbear - "I", # isort - "ARG", # flake8-unused-arguments - "C4", # flake8-comprehensions - "EM", # flake8-errmsg - "ICN", # flake8-import-conventions - "ISC", # flake8-implicit-str-concat - "G", # flake8-logging-format - "PGH", # pygrep-hooks - "PIE", # flake8-pie - "PL", # pylint - "PT", # flake8-pytest-style - "PTH", # flake8-use-pathlib - "RET", # flake8-return - "RUF", # Ruff-specific - "SIM", # flake8-simplify - "T20", # flake8-print - # "TCH", # flake8-type-checking - "UP", # pyupgrade - "YTT", # flake8-2020 - "EXE", # flake8-executable - "NPY", # NumPy specific rules - "PD", # pandas-vet - ] - ignore = [ "PLR0913", "PD011", "RUF012", "PGH001" ] # Temporary ignore - target-version = "py310" + select = [ "ALL" ] + ignore = [ "ANN101", "ANN102" ] [tool.ruff.isort] known-first-party = [ "chemex" ] @@ -82,3 +51,6 @@ [tool.ruff.pep8-naming] classmethod-decorators = [ "pydantic.field_validator", "pydantic.model_validator" ] + + [tool.ruff.lint.pydocstyle] + convention = "google" From 4576a5969fe8e706073b94300826afc513929b91 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Tue, 28 Nov 2023 11:21:30 +0100 Subject: [PATCH 13/18] Add docstrings and refactor for code maintenance --- chemex/configuration/base.py | 61 +++- chemex/configuration/conditions.py | 72 ++++- chemex/containers/data.py | 87 ++++- chemex/containers/experiment.py | 56 ++-- chemex/containers/experiments.py | 159 +++++++++- chemex/containers/profile.py | 59 +++- chemex/experiments/builder.py | 12 +- chemex/experiments/catalog/cest_13c.py | 5 +- chemex/experiments/catalog/cest_15n.py | 5 +- chemex/experiments/catalog/cest_15n_cw.py | 5 +- chemex/experiments/catalog/cest_15n_tr.py | 5 +- chemex/experiments/catalog/cest_1hn_ap.py | 5 +- chemex/experiments/catalog/cest_1hn_ip_ap.py | 3 +- .../experiments/catalog/cest_ch3_1h_ip_ap.py | 5 +- chemex/experiments/catalog/coscest_13c.py | 12 +- .../experiments/catalog/coscest_1hn_ip_ap.py | 11 +- chemex/experiments/catalog/cpmg_13c_ip.py | 3 +- chemex/experiments/catalog/cpmg_13co_ap.py | 7 +- chemex/experiments/catalog/cpmg_15n_ip.py | 7 +- .../experiments/catalog/cpmg_15n_ip_0013.py | 13 +- chemex/experiments/catalog/cpmg_15n_tr.py | 3 +- .../experiments/catalog/cpmg_15n_tr_0013.py | 18 +- chemex/experiments/catalog/cpmg_1hn_ap.py | 7 +- .../experiments/catalog/cpmg_1hn_ap_0013.py | 12 +- .../experiments/catalog/cpmg_ch3_13c_h2c.py | 7 +- chemex/experiments/catalog/cpmg_ch3_1h_dq.py | 3 +- chemex/experiments/catalog/cpmg_ch3_1h_sq.py | 13 +- chemex/experiments/catalog/cpmg_ch3_1h_tq.py | 3 +- .../catalog/cpmg_ch3_1h_tq_diff.py | 8 +- chemex/experiments/catalog/cpmg_ch3_mq.py | 3 +- chemex/experiments/catalog/cpmg_chd2_1h_ap.py | 7 +- chemex/experiments/catalog/cpmg_hn_dq_zq.py | 5 +- chemex/experiments/catalog/dcest_13c.py | 5 +- chemex/experiments/catalog/dcest_15n.py | 5 +- chemex/experiments/catalog/relaxation_hznz.py | 9 +- chemex/experiments/catalog/relaxation_nz.py | 8 +- chemex/experiments/catalog/shift_15n_sq.py | 3 +- chemex/experiments/catalog/shift_15n_sqmq.py | 7 +- chemex/experiments/factories.py | 24 +- chemex/messages.py | 257 +++++++++++++-- chemex/models/constraints.py | 4 +- chemex/models/kinetic/settings_2st.py | 14 +- chemex/models/kinetic/settings_2st_binding.py | 15 +- chemex/models/kinetic/settings_2st_eyring.py | 6 +- .../kinetic/settings_2st_monomer_dimer.py | 6 +- .../kinetic/settings_2st_monomer_tetramer.py | 6 +- .../kinetic/settings_2st_monomer_trimer.py | 6 +- chemex/models/kinetic/settings_2st_rs.py | 9 +- .../settings_3st_binding_2st_partner.py | 11 +- .../models/kinetic/settings_3st_binding_cs.py | 10 +- .../models/kinetic/settings_3st_binding_if.py | 8 +- .../kinetic/settings_3st_double_binding.py | 14 +- chemex/models/kinetic/settings_3st_eyring.py | 4 +- .../settings_3st_monomer_dimer_tetramer.py | 9 +- .../settings_3st_monomer_dimer_trimer.py | 14 +- .../settings_4st_binding_2st_partner.py | 12 +- .../settings_4st_binding_3_bound_states.py | 11 +- chemex/nmr/basis.py | 14 +- chemex/nmr/liouvillian.py | 31 +- chemex/nmr/rates.py | 18 +- chemex/nmr/spectrometer.py | 33 +- chemex/optimize/fitting.py | 23 +- chemex/optimize/gridding.py | 17 +- chemex/optimize/grouping.py | 11 +- chemex/optimize/helper.py | 11 +- chemex/optimize/minimizer.py | 20 +- chemex/parameters/database.py | 299 +++++++++++++++++- chemex/parameters/factory.py | 23 +- chemex/parameters/name.py | 22 +- chemex/parameters/setting.py | 14 +- chemex/parameters/spins.py | 94 ++++-- chemex/parameters/userfunctions.py | 1 + chemex/plotters/cest.py | 31 +- chemex/plotters/cpmg.py | 29 +- chemex/plotters/relaxation.py | 18 +- chemex/plotters/shift.py | 2 +- chemex/printers/data.py | 41 ++- chemex/printers/parameters.py | 7 +- chemex/printers/plot.py | 18 +- chemex/uncertainty.py | 41 ++- 80 files changed, 1563 insertions(+), 413 deletions(-) diff --git a/chemex/configuration/base.py b/chemex/configuration/base.py index 784fb488..4877a0a9 100644 --- a/chemex/configuration/base.py +++ b/chemex/configuration/base.py @@ -1,25 +1,76 @@ +"""Utility module for list and string manipulation in Pydantic models. + +This module provides utility functions for ensuring a variable is in list format and +for converting strings to lowercase. It also includes a Pydantic BaseModel subclass +which applies these utilities to convert all keys in a model to lowercase. + +Typical usage example: + + variable = "Sample" + variable_list = ensure_list(variable) + lower_variable = to_lower("HELLO") + model_instance = BaseModelLowerCase.parse_obj({"Name": "Alice"}) +""" from __future__ import annotations -from typing import Any +from typing import TypeVar, cast from pydantic import BaseModel, model_validator +T = TypeVar("T") + + +def ensure_list(variable: T | list[T] | None) -> T | list[T]: + """Ensures that the input variable is returned as a list. + + If the input variable is already a list, it is returned as-is. + If the variable is None, an empty list is returned. + Otherwise, the variable is wrapped in a list and returned. + + Parameters: + variable (T | list[T] | None): The variable to be ensured as a list. -def ensure_list(variable: Any | list[Any] | None) -> list[Any]: + Returns: + T | list[T]: The input variable as a list. + """ if isinstance(variable, list): - return variable + return cast(list[T], variable) if variable is None: return [] return [variable] -def to_lower(string: Any) -> Any: +def to_lower(string: T) -> T: + """Converts a string to lowercase if it is of type str. + + If the input is not a string, it is returned unchanged. + + Parameters: + string (T): The string to be converted to lowercase. + + Returns: + T: The lowercase string if input is a string; otherwise, the original input. + """ if isinstance(string, str): return string.lower() return string class BaseModelLowerCase(BaseModel): + """A Pydantic BaseModel class that converts all keys in the model to lowercase. + + This is achieved using a model validator that operates before model initialization. + The validator applies the `to_lower` function to each key of the model. + """ + @model_validator(mode="before") - def key_to_lower(cls, model: dict[str, Any]) -> dict[str, Any]: + def key_to_lower(cls, model: dict[str, T]) -> dict[str, T]: + """Model validator to convert all dictionary keys to lowercase. + + Parameters: + model (dict[str, T]): The dictionary model with string keys. + + Returns: + dict[str, T]: The modified dictionary with all keys in lowercase. + """ return {to_lower(k): v for k, v in model.items()} diff --git a/chemex/configuration/conditions.py b/chemex/configuration/conditions.py index 374a0f64..7916cc22 100644 --- a/chemex/configuration/conditions.py +++ b/chemex/configuration/conditions.py @@ -1,7 +1,7 @@ from __future__ import annotations from functools import total_ordering -from typing import TYPE_CHECKING, Annotated, Any, Literal +from typing import TYPE_CHECKING, Annotated, Literal, TypeVar from pydantic import ( BaseModel, @@ -19,11 +19,24 @@ if TYPE_CHECKING: from collections.abc import Hashable +Self = TypeVar("Self", bound="Conditions") +T = TypeVar("T") LabelType = Annotated[Literal["1h", "2h", "13c", "15n"], BeforeValidator(to_lower)] @total_ordering class Conditions(BaseModel, frozen=True): + """Represents experimental conditions for NMR measurements. + + Attributes: + h_larmor_frq (NonNegativeFloat | None): Larmor frequency of Hydrogen in MHz. + temperature (float | None): Experimental temperature in degrees Celsius. + p_total (NonNegativeFloat | None): Total concentration of protein in the sample. + l_total (NonNegativeFloat | None): Total ligand concentration in the sample. + d2o (float | None): Fraction of D2O in the solvent, between 0 and 1. + label (tuple[LabelType, ...]): Tuple of NMR active isotopes used in the experiment. + """ + h_larmor_frq: NonNegativeFloat | None = None temperature: float | None = None p_total: NonNegativeFloat | None = None @@ -31,18 +44,21 @@ class Conditions(BaseModel, frozen=True): d2o: float | None = Field(gt=0.0, lt=1.0, default=None) label: tuple[LabelType, ...] = () - def rounded(self) -> Conditions: + def rounded(self: Self) -> Self: + """Returns a new instance with rounded h_larmor_frq and temperature.""" h_larmor_frq = round(self.h_larmor_frq, 1) if self.h_larmor_frq else None temperature = round(self.temperature, 1) if self.temperature else None return self.model_copy( - update={"h_larmor_frq": h_larmor_frq, "temperature": temperature} + update={"h_larmor_frq": h_larmor_frq, "temperature": temperature}, ) - def match(self, other: Conditions) -> bool: + def match(self: Self, other: Self) -> bool: + """Checks if the current instance is equivalent to another.""" return self == self & other @property def search_keys(self) -> set[Hashable]: + """Creates a set of hashable search keys based on conditions.""" return { self.h_larmor_frq, self.temperature, @@ -53,6 +69,7 @@ def search_keys(self) -> set[Hashable]: @property def section(self) -> str: + """Generates a string representation of the conditions.""" parts: list[str] = [] if self.temperature is not None: parts.append(f"T->{self.temperature:.1f}C") @@ -68,6 +85,7 @@ def section(self) -> str: @property def folder(self): + """Generates a folder name representation of the conditions.""" parts: list[str] = [] if self.temperature is not None: parts.append(f"{self.temperature:.1f}C") @@ -83,26 +101,41 @@ def folder(self): @property def is_deuterated(self) -> bool: + """Checks if the conditions include deuterium.""" return "2h" in self.label - def select_conditions(self, conditions_selection: tuple[str, ...]) -> Conditions: - return Conditions.model_construct( + def select_conditions(self: Self, conditions_selection: tuple[str, ...]) -> Self: + """Selects specific conditions based on given keys. + + Args: + conditions_selection (tuple[str, ...]): Keys to select conditions by. + + Returns: + A new instance of Conditions with selected conditions. + """ + return type(self).model_construct( **{ key: value for key, value in self.model_dump().items() if key in conditions_selection - } + }, ) - def __and__(self, other: Conditions) -> Conditions: + def __and__(self: Self, other: object) -> Self: + if not isinstance(other, type(self)): + return NotImplemented + """Defines bitwise AND operation for Conditions instances.""" self_dict = self.model_dump() other_dict = other.model_dump() intersection = { key: value for key, value in self_dict.items() if other_dict[key] == value } - return Conditions.model_construct(**intersection) + return type(self).model_construct(**intersection) - def __lt__(self, other: Conditions) -> bool: + def __lt__(self, other: object) -> bool: + """Defines less than operation for Conditions instances.""" + if not isinstance(other, type(self)): + return NotImplemented tuple_self = tuple( value if value is not None else -1e16 for value in self.model_dump().values() @@ -116,12 +149,19 @@ def __lt__(self, other: Conditions) -> bool: @total_ordering class ConditionsFromFile(Conditions, frozen=True): + """Extends Conditions to support loading experimental conditions from a file. + + This class includes additional validations specific to the file-based input. + """ + @model_validator(mode="before") - def key_to_lower(cls, model: dict[str, Any]) -> dict[str, Any]: + def key_to_lower(cls, model: dict[str, T]) -> dict[str, T]: + """Converts keys of the model dictionary to lowercase.""" return {to_lower(k): v for k, v in model.items()} @field_validator("d2o") def validate_d2o(cls, d2o: float | None) -> float | None: + """Validates the d2o field for specific model requirements.""" if "hd" in model.name and d2o is None: msg = 'To use the "hd" model, d2o must be provided' raise ValidationError(msg) @@ -129,17 +169,17 @@ def validate_d2o(cls, d2o: float | None) -> float | None: @field_validator("temperature") def validate_temperature(cls, temperature: float | None) -> float | None: + """Validates temperature field for specific model requirements.""" if "eyring" in model.name and temperature is None: msg = 'To use the "eyring" model, "temperature" must be provided' raise ValidationError(msg) return temperature @model_validator(mode="after") - def validate_p_total_l_total( - cls, conditions: ConditionsFromFile - ) -> ConditionsFromFile: - are_not_both_set = conditions.p_total is None or conditions.l_total is None + def validate_p_total_l_total(self: Self) -> Self: + """Validates both p_total and l_total for specific model requirements.""" + are_not_both_set = self.p_total is None or self.l_total is None if "binding" in model.name and are_not_both_set: msg = 'To use the "binding" model, "p_total" and "l_total" must be provided' raise ValidationError(msg) - return conditions + return self diff --git a/chemex/containers/data.py b/chemex/containers/data.py index fe4a2f30..48c1c534 100644 --- a/chemex/containers/data.py +++ b/chemex/containers/data.py @@ -3,18 +3,34 @@ from copy import deepcopy from dataclasses import dataclass, field from random import choices -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, Any, TypeVar import numpy as np if TYPE_CHECKING: + from numpy.typing import NDArray + from chemex.typing import ArrayBool, ArrayFloat +Self = TypeVar("Self", bound="Data") rng = np.random.default_rng() def get_scale(exp: ArrayFloat, err: ArrayFloat, calc: ArrayFloat) -> float: + """Calculate and return the scale factor for the calculated data. + + Args: + exp (ArrayFloat): The experimental data array. + err (ArrayFloat): The error associated with the experimental data. + calc (ArrayFloat): The calculated data array. + + Returns: + float: The calculated scale factor. + + Raises: + ZeroDivisionError: If division by zero occurs in the scale calculation. + """ if (calc == 0).all(): return 1.0 try: @@ -26,9 +42,22 @@ def get_scale(exp: ArrayFloat, err: ArrayFloat, calc: ArrayFloat) -> float: @dataclass class Data: + """Dataset with experimental, calculated data and metadata. + + Attributes: + exp (ArrayFloat): Experimental data. + err (ArrayFloat): Error in experimental data. + metadata (NDArray[Any]): Data metadata. + scale (float): Scale factor for calculated data. + size (int): Data points count, set post-instantiation. + calc (ArrayFloat): Calculated data, set post-instantiation. + mask (ArrayBool): Mask array, set post-instantiation. + refs (ArrayBool): Reference points array, set post-instantiation. + """ + exp: ArrayFloat err: ArrayFloat - metadata: ArrayFloat = field(default_factory=lambda: np.array([])) + metadata: NDArray[Any] = field(default_factory=lambda: np.array([])) scale: float = 1.0 size: int = field(init=False) calc: ArrayFloat = field(init=False) @@ -36,18 +65,24 @@ class Data: refs: ArrayBool = field(init=False) def __post_init__(self): + """Initialize computed attributes of the Data class.""" self.size = self.exp.size self.calc = np.full_like(self.exp, 1e32) self.mask = np.full_like(self.exp, True, dtype=np.bool_) self.refs = np.full_like(self.exp, False, dtype=np.bool_) def scale_calc(self) -> None: + """Scale the calculated data based on the experimental data and mask.""" mask = self.mask scale = get_scale(self.exp[mask], self.err[mask], self.calc[mask]) self.calc *= scale self.scale = scale def prepare_for_simulation(self) -> None: + """Prepare the dataset for simulation. + + Set experimental data to calculated values and errors to zero. + """ self.exp = self.calc.copy() self.err *= 0.0 if any(self.refs): @@ -56,19 +91,27 @@ def prepare_for_simulation(self) -> None: self.calc *= scale self.scale *= scale - def monte_carlo(self) -> Data: - """Generate a data set to run Monte-Carlo simulation.""" + def monte_carlo(self: Self) -> Self: + """Generate Data instance for Monte-Carlo simulation. + + Returns: + Self: New Data instance for Monte-Carlo simulation. + """ data = deepcopy(self) data.exp = rng.normal(self.calc, self.err) return data - def bootstrap(self: Data) -> Data: - """Generate a data set to run Bootstrap simulation.""" + def bootstrap(self: Self) -> Self: + """Generate Data instance using Bootstrap resampling. + + Returns: + Self: New Data instance for Bootstrap simulation. + """ indexes = np.arange(self.metadata.size) pool1 = indexes[self.refs & self.mask] pool2 = indexes[~self.refs & self.mask] bs_indexes: list[int] = sorted( - [*choices(pool1, k=pool1.size), *choices(pool2, k=pool2.size)] + [*choices(pool1, k=pool1.size), *choices(pool2, k=pool2.size)], ) data = deepcopy(self) data.metadata[self.mask] = self.metadata[bs_indexes] @@ -77,6 +120,7 @@ def bootstrap(self: Data) -> Data: return data def sort(self) -> None: + """Sort the data based on metadata values.""" sorted_indexes = self.metadata.argsort() self.metadata = self.metadata[sorted_indexes] self.exp = self.exp[sorted_indexes] @@ -86,12 +130,35 @@ def sort(self) -> None: self.mask = self.mask[sorted_indexes] def any_duplicate(self): + """Check for duplicate entries in metadata. + + Returns: + bool: True if duplicates exist, False otherwise. + """ return np.unique(self.metadata).size != self.metadata.size - def __add__(self: Data, other: Data) -> Data: - # Make sure that both datasets have the same number of points - assert self.size == other.size + def __add__(self: Self, other: Self) -> Self: + """Add two Data instances, combining their experimental data and errors. + + Both Data instances must have the same number of points. + + Args: + other (Self): Another Data instance. + + Returns: + Self: New Data instance representing the sum of the two datasets. + + Raises: + ValueError: If the sizes of the datasets do not match. + """ + # Check if the sizes of the datasets match + if self.size != other.size: + msg = "Sizes of the datasets must be identical to add them." + raise ValueError(msg) + + # Perform addition if sizes match result = deepcopy(self) result.exp = self.exp + other.exp result.err = np.sqrt(self.err**2 + other.err**2) + return result diff --git a/chemex/containers/experiment.py b/chemex/containers/experiment.py index 6f676863..0830857e 100644 --- a/chemex/containers/experiment.py +++ b/chemex/containers/experiment.py @@ -2,7 +2,7 @@ from dataclasses import dataclass, field from itertools import chain -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, TypeVar import numpy as np @@ -25,6 +25,8 @@ from chemex.plotters.plotter import Plotter from chemex.printers.data import Printer +Self = TypeVar("Self", bound="Experiment") + @dataclass class Experiment: @@ -37,7 +39,7 @@ class Experiment: def residuals(self, params: ParametersLF) -> list[float]: return list( - chain.from_iterable(profile.residuals(params) for profile in self.profiles) + chain.from_iterable(profile.residuals(params) for profile in self.profiles), ) def plot(self, path: Path): @@ -60,8 +62,8 @@ def select(self, selection: Selection): profiles: list[Profile] = [] filtered: list[Profile] = [] for profile in profiles_all: - included = include is None or profile.name.part_of(include) - excluded = exclude is not None and profile.name.part_of(exclude) + included = include is None or profile.spin_system.part_of(include) + excluded = exclude is not None and profile.spin_system.part_of(exclude) if included and not excluded: profiles.append(profile) else: @@ -76,7 +78,7 @@ def filter(self, params: ParametersLF): def _any_duplicate(self): return any(profile.any_duplicate() for profile in self.profiles) - def estimate_noise(self, kind: str): + def estimate_noise(self, kind: str) -> None: # TODO: Validation should be moved to the configuration file module implemented = ("file", "scatter", "duplicates") if kind not in implemented: @@ -98,33 +100,45 @@ def prepare_for_simulation(self) -> None: for profile in self.profiles: profile.prepare_for_simulation() - def monte_carlo(self) -> Experiment: + def monte_carlo(self: Self) -> Self: profiles = [profile.monte_carlo() for profile in self.profiles] - return Experiment( - self.filename, self.name, profiles, self.printer, self.plotter + return type(self)( + self.filename, + self.name, + profiles, + self.printer, + self.plotter, ) - def bootstrap(self) -> Experiment: + def bootstrap(self: Self) -> Self: profiles = [profile.bootstrap() for profile in self.profiles] - return Experiment( - self.filename, self.name, profiles, self.printer, self.plotter + return type(self)( + self.filename, + self.name, + profiles, + self.printer, + self.plotter, ) - def bootstrap_ns(self, groups: list[Group]) -> Experiment: + def bootstrap_ns(self: Self, groups: list[Group]) -> Self: """Residue-specific bootstrap.""" profiles: dict[Group, list[Profile]] = {} for profile in self.profiles: - profiles.setdefault(profile.name.groups["i"], []).append(profile) + profiles.setdefault(profile.spin_system.groups["i"], []).append(profile) profiles_bs_ns: list[Profile] = [] for group in groups: profiles_bs_ns.extend(profiles.get(group, [])) - return Experiment( - self.filename, self.name, profiles_bs_ns, self.printer, self.plotter + return type(self)( + self.filename, + self.name, + profiles_bs_ns, + self.printer, + self.plotter, ) @property def groups(self) -> set[Group]: - return {profile.name.groups["i"] for profile in self.profiles} + return {profile.spin_system.groups["i"] for profile in self.profiles} @property def param_id_sets(self) -> list[set[str]]: @@ -132,15 +146,19 @@ def param_id_sets(self) -> list[set[str]]: set(database.get_parameters(profile.param_ids)) for profile in self.profiles ] - def get_relevant_subset(self, param_ids: set[str]) -> Experiment: + def get_relevant_subset(self: Self, param_ids: set[str]) -> Self: profiles = [ profile for profile in self.profiles if set(database.get_parameters(profile.param_ids)) & param_ids ] - return Experiment( - self.filename, self.name, profiles, self.printer, self.plotter + return type(self)( + self.filename, + self.name, + profiles, + self.printer, + self.plotter, ) def __iter__(self) -> Iterator[Profile]: diff --git a/chemex/containers/experiments.py b/chemex/containers/experiments.py index 0e2805b1..72de3ccf 100644 --- a/chemex/containers/experiments.py +++ b/chemex/containers/experiments.py @@ -1,8 +1,13 @@ +"""Module for managing and manipulating collections of NMR experiments. + +This module contains the Experiments class and functions for generating different +types of simulated experiment datasets for statistical analysis. +""" from __future__ import annotations from itertools import chain from random import choices -from typing import TYPE_CHECKING, Literal +from typing import TYPE_CHECKING, Literal, TypeVar import numpy as np @@ -24,50 +29,104 @@ # Type definitions SelectionType = list[SpinSystem] | Literal["*", "all"], None +Self = TypeVar("Self", bound="Experiments") + class Experiments: + """A collection of NMR experiments. + + This class manages a set of NMR experiments, providing functionalities for + adding experiments, calculating residuals, simulation preparation, writing + data, plotting, and more. + """ + def __init__(self) -> None: + """Initialize an empty Experiments collection.""" self._experiments: dict[Path, Experiment] = {} @property def groups(self) -> set[Group]: - groups: set[Group] = set() - return groups.union(*(experiment.groups for experiment in self)) - - def add(self, experiment: Experiment): + """Get the set of unique groups across all experiments. + + Returns: + set[Group]: A set of unique groups. + """ + return {group for experiment in self for group in experiment.groups} + + def add(self, experiment: Experiment) -> None: + """Add an experiment to the collection. + + Args: + experiment (Experiment): The experiment to be added. + """ + if experiment.filename in self._experiments: + msg = "Experiment already exists." + raise ValueError(msg) self._experiments[experiment.filename] = experiment def residuals(self, params: Parameters) -> ArrayFloat: + """Calculate the residuals for all experiments in the collection. + + Args: + params (Parameters): Parameters for residual calculation. + + Returns: + ArrayFloat: Residuals as a NumPy array. + """ return np.asarray( list( - chain.from_iterable(experiment.residuals(params) for experiment in self) - ) + chain.from_iterable( + experiment.residuals(params) for experiment in self + ), + ), ) def back_calculate(self) -> None: + """Back calculate experiments' parameters from the database.""" params_lf = database.build_lmfit_params(self.param_ids) self.residuals(params_lf) def prepare_for_simulation(self) -> None: + """Prepare each experiment in the collection for simulation.""" self.back_calculate() for experiment in self: experiment.prepare_for_simulation() def write(self, path: Path): + """Write experiment data to a specified path. + + Args: + path (Path): Directory path to write data. + """ path_dat = path / "Data" path_dat.mkdir(parents=True, exist_ok=True) for experiment in self: experiment.write(path_dat) def plot(self, path: Path): + """Plot each experiment in the collection. + + Args: + path (Path): Directory path for saving plots. + """ for experiment in self: experiment.plot(path) def plot_simulation(self, path: Path): + """Plot simulations for each experiment. + + Args: + path (Path): Directory path for saving simulation plots. + """ for experiment in self: experiment.plot_simulation(path) - def select(self, selection: Selection): + def select(self, selection: Selection) -> None: + """Select experiments based on the given selection criteria. + + Args: + selection (Selection): Criteria for selecting experiments. + """ if selection.include is None and selection.exclude is None: return for experiment in self: @@ -76,38 +135,84 @@ def select(self, selection: Selection): @property def param_id_sets(self) -> list[set[str]]: + """Get a list of parameter ID sets for all experiments. + + Returns: + list[set[str]]: List of sets containing parameter IDs. + """ return list( - chain.from_iterable(experiment.param_id_sets for experiment in self) + chain.from_iterable(experiment.param_id_sets for experiment in self), ) @property def param_ids(self) -> set[str]: + """Get a set of all unique parameter IDs across experiments. + + Returns: + set[str]: Set of unique parameter IDs. + """ result: set[str] = set() return result.union(*(self.param_id_sets)) def filter(self) -> None: + """Get a set of all unique parameter IDs across experiments. + + Returns: + set[str]: Set of unique parameter IDs. + """ params = database.build_lmfit_params(self.param_ids) for experiment in self: experiment.filter(params) - def get_relevant_subset(self, param_ids: set[str]) -> Experiments: - relevant_subset = Experiments() + def get_relevant_subset(self: Self, param_ids: set[str]) -> Self: + """Get a subset of experiments relevant to specified parameter IDs. + + Args: + param_ids (set[str]): Parameter IDs to filter experiments. + + Returns: + Self: Subset of Experiments relevant to given parameter IDs. + """ + relevant_subset = type(self)() for experiment in self: if subset := experiment.get_relevant_subset(param_ids): relevant_subset.add(subset) return relevant_subset def __iter__(self) -> Iterator[Experiment]: - yield from self._experiments.values() + """Iterate over the experiments in the collection. + + Returns: + Iterator[Experiment]: An iterator over experiments. + """ + return iter(self._experiments.values()) def __len__(self) -> int: + """Get the total number of data points in the collection. + + Returns: + int: Total number of data points. + """ return sum(len(experiment) for experiment in self) def __bool__(self) -> bool: - return bool(len(self)) + """Check if the collection contains any experiments. + + Returns: + bool: True if collection is non-empty, False otherwise. + """ + return bool(self._experiments) def generate_monte_carlo_experiments(experiments: Experiments) -> Experiments: + """Generate a new Experiments collection for Monte Carlo simulation. + + Args: + experiments (Experiments): Original experiments. + + Returns: + Experiments: Collection with Monte Carlo simulated data. + """ experiments_mc = Experiments() for experiment in experiments: experiments_mc.add(experiment.monte_carlo()) @@ -115,6 +220,14 @@ def generate_monte_carlo_experiments(experiments: Experiments) -> Experiments: def generate_bootstrap_experiments(experiments: Experiments) -> Experiments: + """Generate a new Experiments collection for Bootstrap simulation. + + Args: + experiments (Experiments): Original experiments. + + Returns: + Experiments: Collection with Bootstrap simulated data. + """ experiments_mc = Experiments() for experiment in experiments: experiments_mc.add(experiment.bootstrap()) @@ -122,6 +235,14 @@ def generate_bootstrap_experiments(experiments: Experiments) -> Experiments: def generate_bootstrap_ns_experiments(experiments: Experiments) -> Experiments: + """Generate a new Experiments collection for Bootstrap NS simulation. + + Args: + experiments (Experiments): Original experiments. + + Returns: + Experiments: Collection with Bootstrap NS simulated data. + """ groups = experiments.groups groups_bs = choices(tuple(groups), k=len(groups)) experiments_bs = Experiments() @@ -131,8 +252,18 @@ def generate_bootstrap_ns_experiments(experiments: Experiments) -> Experiments: def generate_exp_for_statistics( - experiments: Experiments, statistic_name: str + experiments: Experiments, + statistic_name: str, ) -> Experiments: + """Generate experiments for a specific statistical method. + + Args: + experiments (Experiments): Original experiments. + statistic_name (str): Name of the statistical method. + + Returns: + Experiments: Collection with simulated data for statistics. + """ generators = { "mc": generate_monte_carlo_experiments, "bs": generate_bootstrap_experiments, diff --git a/chemex/containers/profile.py b/chemex/containers/profile.py index 3e6a0013..fa47f90f 100644 --- a/chemex/containers/profile.py +++ b/chemex/containers/profile.py @@ -4,11 +4,13 @@ from dataclasses import dataclass, field from functools import cached_property from operator import attrgetter -from typing import TYPE_CHECKING, Protocol +from typing import TYPE_CHECKING, Protocol, TypeVar from cachetools import LRUCache, cachedmethod if TYPE_CHECKING: + from collections.abc import Hashable + from lmfit import Parameters as ParametersLF from chemex.containers.data import Data @@ -17,22 +19,33 @@ from chemex.printers.data import Printer from chemex.typing import ArrayBool, ArrayFloat +Self = TypeVar("Self", bound="Profile") + class PulseSequence(Protocol): + """Defines a protocol for pulse sequence classes.""" + def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: + """Calculate the ArrayFloat given a Spectrometer and Data.""" ... def is_reference(self, metadata: ArrayFloat) -> ArrayBool: + """Check if the metadata is a reference.""" ... class Filterer(Protocol): + """Defines a protocol for filterer classes.""" + def filter(self, data: Data) -> None: + """Filter the given Data.""" ... @dataclass(order=True) class Profile: + """Represents the profile for a specific experiment.""" + data: Data = field(compare=False) spectrometer: Spectrometer = field(compare=False) pulse_sequence: PulseSequence = field(compare=False) @@ -40,35 +53,40 @@ class Profile: printer: Printer = field(compare=False) filterer: Filterer | None = field(compare=False, default=None) is_scaled: bool = field(compare=False, default=True) - name: SpinSystem = field(compare=True, init=False) + spin_system: SpinSystem = field(compare=True, init=False) cache: LRUCache = field(compare=False, init=False) - def _cache_key(self, params: ParametersLF) -> tuple[float, ...]: + def _cache_key(self, params: ParametersLF) -> tuple[Hashable, ...]: return ( *(params[param_id].value for param_id in self.param_ids), - *self.data.metadata, + self.data.metadata.tostring(), ) def __post_init__(self): - self.name = self.spectrometer.liouvillian.spin_system + """Initialize derived attributes.""" + self.spin_system = self.spectrometer.liouvillian.spin_system self.data.refs = self.pulse_sequence.is_reference(self.data.metadata) self.cache = LRUCache(maxsize=5) @cached_property def param_ids(self) -> set[str]: + """Get the set of parameter IDs.""" return set(self.name_map.values()) - def _get_par_values(self, params: ParametersLF) -> dict[str, float]: + def _get_parameter_values(self, params: ParametersLF) -> dict[str, float]: + """Get the parameter values from the provided parameters.""" return { local_name: params[param_id].value for local_name, param_id in self.name_map.items() } def update_spectrometer(self, params: ParametersLF) -> None: - par_values = self._get_par_values(params) - self.spectrometer.update(par_values) + """Update the spectrometer settings.""" + parameter_values = self._get_parameter_values(params) + self.spectrometer.update(parameter_values) def calculate(self, params: ParametersLF) -> ArrayFloat: + """Calculate and return the ArrayFloat.""" self.update_spectrometer(params) self.data.calc = self.pulse_sequence.calculate(self.spectrometer, self.data) if self.is_scaled: @@ -77,39 +95,46 @@ def calculate(self, params: ParametersLF) -> ArrayFloat: @cachedmethod(attrgetter("cache"), key=_cache_key) def residuals(self, params: ParametersLF) -> ArrayFloat: + """Calculate and return residuals.""" residuals = (self.calculate(params) - self.data.exp) / self.data.err return residuals[self.data.mask] def filter(self, params: ParametersLF) -> None: - if self.filterer is None: - return - self.update_spectrometer(params) - self.filterer.filter(self.data) + """Apply a filter to the data, if a filterer is available.""" + if self.filterer is not None: + self.update_spectrometer(params) + self.filterer.filter(self.data) def set_noise(self, value: float): + """Set the noise value.""" self.data.err[:] = value def prepare_for_simulation(self) -> None: + """Prepare data for simulation.""" self.data.prepare_for_simulation() - def monte_carlo(self) -> Profile: + def monte_carlo(self: Self) -> Self: + """Generate a Monte Carlo variant of the profile.""" profile = deepcopy(self) profile.data = profile.data.monte_carlo() return profile - def bootstrap(self) -> Profile: - """Make a profile for bootstrap analysis.""" + def bootstrap(self: Self) -> Self: + """Generate a bootstrap variant of the profile.""" profile = deepcopy(self) profile.data = profile.data.bootstrap() return profile def any_duplicate(self): + """Check for duplicate data points.""" return self.data.any_duplicate() - def __add__(self: Profile, other: Profile) -> Profile: + def __add__(self: Self, other: Self) -> Self: + """Combine two profiles.""" profile = deepcopy(self) profile.data = self.data + other.data return profile def __str__(self) -> str: - return self.printer.print(str(self.name), self.data) + """String representation of the Profile.""" + return self.printer.print(str(self.spin_system), self.data) diff --git a/chemex/experiments/builder.py b/chemex/experiments/builder.py index 2f31718b..cbb9e337 100644 --- a/chemex/experiments/builder.py +++ b/chemex/experiments/builder.py @@ -61,7 +61,10 @@ def _apply_selection(dataset: Dataset, selection: Selection) -> Dataset: def _create_dataset( - filename: Path, live: Live, factory: Creators, config: ConfigType + filename: Path, + live: Live, + factory: Creators, + config: ConfigType, ) -> Dataset: try: dataset = factory.create_dataset(filename.parent, config) @@ -73,7 +76,10 @@ def _create_dataset( def _create_config( - filename: Path, live: Live, factory: Creators, config_dict: MutableMapping[str, Any] + filename: Path, + live: Live, + factory: Creators, + config_dict: MutableMapping[str, Any], ) -> ConfigType: try: config = factory.create_config(config_dict) @@ -116,7 +122,7 @@ def build_experiment(filename: Path, selection: Selection) -> Experiment: printer, filterer, config.data.scaled, - ) + ), ) live.update(get_reading_exp_text(filename, experiment_name, len(profiles))) diff --git a/chemex/experiments/catalog/cest_13c.py b/chemex/experiments/catalog/cest_13c.py index 73713ce9..f2fcf8fd 100644 --- a/chemex/experiments/catalog/cest_13c.py +++ b/chemex/experiments/catalog/cest_13c.py @@ -46,7 +46,8 @@ class Cest13CConfig(ExperimentConfig[Cest13CSettings, CestDataSettings]): def to_be_fitted(self) -> ToBeFitted: state = self.experiment.observed_state return ToBeFitted( - rates=["r2_i", f"r1_i_{state}"], model_free=[f"tauc_{state}", f"s2_{state}"] + rates=["r2_i", f"r1_i_{state}"], + model_free=[f"tauc_{state}", f"s2_{state}"], ) @@ -101,7 +102,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: ) return np.array( - [spectrometer.detect(intensities[offset]) for offset in offsets] + [spectrometer.detect(intensities[offset]) for offset in offsets], ) diff --git a/chemex/experiments/catalog/cest_15n.py b/chemex/experiments/catalog/cest_15n.py index 9b339839..9f7e81b7 100644 --- a/chemex/experiments/catalog/cest_15n.py +++ b/chemex/experiments/catalog/cest_15n.py @@ -47,7 +47,8 @@ class Cest15NConfig(ExperimentConfig[Cest15NSettings, CestDataSettings]): def to_be_fitted(self) -> ToBeFitted: state = self.experiment.observed_state return ToBeFitted( - rates=["r2_i", f"r1_i_{state}"], model_free=[f"tauc_{state}", f"s2_{state}"] + rates=["r2_i", f"r1_i_{state}"], + model_free=[f"tauc_{state}", f"s2_{state}"], ) @@ -100,7 +101,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: ) return np.array( - [spectrometer.detect(intensities[offset]) for offset in offsets] + [spectrometer.detect(intensities[offset]) for offset in offsets], ) diff --git a/chemex/experiments/catalog/cest_15n_cw.py b/chemex/experiments/catalog/cest_15n_cw.py index 8a0d239a..86bc8879 100644 --- a/chemex/experiments/catalog/cest_15n_cw.py +++ b/chemex/experiments/catalog/cest_15n_cw.py @@ -63,7 +63,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cest15NCwConfig, spin_system: SpinSystem + config: Cest15NCwConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -116,7 +117,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: ) return np.array( - [spectrometer.detect(intensities[offset]) for offset in offsets] + [spectrometer.detect(intensities[offset]) for offset in offsets], ) diff --git a/chemex/experiments/catalog/cest_15n_tr.py b/chemex/experiments/catalog/cest_15n_tr.py index 9520e63c..4f80900b 100644 --- a/chemex/experiments/catalog/cest_15n_tr.py +++ b/chemex/experiments/catalog/cest_15n_tr.py @@ -62,7 +62,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cest15NTrConfig, spin_system: SpinSystem + config: Cest15NTrConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -121,7 +122,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: ) return np.array( - [spectrometer.detect(intensities[offset]) for offset in offsets] + [spectrometer.detect(intensities[offset]) for offset in offsets], ) diff --git a/chemex/experiments/catalog/cest_1hn_ap.py b/chemex/experiments/catalog/cest_1hn_ap.py index 44ce8002..556dc6e5 100644 --- a/chemex/experiments/catalog/cest_1hn_ap.py +++ b/chemex/experiments/catalog/cest_1hn_ap.py @@ -56,7 +56,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cest1HnApConfig, spin_system: SpinSystem + config: Cest1HnApConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -103,7 +104,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: ) return np.array( - [spectrometer.detect(intensities[offset]) for offset in offsets] + [spectrometer.detect(intensities[offset]) for offset in offsets], ) diff --git a/chemex/experiments/catalog/cest_1hn_ip_ap.py b/chemex/experiments/catalog/cest_1hn_ip_ap.py index 11e4f09d..1c0d1404 100644 --- a/chemex/experiments/catalog/cest_1hn_ip_ap.py +++ b/chemex/experiments/catalog/cest_1hn_ip_ap.py @@ -70,7 +70,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cest1HnIpApConfig, spin_system: SpinSystem + config: Cest1HnIpApConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/cest_ch3_1h_ip_ap.py b/chemex/experiments/catalog/cest_ch3_1h_ip_ap.py index 6caa7bc6..c76dfd02 100644 --- a/chemex/experiments/catalog/cest_ch3_1h_ip_ap.py +++ b/chemex/experiments/catalog/cest_ch3_1h_ip_ap.py @@ -44,7 +44,7 @@ def detection(self) -> str: class CestCh31HIpApConfig( - ExperimentConfig[CestCh31HIpApSettings, CestDataSettingsNoRef] + ExperimentConfig[CestCh31HIpApSettings, CestDataSettingsNoRef], ): @property def to_be_fitted(self) -> ToBeFitted: @@ -62,7 +62,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CestCh31HIpApConfig, spin_system: SpinSystem + config: CestCh31HIpApConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/coscest_13c.py b/chemex/experiments/catalog/coscest_13c.py index f583bd11..b0d12728 100644 --- a/chemex/experiments/catalog/coscest_13c.py +++ b/chemex/experiments/catalog/coscest_13c.py @@ -52,12 +52,14 @@ class CosCest13CConfig(ExperimentConfig[CosCest13CSettings, CestDataSettings]): def to_be_fitted(self) -> ToBeFitted: state = self.experiment.observed_state return ToBeFitted( - rates=["r2_i", f"r1_i_{state}"], model_free=[f"tauc_{state}", f"s2_{state}"] + rates=["r2_i", f"r1_i_{state}"], + model_free=[f"tauc_{state}", f"s2_{state}"], ) def build_spectrometer( - config: CosCest13CConfig, spin_system: SpinSystem + config: CosCest13CConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -117,7 +119,9 @@ def _calc_cosine_shape(self, spectrometer: Spectrometer) -> ArrayFloat: if n_left: pulse_left = spectrometer.shaped_pulse_i( - n_left * dt, amplitudes[:n_left], phases[:n_left] + n_left * dt, + amplitudes[:n_left], + phases[:n_left], ) pulse = pulse_left[phase_left] @ pulse @@ -146,7 +150,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: intensities[offset] = d_eq @ self._calc_cosine_shape(spectrometer) @ start return np.array( - [spectrometer.detect(intensities[offset]) for offset in offsets] + [spectrometer.detect(intensities[offset]) for offset in offsets], ) diff --git a/chemex/experiments/catalog/coscest_1hn_ip_ap.py b/chemex/experiments/catalog/coscest_1hn_ip_ap.py index 92c6a9c2..ba50f81d 100644 --- a/chemex/experiments/catalog/coscest_1hn_ip_ap.py +++ b/chemex/experiments/catalog/coscest_1hn_ip_ap.py @@ -48,7 +48,7 @@ def detection(self) -> str: class CosCest1HnIpApConfig( - ExperimentConfig[CosCest1HnIpApSettings, CestDataSettingsNoRef] + ExperimentConfig[CosCest1HnIpApSettings, CestDataSettingsNoRef], ): @property def to_be_fitted(self) -> ToBeFitted: @@ -66,7 +66,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CosCest1HnIpApConfig, spin_system: SpinSystem + config: CosCest1HnIpApConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -121,7 +122,9 @@ def _calc_cosine_shape(self, spectrometer: Spectrometer) -> ArrayFloat: if n_left: pulse_left = spectrometer.shaped_pulse_i( - n_left * dt, amplitudes[:n_left], phases[:n_left] + n_left * dt, + amplitudes[:n_left], + phases[:n_left], ) pulse = pulse_left[phase_left] @ pulse @@ -132,7 +135,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: spectrometer.offset_i = 0.0 d_d1, d_taua, d_t1 = spectrometer.delays( - [self.settings.d1, self.settings.taua, self.settings.time_t1] + [self.settings.d1, self.settings.taua, self.settings.time_t1], ) pp90_i = spectrometer.perfect90_i diff --git a/chemex/experiments/catalog/cpmg_13c_ip.py b/chemex/experiments/catalog/cpmg_13c_ip.py index d61669e2..6a4cbeb3 100644 --- a/chemex/experiments/catalog/cpmg_13c_ip.py +++ b/chemex/experiments/catalog/cpmg_13c_ip.py @@ -51,7 +51,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cpmg13CIpConfig, spin_system: SpinSystem + config: Cpmg13CIpConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/cpmg_13co_ap.py b/chemex/experiments/catalog/cpmg_13co_ap.py index 7edd81d8..a5362f28 100644 --- a/chemex/experiments/catalog/cpmg_13co_ap.py +++ b/chemex/experiments/catalog/cpmg_13co_ap.py @@ -57,7 +57,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cpmg13CoApConfig, spin_system: SpinSystem + config: Cpmg13CoApConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -120,7 +121,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: # Calculating the instensities as a function of ncyc intensities = { - 0.0: spectrometer.detect(d_eq @ p90[1] @ p_flip0 @ p90[1] @ start) + 0.0: spectrometer.detect(d_eq @ p90[1] @ p_flip0 @ p90[1] @ start), } part1 = d_neg @ p90[1] @ start @@ -130,7 +131,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: echo = d_cp[ncyc] @ perfect180x @ d_cp[ncyc] cpmg = matrix_power(echo, int(ncyc)) intensities[ncyc] = spectrometer.detect( - part2 @ cpmg @ p_flip @ cpmg @ part1 + part2 @ cpmg @ p_flip @ cpmg @ part1, ) # Return profile diff --git a/chemex/experiments/catalog/cpmg_15n_ip.py b/chemex/experiments/catalog/cpmg_15n_ip.py index 267bd2f2..5090d329 100644 --- a/chemex/experiments/catalog/cpmg_15n_ip.py +++ b/chemex/experiments/catalog/cpmg_15n_ip.py @@ -51,7 +51,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cpmg15NIpConfig, spin_system: SpinSystem + config: Cpmg15NIpConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -107,14 +108,14 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: intensities = { 0.0: spectrometer.detect(d_eq @ p90[0] @ p180pmx @ p90[0] @ start), -1.0: spectrometer.detect( - part2 @ d_cp[-1.0] @ p180pmx @ d_cp[-1.0] @ part1 + part2 @ d_cp[-1.0] @ p180pmx @ d_cp[-1.0] @ part1, ), } for ncyc in set(ncycs) - {0.0, -1.0}: echo = d_cp[ncyc] @ p180[1] @ d_cp[ncyc] cpmg = matrix_power(echo, int(ncyc)) intensities[ncyc] = spectrometer.detect( - part2 @ cpmg @ p180pmx @ cpmg @ part1 + part2 @ cpmg @ p180pmx @ cpmg @ part1, ) # Return profile diff --git a/chemex/experiments/catalog/cpmg_15n_ip_0013.py b/chemex/experiments/catalog/cpmg_15n_ip_0013.py index 595a4b0a..876d6596 100644 --- a/chemex/experiments/catalog/cpmg_15n_ip_0013.py +++ b/chemex/experiments/catalog/cpmg_15n_ip_0013.py @@ -51,7 +51,7 @@ def detection(self) -> str: class Cpmg15N0013IpConfig( - ExperimentConfig[Cpmg15N0013IpSettings, RelaxationDataSettings] + ExperimentConfig[Cpmg15N0013IpSettings, RelaxationDataSettings], ): @property def to_be_fitted(self) -> ToBeFitted: @@ -60,7 +60,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cpmg15N0013IpConfig, spin_system: SpinSystem + config: Cpmg15N0013IpConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -108,7 +109,7 @@ def _get_phases(self, ncyc: ArrayFloat) -> ArrayInt: [ [0, 0, 1, 3, 0, 0, 3, 1, 0, 0, 3, 1, 0, 0, 1, 3], [1, 3, 2, 2, 3, 1, 2, 2, 3, 1, 2, 2, 1, 3, 2, 2], - ] + ], ) indexes = np.flip(np.arange(2 * int(ncyc))) return np.take(cp_phases, indexes, mode="wrap", axis=1) @@ -140,15 +141,15 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: @ d_pos @ p180[[0, 1]] @ p90[1] - @ start - ) + @ start, + ), } for ncyc in set(ncycs) - {0.0}: phases = self._get_phases(ncyc) echo = d_cp[ncyc] @ p180 @ d_cp[ncyc] cpmg = reduce(np.matmul, echo[phases.T]) intensities[ncyc] = spectrometer.detect( - d_delta[ncyc] @ p90[3] @ d_neg @ cpmg @ d_neg @ p90[1] @ start + d_delta[ncyc] @ p90[3] @ d_neg @ cpmg @ d_neg @ p90[1] @ start, ) # Return profile diff --git a/chemex/experiments/catalog/cpmg_15n_tr.py b/chemex/experiments/catalog/cpmg_15n_tr.py index 9ef98eba..0eee71b1 100644 --- a/chemex/experiments/catalog/cpmg_15n_tr.py +++ b/chemex/experiments/catalog/cpmg_15n_tr.py @@ -66,7 +66,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cpmg15NTrConfig, spin_system: SpinSystem + config: Cpmg15NTrConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/cpmg_15n_tr_0013.py b/chemex/experiments/catalog/cpmg_15n_tr_0013.py index 6e9ed771..a9fc4c9d 100644 --- a/chemex/experiments/catalog/cpmg_15n_tr_0013.py +++ b/chemex/experiments/catalog/cpmg_15n_tr_0013.py @@ -57,7 +57,7 @@ def detection(self) -> str: class Cpmg15NTr0013Config( - ExperimentConfig[Cpmg15NTr0013Settings, RelaxationDataSettings] + ExperimentConfig[Cpmg15NTr0013Settings, RelaxationDataSettings], ): @property def to_be_fitted(self) -> ToBeFitted: @@ -73,7 +73,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cpmg15NTr0013Config, spin_system: SpinSystem + config: Cpmg15NTr0013Config, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -118,13 +119,13 @@ def _get_phases(self, ncyc: float) -> tuple[ArrayInt, ArrayInt]: [ [1, 1, 0, 2, 1, 1, 2, 0, 1, 1, 2, 0, 1, 1, 0, 2], [0, 2, 3, 3, 2, 0, 3, 3, 2, 0, 3, 3, 0, 2, 3, 3], - ] + ], ) cp_phases2 = np.array( [ [0, 0, 1, 3, 0, 0, 3, 1, 0, 0, 3, 1, 0, 0, 1, 3], [1, 3, 2, 2, 3, 1, 2, 2, 3, 1, 2, 2, 1, 3, 2, 2], - ] + ], ) indexes = np.arange(int(ncyc)) phases1 = np.take(cp_phases1, np.flip(indexes), mode="wrap", axis=1) @@ -167,7 +168,8 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: else: p180_is = p90[0] @ p90[1] @ p180_sx @ p90[1] @ p90[0] palmer = np.mean( - p90[[0, 2]] @ d_taub @ p180_is @ d_taub @ p180_sx @ p90[[1, 3]], axis=0 + p90[[0, 2]] @ d_taub @ p180_is @ d_taub @ p180_sx @ p90[[1, 3]], + axis=0, ) # Calculating the instensities as a function of ncyc @@ -181,8 +183,8 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: @ p180[[0, 1]] @ p90[0] @ d_delta[0] - @ start - ) + @ start, + ), } for ncyc in set(ncycs) - {0.0}: phases1, phases2 = self._get_phases(ncyc) @@ -198,7 +200,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: @ cpmg1 @ p90[0] @ d_delta[ncyc] - @ start + @ start, ) # Return profile diff --git a/chemex/experiments/catalog/cpmg_1hn_ap.py b/chemex/experiments/catalog/cpmg_1hn_ap.py index f8387c86..18500523 100644 --- a/chemex/experiments/catalog/cpmg_1hn_ap.py +++ b/chemex/experiments/catalog/cpmg_1hn_ap.py @@ -56,7 +56,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cpmg1HnApConfig, spin_system: SpinSystem + config: Cpmg1HnApConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -117,7 +118,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: part2 = d_eq_2 @ p90[0] @ d_neg intensities = { 0.0: spectrometer.detect( - d_eq_2 @ p90[0] @ p180pmx @ p90[0] @ d_eq_1 @ start + d_eq_2 @ p90[0] @ p180pmx @ p90[0] @ d_eq_1 @ start, ), -1.0: spectrometer.detect(part2 @ d_cp[-1] @ p180pmx @ d_cp[-1] @ part1), } @@ -125,7 +126,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: echo = d_cp[ncyc] @ p180[1] @ d_cp[ncyc] cpmg = matrix_power(echo, int(ncyc)) intensities[ncyc] = spectrometer.detect( - part2 @ cpmg @ p180pmx @ cpmg @ part1 + part2 @ cpmg @ p180pmx @ cpmg @ part1, ) # Return profile diff --git a/chemex/experiments/catalog/cpmg_1hn_ap_0013.py b/chemex/experiments/catalog/cpmg_1hn_ap_0013.py index 211b0ef0..c3140aaa 100644 --- a/chemex/experiments/catalog/cpmg_1hn_ap_0013.py +++ b/chemex/experiments/catalog/cpmg_1hn_ap_0013.py @@ -56,7 +56,7 @@ def detection(self) -> str: class Cpmg1HnAp0013Config( - ExperimentConfig[Cpmg1HnAp0013Settings, RelaxationDataSettings] + ExperimentConfig[Cpmg1HnAp0013Settings, RelaxationDataSettings], ): @property def to_be_fitted(self) -> ToBeFitted: @@ -65,7 +65,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Cpmg1HnAp0013Config, spin_system: SpinSystem + config: Cpmg1HnAp0013Config, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -86,7 +87,8 @@ class Cpmg1HnAp0013Sequence: settings: Cpmg1HnAp0013Settings def _get_delays( - self, ncycs: ArrayFloat + self, + ncycs: ArrayFloat, ) -> tuple[dict[float, float], dict[float, float], list[float]]: ncycs_no_ref = ncycs[ncycs > 0] tau_cps = { @@ -115,13 +117,13 @@ def _get_phases(self, ncyc: ArrayFloat) -> tuple[ArrayInt, ArrayInt]: [ [1, 1, 2, 0, 1, 1, 0, 2, 1, 1, 0, 2, 1, 1, 2, 0], [2, 0, 3, 3, 0, 2, 3, 3, 0, 2, 3, 3, 2, 0, 3, 3], - ] + ], ) cp_phases2 = np.array( [ [3, 3, 2, 0, 3, 3, 0, 2, 3, 3, 0, 2, 3, 3, 2, 0], [2, 0, 1, 1, 0, 2, 1, 1, 0, 2, 1, 1, 2, 0, 1, 1], - ] + ], ) indexes = np.arange(int(ncyc)) phases1 = np.take(cp_phases1, np.flip(indexes), mode="wrap", axis=1) diff --git a/chemex/experiments/catalog/cpmg_ch3_13c_h2c.py b/chemex/experiments/catalog/cpmg_ch3_13c_h2c.py index c7608439..3fdecd04 100644 --- a/chemex/experiments/catalog/cpmg_ch3_13c_h2c.py +++ b/chemex/experiments/catalog/cpmg_ch3_13c_h2c.py @@ -53,7 +53,7 @@ def detection(self) -> str: class CpmgCh313CH2cConfig( - ExperimentConfig[CpmgCh313CH2cSettings, RelaxationDataSettings] + ExperimentConfig[CpmgCh313CH2cSettings, RelaxationDataSettings], ): @property def to_be_fitted(self) -> ToBeFitted: @@ -62,7 +62,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CpmgCh313CH2cConfig, spin_system: SpinSystem + config: CpmgCh313CH2cConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -120,7 +121,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: # Calculating the instensities as a function of ncyc intensities = { - 0.0: spectrometer.detect(d_eq @ p90[1] @ palmer @ p90[0] @ start) + 0.0: spectrometer.detect(d_eq @ p90[1] @ palmer @ p90[0] @ start), } part1 = d_neg @ p90[0] @ start part2 = d_eq @ p90[1] @ d_neg diff --git a/chemex/experiments/catalog/cpmg_ch3_1h_dq.py b/chemex/experiments/catalog/cpmg_ch3_1h_dq.py index 1a81a94e..f50d9f4d 100644 --- a/chemex/experiments/catalog/cpmg_ch3_1h_dq.py +++ b/chemex/experiments/catalog/cpmg_ch3_1h_dq.py @@ -56,7 +56,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CpmgCh31HDqConfig, spin_system: SpinSystem + config: CpmgCh31HDqConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/cpmg_ch3_1h_sq.py b/chemex/experiments/catalog/cpmg_ch3_1h_sq.py index 0740e443..ca22ce32 100644 --- a/chemex/experiments/catalog/cpmg_ch3_1h_sq.py +++ b/chemex/experiments/catalog/cpmg_ch3_1h_sq.py @@ -57,7 +57,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CpmgCh31HSqConfig, spin_system: SpinSystem + config: CpmgCh31HSqConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -129,12 +130,12 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: if self.settings.ipap_flg: intensities = { 0.0: spectrometer.detect( - d_taua @ (p180pmy @ p180c_py + p180c_my @ p180pmy) @ d_taua @ start - ) + d_taua @ (p180pmy @ p180c_py + p180c_my @ p180pmy) @ d_taua @ start, + ), } else: intensities = { - 0.0: spectrometer.detect(d_taua @ d_taua @ p180pmy @ p180c_py @ start) + 0.0: spectrometer.detect(d_taua @ d_taua @ p180pmy @ p180c_py @ start), } phases1, phases2 = self._get_phases() @@ -153,11 +154,11 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: centre = cpmg2 @ p180pmy @ cpmg1 if self.settings.ipap_flg: intensities[ncyc] = spectrometer.detect( - d_taua @ (centre @ p180c_py + p180c_my @ centre) @ d_taua @ start + d_taua @ (centre @ p180c_py + p180c_my @ centre) @ d_taua @ start, ) else: intensities[ncyc] = spectrometer.detect( - d_taua @ d_taua @ centre @ p180c_py @ start + d_taua @ d_taua @ centre @ p180c_py @ start, ) # Return profile diff --git a/chemex/experiments/catalog/cpmg_ch3_1h_tq.py b/chemex/experiments/catalog/cpmg_ch3_1h_tq.py index b6e735df..a2b30680 100644 --- a/chemex/experiments/catalog/cpmg_ch3_1h_tq.py +++ b/chemex/experiments/catalog/cpmg_ch3_1h_tq.py @@ -56,7 +56,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CpmgCh31HTqConfig, spin_system: SpinSystem + config: CpmgCh31HTqConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/cpmg_ch3_1h_tq_diff.py b/chemex/experiments/catalog/cpmg_ch3_1h_tq_diff.py index 83f98c8e..54b44f9f 100644 --- a/chemex/experiments/catalog/cpmg_ch3_1h_tq_diff.py +++ b/chemex/experiments/catalog/cpmg_ch3_1h_tq_diff.py @@ -50,14 +50,15 @@ def detection(self) -> str: class CpmgCh31HTqDiffConfig( - ExperimentConfig[CpmgCh31HTqDiffSettings, RelaxationDataSettings] + ExperimentConfig[CpmgCh31HTqDiffSettings, RelaxationDataSettings], ): @property def to_be_fitted(self) -> ToBeFitted: state = self.experiment.observed_state to_be_fitted = ToBeFitted( - rates=[f"r2_i_{state}", "d_"], model_free=[f"tauc_{state}", "d_"] + rates=[f"r2_i_{state}", "d_"], + model_free=[f"tauc_{state}", "d_"], ) if self.experiment.ipap_flg: @@ -68,7 +69,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CpmgCh31HTqDiffConfig, spin_system: SpinSystem + config: CpmgCh31HTqDiffConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/cpmg_ch3_mq.py b/chemex/experiments/catalog/cpmg_ch3_mq.py index 5929d0b6..777df691 100644 --- a/chemex/experiments/catalog/cpmg_ch3_mq.py +++ b/chemex/experiments/catalog/cpmg_ch3_mq.py @@ -46,7 +46,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CpmgCh3MqConfig, spin_system: SpinSystem + config: CpmgCh3MqConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/cpmg_chd2_1h_ap.py b/chemex/experiments/catalog/cpmg_chd2_1h_ap.py index 578335f4..ceee467c 100644 --- a/chemex/experiments/catalog/cpmg_chd2_1h_ap.py +++ b/chemex/experiments/catalog/cpmg_chd2_1h_ap.py @@ -44,7 +44,7 @@ def detection(self) -> str: class CpmgChd21HApConfig( - ExperimentConfig[CpmgChd21HApSettings, RelaxationDataSettings] + ExperimentConfig[CpmgChd21HApSettings, RelaxationDataSettings], ): @property def to_be_fitted(self) -> ToBeFitted: @@ -53,7 +53,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CpmgChd21HApConfig, spin_system: SpinSystem + config: CpmgChd21HApConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -114,7 +115,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: echo = d_cp[ncyc] @ p180[1] @ d_cp[ncyc] cpmg = matrix_power(echo, int(ncyc)) intensities[ncyc] = spectrometer.detect( - part2 @ cpmg @ p180pmx @ cpmg @ part1 + part2 @ cpmg @ p180pmx @ cpmg @ part1, ) # Return profile diff --git a/chemex/experiments/catalog/cpmg_hn_dq_zq.py b/chemex/experiments/catalog/cpmg_hn_dq_zq.py index a3ee3036..056a4f64 100644 --- a/chemex/experiments/catalog/cpmg_hn_dq_zq.py +++ b/chemex/experiments/catalog/cpmg_hn_dq_zq.py @@ -61,7 +61,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: CpmgHNDqZqConfig, spin_system: SpinSystem + config: CpmgHNDqZqConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -91,7 +92,7 @@ def _get_tau_cps(self, ncycs: ArrayFloat) -> dict[float, float]: self.settings.time_t2 / (4.0 * ncycs_no_ref) - 7.0 / 3.0 * self.settings.pw90_n, strict=True, - ) + ), ) def _get_phases(self, ncyc: float) -> tuple[ArrayInt, ArrayInt]: diff --git a/chemex/experiments/catalog/dcest_13c.py b/chemex/experiments/catalog/dcest_13c.py index cbcb2829..7bfde004 100644 --- a/chemex/experiments/catalog/dcest_13c.py +++ b/chemex/experiments/catalog/dcest_13c.py @@ -63,7 +63,8 @@ class DCest13CConfig(ExperimentConfig[DCest13CSettings, CestDataSettings]): def to_be_fitted(self) -> ToBeFitted: state = self.experiment.observed_state return ToBeFitted( - rates=["r2_i", f"r1_i_{state}"], model_free=[f"tauc_{state}", f"s2_{state}"] + rates=["r2_i", f"r1_i_{state}"], + model_free=[f"tauc_{state}", f"s2_{state}"], ) @@ -125,7 +126,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: ) return np.array( - [spectrometer.detect(intensities[offset]) for offset in offsets] + [spectrometer.detect(intensities[offset]) for offset in offsets], ) diff --git a/chemex/experiments/catalog/dcest_15n.py b/chemex/experiments/catalog/dcest_15n.py index 75b51a9f..dc3379d9 100644 --- a/chemex/experiments/catalog/dcest_15n.py +++ b/chemex/experiments/catalog/dcest_15n.py @@ -69,7 +69,8 @@ class DCest15NConfig(ExperimentConfig[DCest15NSettings, CestDataSettings]): def to_be_fitted(self) -> ToBeFitted: state = self.experiment.observed_state return ToBeFitted( - rates=["r2_i", f"r1_i_{state}"], model_free=[f"tauc_{state}", f"s2_{state}"] + rates=["r2_i", f"r1_i_{state}"], + model_free=[f"tauc_{state}", f"s2_{state}"], ) @@ -131,7 +132,7 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: ) return np.array( - [spectrometer.detect(intensities[offset]) for offset in offsets] + [spectrometer.detect(intensities[offset]) for offset in offsets], ) diff --git a/chemex/experiments/catalog/relaxation_hznz.py b/chemex/experiments/catalog/relaxation_hznz.py index 47f2c978..50d88a09 100644 --- a/chemex/experiments/catalog/relaxation_hznz.py +++ b/chemex/experiments/catalog/relaxation_hznz.py @@ -39,7 +39,7 @@ def detection(self) -> str: class RelaxationHzNzConfig( - ExperimentConfig[RelaxationHzNzSettings, RelaxationDataSettings] + ExperimentConfig[RelaxationHzNzSettings, RelaxationDataSettings], ): @property def to_be_fitted(self) -> ToBeFitted: @@ -51,7 +51,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: RelaxationHzNzConfig, spin_system: SpinSystem + config: RelaxationHzNzConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions @@ -82,10 +83,10 @@ def calculate(self, spectrometer: Spectrometer, data: Data) -> ArrayFloat: return np.array( [ spectrometer.detect( - delay @ p180_s @ delay @ p180_i @ delay @ p180_s @ delay @ start + delay @ p180_s @ delay @ p180_i @ delay @ p180_s @ delay @ start, ) for delay in delays - ] + ], ) def is_reference(self, metadata: ArrayFloat) -> ArrayBool: diff --git a/chemex/experiments/catalog/relaxation_nz.py b/chemex/experiments/catalog/relaxation_nz.py index 22dcd5c1..114a2509 100644 --- a/chemex/experiments/catalog/relaxation_nz.py +++ b/chemex/experiments/catalog/relaxation_nz.py @@ -39,18 +39,20 @@ def detection(self) -> str: class RelaxationNzConfig( - ExperimentConfig[RelaxationNzSettings, RelaxationDataSettings] + ExperimentConfig[RelaxationNzSettings, RelaxationDataSettings], ): @property def to_be_fitted(self) -> ToBeFitted: state = self.experiment.observed_state return ToBeFitted( - rates=[f"r1_i_{state}"], model_free=[f"tauc_{state}", f"s2_{state}"] + rates=[f"r1_i_{state}"], + model_free=[f"tauc_{state}", f"s2_{state}"], ) def build_spectrometer( - config: RelaxationNzConfig, spin_system: SpinSystem + config: RelaxationNzConfig, + spin_system: SpinSystem, ) -> Spectrometer: settings = config.experiment conditions = config.conditions diff --git a/chemex/experiments/catalog/shift_15n_sq.py b/chemex/experiments/catalog/shift_15n_sq.py index f121857a..2e02f40b 100644 --- a/chemex/experiments/catalog/shift_15n_sq.py +++ b/chemex/experiments/catalog/shift_15n_sq.py @@ -45,7 +45,8 @@ def to_be_fitted(self) -> ToBeFitted: def build_spectrometer( - config: Shift15NSqConfig, spin_system: SpinSystem + config: Shift15NSqConfig, + spin_system: SpinSystem, ) -> Spectrometer: conditions = config.conditions diff --git a/chemex/experiments/catalog/shift_15n_sqmq.py b/chemex/experiments/catalog/shift_15n_sqmq.py index 927eab32..4f8a235b 100644 --- a/chemex/experiments/catalog/shift_15n_sqmq.py +++ b/chemex/experiments/catalog/shift_15n_sqmq.py @@ -43,7 +43,8 @@ class Shift15NSqMqConfig(ExperimentConfig[Shift15NSqMqSettings, ShiftDataSetting def build_spectrometer( - config: Shift15NSqMqConfig, spin_system: SpinSystem + config: Shift15NSqMqConfig, + spin_system: SpinSystem, ) -> Spectrometer: conditions = config.conditions @@ -81,8 +82,8 @@ def calculate(self, spectrometer: Spectrometer, _data: Data) -> ArrayFloat: [ 1e3 * (shift_sq - 0.5 * (shift_dq + shift_zq)) - / spectrometer.liouvillian.ppm_i - ] + / spectrometer.liouvillian.ppm_i, + ], ) def is_reference(self, metadata: ArrayFloat) -> ArrayBool: diff --git a/chemex/experiments/factories.py b/chemex/experiments/factories.py index f8f2d04b..bed4aaf4 100644 --- a/chemex/experiments/factories.py +++ b/chemex/experiments/factories.py @@ -1,20 +1,20 @@ """Factories for creating different parts of an experiment.""" from __future__ import annotations -from collections.abc import Callable, MutableMapping from dataclasses import dataclass -from pathlib import Path from typing import TYPE_CHECKING, Any, ClassVar -from chemex.configuration.experiment import ExperimentConfig -from chemex.containers.profile import Filterer, PulseSequence -from chemex.nmr.spectrometer import Spectrometer -from chemex.plotters.plotter import Plotter -from chemex.printers.data import Printer - if TYPE_CHECKING: + from collections.abc import Callable, MutableMapping + from pathlib import Path + + from chemex.configuration.experiment import ExperimentConfig from chemex.containers.data import Data + from chemex.containers.profile import Filterer, PulseSequence + from chemex.nmr.spectrometer import Spectrometer from chemex.parameters.spin_system import SpinSystem + from chemex.plotters.plotter import Plotter + from chemex.printers.data import Printer Dataset = list[tuple[SpinSystem, Data]] ConfigType = ExperimentConfig[Any, Any] @@ -43,7 +43,9 @@ def create_config(self, config_dict: MutableMapping[str, Any]) -> ConfigType: return self.config_creator(**config_dict) def create_spectrometer( - self, config: ConfigType, spin_system: SpinSystem + self, + config: ConfigType, + spin_system: SpinSystem, ) -> Spectrometer: """Create and initialize a spectrometer of a specific type.""" return self.spectrometer_creator(config, spin_system) @@ -57,7 +59,9 @@ def create_dataset(self, base_path: Path, settings: ConfigType) -> Dataset: return self.dataset_creator(base_path, settings) def create_filterer( - self, config: ConfigType, spectrometer: Spectrometer + self, + config: ConfigType, + spectrometer: Spectrometer, ) -> Filterer: """Create a filterer used to remove undesired data points.""" return self.filterer_creator(config=config, spectrometer=spectrometer) diff --git a/chemex/messages.py b/chemex/messages.py index 09b26002..94007c68 100644 --- a/chemex/messages.py +++ b/chemex/messages.py @@ -1,3 +1,18 @@ +"""Module for command-line interface functionalities in ChemEx software package. + +This module is an integral part of the ChemEx software, dedicated to enhancing user +interaction with a command-line interface for analyzing NMR chemical exchange data. +It leverages the 'rich' Python library to provide rich text and table formatting, +making the data presentation more readable and engaging. The module includes various +functions for displaying progress, handling errors, and showing results of data +analysis steps such as dataset loading, fitting processes, simulations, and plotting. + +Typical usage example: + + from your_module import print_logo, print_loading_experiments + print_logo() + print_loading_experiments() +""" from __future__ import annotations from typing import TYPE_CHECKING @@ -22,26 +37,27 @@ console = Console() -LOGO = "\n".join( - [ - r" ________ ______", - r" / ____/ /_ ___ ____ ___ / ____/ __", - r" / / / __ \/ _ \/ __ `__ \/ __/ | |/_/", - r"/ /___/ / / / __/ / / / / / /____> <", - r"\____/_/ /_/\___/_/ /_/ /_/_____/_/|_|", - "", - "", - ] -) +LOGO = r""" + ________ ______ + / ____/ /_ ___ ____ ___ / ____/ __ + / / / __ \/ _ \/ __ `__ \/ __/ | |/_/ +/ /___/ / / / __/ / / / / / /____> < +\____/_/ /_/\___/_/ /_/ /_/_____/_/|_| + + +""" +"""ASCII art logo of the ChemEx software.""" EXPERIMENT_NAME = """ [experiment] name = "experiment_name" ... """ +"""Template for the experiment name in configuration files.""" def print_logo() -> None: + """Print the ChemEx software logo with version information.""" logo = Text(LOGO, style="blue") description = "Analysis of NMR chemical exchange data\n\n" version = "Version: " @@ -52,15 +68,26 @@ def print_logo() -> None: def print_loading_experiments() -> None: + """Display a loading message for datasets.""" console.print("\nLoading datasets...", style="bold yellow") -def get_reading_exp_text(filename: Path, type: str = "", total_nb: int = 0) -> Text: +def get_reading_exp_text(filename: Path, name: str = "", total_nb: int = 0) -> Text: + """Generate a formatted message for reading an experiment file. + + Args: + filename (Path): The path of the file being read. + name (str, optional): The experiment name. Defaults to an empty string. + total_nb (int, optional): The total number of profiles. Defaults to 0. + + Returns: + Text: A formatted message indicating the file name, type, and profile count. + """ parts = ( " • Reading ", (f"{filename}", "green"), " (", - (f"{type}", "blue"), + (f"{name}", "blue"), ")", ) @@ -73,22 +100,33 @@ def get_reading_exp_text(filename: Path, type: str = "", total_nb: int = 0) -> T def print_reading_defaults() -> None: + """Print a message indicating the reading of default parameters.""" console.print("\nReading default parameters...", style="bold yellow") def print_reading_methods() -> None: + """Display a message indicating that methods are being read.""" console.print("\nReading methods...", style="bold yellow") def print_start_fit() -> None: + """Display a message indicating the start of the fitting process.""" console.print("\nStarting the fits...", style="bold yellow") def print_running_simulations() -> None: + """Display a message indicating that simulations are running.""" console.print("\nRunning simulations...", style="bold yellow") def print_step_name(name: str, index: int, total: int) -> None: + """Print the name of the current step in the analysis process. + + Args: + name (str): Name of the step. + index (int): Current step index. + total (int): Total number of steps. + """ text = Text.assemble( "Running ", (f"{name}", "magenta"), @@ -98,22 +136,42 @@ def print_step_name(name: str, index: int, total: int) -> None: def print_selecting_profiles(selected_nb: int) -> None: + """Display a message indicating the number of profiles selected. + + Args: + selected_nb (int): The number of selected profiles. + """ console.print( - Text.from_markup(f" • Selecting profiles -> [blue]{selected_nb}[/] profiles") + Text.from_markup(f" • Selecting profiles -> [blue]{selected_nb}[/] profiles"), ) def print_no_data() -> None: + """Inform the user that no data is available for fitting.""" console.print(" • No data to fit") def print_fitmethod(fit_method: str) -> None: + """Display the chosen method for fitting. + + Args: + fit_method (str): The method being used for fitting. + """ console.print(Text.assemble(" • Fit method -> ", (f"{fit_method}", "blue"))) def print_status_changes( - vary: Counter[str], fixed: Counter[str], constrained: Counter[str] + vary: Counter[str], + fixed: Counter[str], + constrained: Counter[str], ) -> None: + """Print changes in parameter status like varied, fixed, or constrained. + + Args: + vary (Counter[str]): Parameters varied during fitting. + fixed (Counter[str]): Parameters fixed during fitting. + constrained (Counter[str]): Parameters constrained during fitting. + """ if not any([vary, fixed, constrained]): return @@ -139,22 +197,35 @@ def print_status_changes( def print_minimizing() -> None: + """Display a message indicating that the minimization process is running.""" console.print(Text(" • Running the minimization...")) def print_running_grid() -> None: + """Inform the user that the grid search is in progress.""" console.print(Text(" • Running the grid search...")) def print_running_statistics(name: str) -> None: + """Display a message indicating that statistical simulations are running. + + Args: + name (str): The name of the statistical simulation. + """ console.print(Text(f" • Running {name} simulations...")) def print_section(name: str) -> None: + """Print the name of the current section in the analysis process. + + Args: + name (str): Name of the section. + """ console.print(Text(f" • Section {name}")) def print_chi2_table_header() -> None: + """Print the header for the chi-squared table.""" header = Text(f"{'Iteration':>9s} {'χ²':>12s} {'Reduced χ²':>12s}") console.print() console.print(Padding.indent(header, 5), style="bold") @@ -162,11 +233,25 @@ def print_chi2_table_header() -> None: def print_chi2_table_line(iteration: int, chisqr: float, redchi: float) -> None: + """Print a line in the chi-squared table with iteration and chi-squared values. + + Args: + iteration (int): Iteration number. + chisqr (float): Chi-squared value. + redchi (float): Reduced chi-squared value. + """ line = Text(f"{iteration:>9d} {chisqr:>12.1f} {redchi:>12.3f}") console.print(Padding.indent(line, 5)) def print_chi2_table_footer(iteration: int, chisqr: float, redchi: float) -> None: + """Print the footer for the chi-squared table. + + Args: + iteration (int): Iteration number. + chisqr (float): Chi-squared value. + redchi (float): Reduced chi-squared value. + """ footer = Text(f"{iteration:>9d} {chisqr:>12.1f} {redchi:>12.3f}") console.print(Padding.indent("─" * 39, 4)) console.print(Padding.indent(footer, 5), style="bold") @@ -174,25 +259,44 @@ def print_chi2_table_footer(iteration: int, chisqr: float, redchi: float) -> Non def print_chi2(chisqr: float, redchi: float) -> None: + """Display the chi-squared and reduced chi-squared values. + + Args: + chisqr (float): Chi-squared value. + redchi (float): Reduced chi-squared value. + """ console.print() console.print( - Padding.indent(Text.from_markup(f" χ²: [bold]{chisqr:15.1f}[/]"), 3) + Padding.indent(Text.from_markup(f" χ²: [bold]{chisqr:15.1f}[/]"), 3), ) console.print( - Padding.indent(Text.from_markup(f"Reduced χ²: [bold]{redchi:15.3f}[/]"), 3) + Padding.indent(Text.from_markup(f"Reduced χ²: [bold]{redchi:15.3f}[/]"), 3), ) console.print() def print_writing_results(path: Path) -> None: + """Inform the user about the location where results are being written. + + Args: + path (Path): Path to the file or directory where results are saved. + """ console.print(f" • Writing results in [green]{path}") def print_making_plots() -> None: + """Display a message indicating that plots are being generated.""" console.print(Text(" • Making plots...")) -def print_plot_filename(filename: Path, extra: bool = True) -> None: +def print_plot_filename(filename: Path, *, extra: bool = True) -> None: + """Display the filename of the plot being generated. + + Args: + filename (Path): The path of the plot file. + extra (bool, optional): Indicates if extra information is included. + Defaults to True. + """ text = f" ‣ [green]{filename}[/]" if extra: @@ -202,20 +306,41 @@ def print_plot_filename(filename: Path, extra: bool = True) -> None: def print_group_name(text: str) -> None: + """Print the name of the group in the analysis process. + + Args: + text (str): Name of the group. + """ console.print(Padding(Rule(text, characters="⋅"), (1, 0, 0, 3)), width=49) def print_file_not_found(filename: Path) -> None: + """Inform the user that a specified file was not found. + + Args: + filename (Path): The path of the file that was not found. + """ console.print() console.print(f"[red]The file '{filename}' is empty or does not exist!") def print_file_not_found_error(error: FileNotFoundError) -> None: + """Display the file not found error message. + + Args: + error (FileNotFoundError): The FileNotFoundError exception instance. + """ console.print() console.print(f"[red]Error: {error}") def print_toml_error(filename: Path, error_message: Exception) -> None: + """Display an error related to TOML file parsing. + + Args: + filename (Path): Path of the TOML file. + error_message (Exception): The exception instance with the error message. + """ console.print() console.print(Text.from_markup(f"[red]Error in the TOML file '{filename}'")) console.print( @@ -223,15 +348,20 @@ def print_toml_error(filename: Path, error_message: Exception) -> None: ) console.print( "Please check the website [link]https://toml.io[/]" - " for a complete description of the TOML format." + " for a complete description of the TOML format.", ) def print_experiment_name_error(filename: Path) -> None: + """Display an error message when the experiment name is missing from a file. + + Args: + filename (Path): Path of the file with the missing experiment name. + """ console.print() console.print(f"[red]The experiment name is missing from the file '{filename}'\n") console.print( - f"Please make sure that the 'name' field is provided in '{filename}':\n" + f"Please make sure that the 'name' field is provided in '{filename}':\n", ) console.print( Syntax(EXPERIMENT_NAME, "toml"), @@ -240,6 +370,12 @@ def print_experiment_name_error(filename: Path) -> None: def print_pydantic_parsing_error(filename: Path, error: ValidationError) -> None: + """Display errors encountered while parsing a file using Pydantic. + + Args: + filename (Path): Path of the file being parsed. + error (ValidationError): Instance detailing parsing errors. + """ console.print() console.print(Text.from_markup(f"[red]Error(s) while parsing '{filename}'")) for err in error.errors(): @@ -248,54 +384,64 @@ def print_pydantic_parsing_error(filename: Path, error: ValidationError) -> None def print_calculation_stopped_error() -> None: + """Inform the user that the calculation was manually stopped.""" console.print() console.print("[red] -- Keyboard Interrupt: Calculation stopped --") console.print() def print_plotting_canceled() -> None: + """Display a message indicating that the plotting process was cancelled.""" console.print() console.print("[red] -- Keyboard Interrupt: Plotting cancelled --") console.print() def print_value_error() -> None: + """Inform the user that a ValueError occurred, stopping the calculation.""" console.print() console.print("[red] -- Got a ValueError: Calculation stopped --") console.print() def print_warning_positive_jnh() -> None: + """Warn about positive 1J(NH) coupling values.""" console.print() console.print( - "[yellow] -- WARNING: Some 1J(NH) couplings are set with positive values --" + "[yellow] -- WARNING: Some 1J(NH) couplings are set with positive values --", ) console.print( "This can cause the TROSY and anti-TROSY components to be switched in some" - " experiments." + " experiments.", ) console.print() def print_warning_negative_jch() -> None: + """Warn about negative 1J(CH) coupling values.""" console.print() console.print( - "[yellow] -- WARNING: Some 1J(CH) couplings are set with negative values --" + "[yellow] -- WARNING: Some 1J(CH) couplings are set with negative values --", ) console.print( "This can cause the TROSY and anti-TROSY components to be switched in some" - " experiments." + " experiments.", ) console.print() def print_error_grid_settings(entry: str) -> None: + """Display an error related to grid settings. + + Args: + entry (str): The problematic entry in the grid settings. + """ console.print() console.print("[red] -- ERROR: Error reading grid settings:") console.print(Text(f' "{entry}"', style="red")) console.print() console.print( - "Please make sure that the grid settings are provided in the correct format" + "Please make sure that the grid settings are provided in the correct format", ) console.print(Text(" [PB] = lin(, , )")) console.print(Text(" [PB] = log(, , )")) @@ -304,21 +450,32 @@ def print_error_grid_settings(entry: str) -> None: def print_error_constraints(expression: str) -> None: + """Display an error message for issues with constraints expressions. + + Args: + expression (str): The problematic constraint expression. + """ console.print() console.print(f'[red] -- ERROR: Error reading constraints -> "{expression}" --') console.print() def print_grid_statistic_warning() -> None: + """Warn that 'GRID' and 'STATISTICS' options are mutually exclusive.""" console.print() console.print( "[yellow] -- WARNING: The 'GRID' and 'STATISTICS' options are mutually " - "exclusive. Only the 'GRID' calculation will be run." + "exclusive. Only the 'GRID' calculation will be run.", ) console.print() def print_model_error(name: str) -> None: + """Display an error message for unavailable models. + + Args: + name (str): The name of the model that is not available. + """ from chemex.models.factory import model_factory console.print() @@ -331,8 +488,17 @@ def print_model_error(name: str) -> None: def print_not_implemented_noise_method_warning( - filename: Path, kind: str, implemented: tuple[str, ...] + filename: Path, + kind: str, + implemented: tuple[str, ...], ) -> None: + """Warn about unimplemented noise methods for an experiment. + + Args: + filename (Path): Path of the experiment file. + kind (str): The kind of noise method that is not implemented. + implemented (tuple[str, ...]): Tuple of implemented methods. + """ warning_message = ( f"[yellow] -- WARNING: Experiment {filename.name}[/yellow]: " f"The '{kind}' method is not implemented. " @@ -345,6 +511,11 @@ def print_not_implemented_noise_method_warning( def print_no_duplicate_warning(filename: Path) -> None: + """Warn about the absence of duplicate points in some profiles. + + Args: + filename (Path): Path of the experiment file. + """ warning_message = ( f"[yellow] -- WARNING: Experiment {filename.name}[/yellow]: " f"Some profiles do not have duplicate points. " @@ -433,11 +604,39 @@ def print_no_duplicate_warning(filename: Path) -> None: } +def print_wrong_option(option: str) -> str: + """Display a message for an invalid option in configuration files. + + Args: + option (str): The option that is invalid or incorrectly formatted. + + Returns: + str: A message indicating the error with the specific option. + """ + return ( + f"\n - '{option.upper()}' is not a valid option.\n" + "\nPlease check the website " + "[link]" + "https://gbouvignies.github.io/ChemEx/docs/user_guide/fitting/method_files" + "[/] " + "for a complete list of valid options." + ) + + def print_method_error(filename: Path, section: str, options: set[int | str]) -> None: + """Display errors for invalid methods or options in a specific section of a file. + + Args: + filename (Path): The file containing the error. + section (str): The section of the file with the erroneous method or option. + options (set[int | str]): Set of options or methods that are incorrect. + """ console.print() console.print( - f"[red] -- ERROR: Error reading section '[{section}]' of '{filename}' --" + f"[red] -- ERROR: Error reading section '[{section}]' of '{filename}' --", ) for option in options: - console.print(METHOD_ERROR_MESSAGES.get(str(option))) + console.print( + METHOD_ERROR_MESSAGES.get(str(option), print_wrong_option(str(option))), + ) console.print() diff --git a/chemex/models/constraints.py b/chemex/models/constraints.py index 6f1e411e..5db9c272 100644 --- a/chemex/models/constraints.py +++ b/chemex/models/constraints.py @@ -45,7 +45,7 @@ def pop_3st( [-kab - kac, kba, kca], [kab, -kba - kbc, kcb], [1.0, 1.0, 1.0], - ] + ], ) if np.isclose(np.linalg.det(mat), 0.0): @@ -94,7 +94,7 @@ def pop_4st( [kab, -kba - kbc - kbd, kcb, kdb], [kac, kbc, -kca - kcb - kcd, kdc], [1.0, 1.0, 1.0, 1.0], - ] + ], ) if np.isclose(np.linalg.det(mat), 0.0): diff --git a/chemex/models/kinetic/settings_2st.py b/chemex/models/kinetic/settings_2st.py index 32a56f86..45d75d81 100644 --- a/chemex/models/kinetic/settings_2st.py +++ b/chemex/models/kinetic/settings_2st.py @@ -17,7 +17,10 @@ def make_settings_2st(_conditions: Conditions) -> dict[str, ParamLocalSetting]: return { "kex_ab": ParamLocalSetting( - name_setting=NameSetting("kex_ab", "", TPL), value=200.0, min=0.0, vary=True + name_setting=NameSetting("kex_ab", "", TPL), + value=200.0, + min=0.0, + vary=True, ), "pb": ParamLocalSetting( name_setting=NameSetting("pb", "", TPL), @@ -27,13 +30,16 @@ def make_settings_2st(_conditions: Conditions) -> dict[str, ParamLocalSetting]: vary=True, ), "pa": ParamLocalSetting( - name_setting=NameSetting("pa", "", TPL), expr="1.0 - {pb}" + name_setting=NameSetting("pa", "", TPL), + expr="1.0 - {pb}", ), "kab": ParamLocalSetting( - name_setting=NameSetting("kab", "", TPL), expr="{kex_ab} * {pb}" + name_setting=NameSetting("kab", "", TPL), + expr="{kex_ab} * {pb}", ), "kba": ParamLocalSetting( - name_setting=NameSetting("kba", "", TPL), expr="{kex_ab} * {pa}" + name_setting=NameSetting("kba", "", TPL), + expr="{kex_ab} * {pa}", ), } diff --git a/chemex/models/kinetic/settings_2st_binding.py b/chemex/models/kinetic/settings_2st_binding.py index fc94fda2..42311f6b 100644 --- a/chemex/models/kinetic/settings_2st_binding.py +++ b/chemex/models/kinetic/settings_2st_binding.py @@ -20,7 +20,10 @@ def calculate_residuals( - concentrations: ArrayFloat, p_total: float, l_total: float, kd: float + concentrations: ArrayFloat, + p_total: float, + l_total: float, + kd: float, ) -> ArrayFloat: p_free, l_free, pl = concentrations return np.array( @@ -28,17 +31,21 @@ def calculate_residuals( l_total - l_free - pl, p_total - p_free - pl, kd * pl - p_free * l_free, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, l_total: float, kd: float + p_total: float, + l_total: float, + kd: float, ) -> dict[str, float]: concentrations_start = (p_total, l_total, 0.0) results = root( - calculate_residuals, concentrations_start, args=(p_total, l_total, kd) + calculate_residuals, + concentrations_start, + args=(p_total, l_total, kd), ) p_free, l_free, pl = results["x"] return {"p_free": p_free, "l_free": l_free, "pl": pl} diff --git a/chemex/models/kinetic/settings_2st_eyring.py b/chemex/models/kinetic/settings_2st_eyring.py index 8801b83e..6f3ae404 100644 --- a/chemex/models/kinetic/settings_2st_eyring.py +++ b/chemex/models/kinetic/settings_2st_eyring.py @@ -22,7 +22,11 @@ @lru_cache(maxsize=100) def calculate_kij_2st_eyring( - dh_b: float, ds_b: float, dh_ab: float, ds_ab: float, temperature: float + dh_b: float, + ds_b: float, + dh_ab: float, + ds_ab: float, + temperature: float, ) -> dict[str, float]: kelvin = temperature + 273.15 kbt_h = constants.k * kelvin / constants.h diff --git a/chemex/models/kinetic/settings_2st_monomer_dimer.py b/chemex/models/kinetic/settings_2st_monomer_dimer.py index 35d2d635..499f8260 100644 --- a/chemex/models/kinetic/settings_2st_monomer_dimer.py +++ b/chemex/models/kinetic/settings_2st_monomer_dimer.py @@ -21,14 +21,16 @@ def calculate_residuals( - concentrations: ArrayFloat, p_total: float, kd: float + concentrations: ArrayFloat, + p_total: float, + kd: float, ) -> ArrayFloat: monomer, dimer = concentrations return np.array( [ monomer + 2.0 * dimer - p_total, kd * dimer - monomer**2, - ] + ], ) diff --git a/chemex/models/kinetic/settings_2st_monomer_tetramer.py b/chemex/models/kinetic/settings_2st_monomer_tetramer.py index 98bd3197..8fbbda57 100644 --- a/chemex/models/kinetic/settings_2st_monomer_tetramer.py +++ b/chemex/models/kinetic/settings_2st_monomer_tetramer.py @@ -21,14 +21,16 @@ def calculate_residuals( - concentrations: ArrayFloat, p_total: float, kd: float + concentrations: ArrayFloat, + p_total: float, + kd: float, ) -> ArrayFloat: monomer, tetramer = concentrations return np.array( [ monomer + 4.0 * tetramer - p_total, kd * tetramer - monomer**4, - ] + ], ) diff --git a/chemex/models/kinetic/settings_2st_monomer_trimer.py b/chemex/models/kinetic/settings_2st_monomer_trimer.py index b6593a4d..e90c42eb 100644 --- a/chemex/models/kinetic/settings_2st_monomer_trimer.py +++ b/chemex/models/kinetic/settings_2st_monomer_trimer.py @@ -21,14 +21,16 @@ def calculate_residuals( - concentrations: ArrayFloat, p_total: float, kd: float + concentrations: ArrayFloat, + p_total: float, + kd: float, ) -> ArrayFloat: monomer, trimer = concentrations return np.array( [ monomer + 3.0 * trimer - p_total, kd * trimer - monomer**3, - ] + ], ) diff --git a/chemex/models/kinetic/settings_2st_rs.py b/chemex/models/kinetic/settings_2st_rs.py index fd39e365..4ba2d3ea 100644 --- a/chemex/models/kinetic/settings_2st_rs.py +++ b/chemex/models/kinetic/settings_2st_rs.py @@ -27,13 +27,16 @@ def make_settings_2st_rs(_conditions: Conditions) -> dict[str, ParamLocalSetting vary=True, ), "pa": ParamLocalSetting( - name_setting=NameSetting("pa", "g", TPL), expr="1.0 - {pb}" + name_setting=NameSetting("pa", "g", TPL), + expr="1.0 - {pb}", ), "kab": ParamLocalSetting( - name_setting=NameSetting("kab", "g", TPL), expr="{kex_ab} * {pb}" + name_setting=NameSetting("kab", "g", TPL), + expr="{kex_ab} * {pb}", ), "kba": ParamLocalSetting( - name_setting=NameSetting("kba", "g", TPL), expr="{kex_ab} * {pa}" + name_setting=NameSetting("kba", "g", TPL), + expr="{kex_ab} * {pa}", ), } diff --git a/chemex/models/kinetic/settings_3st_binding_2st_partner.py b/chemex/models/kinetic/settings_3st_binding_2st_partner.py index 058fa43d..849696f9 100644 --- a/chemex/models/kinetic/settings_3st_binding_2st_partner.py +++ b/chemex/models/kinetic/settings_3st_binding_2st_partner.py @@ -37,13 +37,17 @@ def calculate_residuals( kd1 * pl1 - p * l1, kd2 * pl2 - p * l2, keq * l1 - l2, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, l_total: float, kd1: float, kd2: float, keq: float + p_total: float, + l_total: float, + kd1: float, + kd2: float, + keq: float, ) -> dict[str, float]: concentrations_start = (p_total, l_total / 2, l_total / 2, 0.0, 0.0) results = root( @@ -167,7 +171,8 @@ def make_settings_3st_binding_partner_2st( def register() -> None: model_factory.register( - name=NAME, setting_maker=make_settings_3st_binding_partner_2st + name=NAME, + setting_maker=make_settings_3st_binding_partner_2st, ) user_functions = { "calc_conc": calculate_concentrations, diff --git a/chemex/models/kinetic/settings_3st_binding_cs.py b/chemex/models/kinetic/settings_3st_binding_cs.py index 2fb5440c..7ba7e5d1 100644 --- a/chemex/models/kinetic/settings_3st_binding_cs.py +++ b/chemex/models/kinetic/settings_3st_binding_cs.py @@ -10,10 +10,10 @@ from chemex.models.factory import model_factory from chemex.parameters.setting import NameSetting, ParamLocalSetting from chemex.parameters.userfunctions import user_function_registry -from chemex.typing import ArrayFloat if TYPE_CHECKING: from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat NAME = "3st_binding_cs" @@ -35,13 +35,17 @@ def calculate_residuals( l_total - l_ - pl, kab * p1 - kba * p2, kd * pl - p2 * l_, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, l_total: float, kd: float, kab: float, kba: float + p_total: float, + l_total: float, + kd: float, + kab: float, + kba: float, ) -> dict[str, float]: concentrations_start = (p_total, 0.0, 0.0, l_total) results = root( diff --git a/chemex/models/kinetic/settings_3st_binding_if.py b/chemex/models/kinetic/settings_3st_binding_if.py index 0ed2cf1c..c44e810e 100644 --- a/chemex/models/kinetic/settings_3st_binding_if.py +++ b/chemex/models/kinetic/settings_3st_binding_if.py @@ -35,13 +35,17 @@ def calculate_residuals( pfree + pl1 + pl2 - p_total, lfree * pfree - kd_ab * pl1, kbc * pl1 - kcb * pl2, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, l_total: float, kd_ab: float, kbc: float, kcb: float + p_total: float, + l_total: float, + kd_ab: float, + kbc: float, + kcb: float, ) -> dict[str, float]: concentrations_start = (p_total, 0.0, 0.0) results = root( diff --git a/chemex/models/kinetic/settings_3st_double_binding.py b/chemex/models/kinetic/settings_3st_double_binding.py index 172dc06a..8cab57f3 100644 --- a/chemex/models/kinetic/settings_3st_double_binding.py +++ b/chemex/models/kinetic/settings_3st_double_binding.py @@ -1,3 +1,5 @@ +from __future__ import annotations + """This code imports the necessary modules and functions to define a 3-state double binding model. The model is named "3st_double_binding" and it is registered in the model factory. The model requires two parameters, @@ -7,7 +9,6 @@ given the total protein and ligand concentrations, as well as the dissociation constants for each binding site. """ -from __future__ import annotations from functools import lru_cache from typing import TYPE_CHECKING @@ -43,17 +44,22 @@ def calculate_residuals( pfree + pl1 + pl2 - p_total, lfree * pfree - kd_ab * pl1, lfree * pfree - kd_ac * pl2, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, l_total: float, kd_ab: float, kd_ac: float + p_total: float, + l_total: float, + kd_ab: float, + kd_ac: float, ) -> dict[str, float]: concentrations_start = (p_total, 0.0, 0.0) results = root( - calculate_residuals, concentrations_start, args=(p_total, l_total, kd_ab, kd_ac) + calculate_residuals, + concentrations_start, + args=(p_total, l_total, kd_ab, kd_ac), ) return dict(zip(("pfree", "pl1", "pl2"), results["x"], strict=True)) diff --git a/chemex/models/kinetic/settings_3st_eyring.py b/chemex/models/kinetic/settings_3st_eyring.py index eef2278e..ce58a38d 100644 --- a/chemex/models/kinetic/settings_3st_eyring.py +++ b/chemex/models/kinetic/settings_3st_eyring.py @@ -11,10 +11,10 @@ from chemex.models.factory import model_factory from chemex.parameters.setting import NameSetting, ParamLocalSetting from chemex.parameters.userfunctions import user_function_registry -from chemex.typing import ArrayFloat if TYPE_CHECKING: from chemex.configuration.conditions import Conditions + from chemex.typing import ArrayFloat NAME = "3st_eyring" @@ -48,7 +48,7 @@ def calculate_kij_3st_eyring( dh_bc - dh_b - kelvin * (ds_bc - ds_b), dh_ac - dh_c - kelvin * (ds_ac - ds_c), dh_bc - dh_c - kelvin * (ds_bc - ds_c), - ) + ), ) kij_values: ArrayFloat = kbt_h * np.exp(-ddg_ij / rt) kij_values = np.clip(kij_values, 0.0, 1e16) diff --git a/chemex/models/kinetic/settings_3st_monomer_dimer_tetramer.py b/chemex/models/kinetic/settings_3st_monomer_dimer_tetramer.py index 10b01cbb..4aa9371c 100644 --- a/chemex/models/kinetic/settings_3st_monomer_dimer_tetramer.py +++ b/chemex/models/kinetic/settings_3st_monomer_dimer_tetramer.py @@ -32,13 +32,15 @@ def calculate_residuals( monomer + 2.0 * dimer + 4.0 * tetramer - p_total, kd1 * dimer - monomer**2, kd2 * tetramer - dimer**2, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, kd1: float, kd2: float + p_total: float, + kd1: float, + kd2: float, ) -> dict[str, float]: concentrations_start = (p_total, 0.0, 0.0) results = root(calculate_residuals, concentrations_start, args=(p_total, kd1, kd2)) @@ -132,7 +134,8 @@ def make_settings_3st_monomer_dimer_tetramer( def register() -> None: model_factory.register( - name=NAME, setting_maker=make_settings_3st_monomer_dimer_tetramer + name=NAME, + setting_maker=make_settings_3st_monomer_dimer_tetramer, ) user_functions = { "concentrations": calculate_concentrations, diff --git a/chemex/models/kinetic/settings_3st_monomer_dimer_trimer.py b/chemex/models/kinetic/settings_3st_monomer_dimer_trimer.py index 90a49988..4ad290e1 100644 --- a/chemex/models/kinetic/settings_3st_monomer_dimer_trimer.py +++ b/chemex/models/kinetic/settings_3st_monomer_dimer_trimer.py @@ -21,7 +21,10 @@ def calculate_residuals( - concentrations: ArrayFloat, p_total: float, kd1: float, kd2: float + concentrations: ArrayFloat, + p_total: float, + kd1: float, + kd2: float, ) -> ArrayFloat: monomer, dimer, trimer = concentrations return np.array( @@ -29,13 +32,15 @@ def calculate_residuals( monomer + 2.0 * dimer + 3.0 * trimer - p_total, kd1 * dimer - monomer**2, kd2 * trimer - monomer * dimer, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, kd1: float, kd2: float + p_total: float, + kd1: float, + kd2: float, ) -> dict[str, float]: concentrations_start = (p_total, 0.0, 0.0) results = root(calculate_residuals, concentrations_start, args=(p_total, kd1, kd2)) @@ -141,7 +146,8 @@ def make_settings_3st_monomer_dimer_trimer( def register() -> None: model_factory.register( - name=NAME, setting_maker=make_settings_3st_monomer_dimer_trimer + name=NAME, + setting_maker=make_settings_3st_monomer_dimer_trimer, ) user_functions = { "concetrations": calculate_concentrations, diff --git a/chemex/models/kinetic/settings_4st_binding_2st_partner.py b/chemex/models/kinetic/settings_4st_binding_2st_partner.py index f617aafe..7914df15 100644 --- a/chemex/models/kinetic/settings_4st_binding_2st_partner.py +++ b/chemex/models/kinetic/settings_4st_binding_2st_partner.py @@ -38,13 +38,18 @@ def calculate_residuals( kd2 * pl2 - p * l2, keq_l * l1 - l2, keq_pl * pl2 - pl3, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, l_total: float, kd1: float, kd2: float, keq_l: float, keq_pl: float + p_total: float, + l_total: float, + kd1: float, + kd2: float, + keq_l: float, + keq_pl: float, ) -> dict[str, float]: concentrations_start = (p_total, l_total / 2, l_total / 2, 0.0, 0.0, 0.0) results = root( @@ -200,7 +205,8 @@ def make_settings_4st_binding_partner_2st( def register() -> None: model_factory.register( - name=NAME, setting_maker=make_settings_4st_binding_partner_2st + name=NAME, + setting_maker=make_settings_4st_binding_partner_2st, ) user_functions = { "calc_conc": calculate_concentrations, diff --git a/chemex/models/kinetic/settings_4st_binding_3_bound_states.py b/chemex/models/kinetic/settings_4st_binding_3_bound_states.py index f7c19af3..4a09deea 100644 --- a/chemex/models/kinetic/settings_4st_binding_3_bound_states.py +++ b/chemex/models/kinetic/settings_4st_binding_3_bound_states.py @@ -36,13 +36,17 @@ def calculate_residuals( kd_ab * pl1 - p_ * l_, keq_bc * pl1 - pl2, keq_cd * pl2 - pl3, - ] + ], ) @lru_cache(maxsize=100) def calculate_concentrations( - p_total: float, l_total: float, kd_ab: float, keq_bc: float, keq_cd: float + p_total: float, + l_total: float, + kd_ab: float, + keq_bc: float, + keq_cd: float, ) -> dict[str, float]: concentrations_start = (p_total, l_total, 0.0, 0.0, 0.0) results = root( @@ -185,7 +189,8 @@ def make_settings_4st_binding_3_bound_states( def register() -> None: model_factory.register( - name=NAME, setting_maker=make_settings_4st_binding_3_bound_states + name=NAME, + setting_maker=make_settings_4st_binding_3_bound_states, ) user_functions = { "concentrations": calculate_concentrations, diff --git a/chemex/nmr/basis.py b/chemex/nmr/basis.py index 0065b4ac..89d6a491 100644 --- a/chemex/nmr/basis.py +++ b/chemex/nmr/basis.py @@ -286,7 +286,9 @@ def _build_vectors(basis: Basis) -> DictArrayFloat: def _get_indices( - basis: Basis, transition_name: str, state: str + basis: Basis, + transition_name: str, + state: str, ) -> tuple[tuple[list[int], list[int]], list[float]]: rows: list[int] = [] cols: list[int] = [] @@ -335,15 +337,15 @@ class Basis: spin_system: str = "" @property - def name(self): - return ".".join([self.type, self.extension, self.spin_system]) + def name(self) -> str: + return f"{self.type}.{self.extension}.{self.spin_system}" @property - def components(self): + def components(self) -> list[str]: return _BASES[self.type] @property - def atoms(self): + def atoms(self) -> dict[str, str]: return { letter: atom for letter, atom in _ATOMS.get(self.spin_system, {}).items() @@ -364,5 +366,5 @@ def required_names(self) -> set[str]: required_names |= {f"p{state}" for state in model.states} return required_names - def __len__(self): + def __len__(self) -> int: return len(self.components) diff --git a/chemex/nmr/liouvillian.py b/chemex/nmr/liouvillian.py index 786b8444..bac88607 100644 --- a/chemex/nmr/liouvillian.py +++ b/chemex/nmr/liouvillian.py @@ -1,7 +1,6 @@ -"""The ref module contains the reference matrices and code for calculating the -Liouvillian. +"""The ref module contains the code for calculating the Liouvillians. -Operator basis:: +Operator basis: { Eq, Ix, Iy, Iz, Sx, Sy, Sz, @@ -37,7 +36,9 @@ def _make_gaussian( - value: float, scale: float, res: int + value: float, + scale: float, + res: int, ) -> tuple[ArrayFloat, ArrayFloat]: if scale not in (0.0, np.inf) and res > 1: grid = np.linspace(-2.0, 2.0, res) @@ -56,7 +57,12 @@ def _scale_matrix(self, name: str, value: float): for state_name in state_names & set(self.matrices): self.matrices[state_name] = np.sign(self._matrices_ref[state_name]) * value - def __init__(self, spin_system: SpinSystem, basis: Basis, conditions: Conditions): + def __init__( + self, + spin_system: SpinSystem, + basis: Basis, + conditions: Conditions, + ) -> None: self.spin_system = spin_system.correct(basis) self.basis = basis self.h_frq = 0.0 if conditions.h_larmor_frq is None else conditions.h_larmor_frq @@ -183,7 +189,9 @@ def b1_i(self) -> float: def b1_i(self, value: float): self._b1_i = value self._b1_i_dist, self._b1_i_weights = _make_gaussian( - self.b1_i, self.b1_i_inh_scale, self.b1_i_inh_res + self.b1_i, + self.b1_i_inh_scale, + self.b1_i_inh_res, ) self._b1_i_dist = self._b1_i_dist.reshape((-1, 1, 1)) self._b1_i_weights = self._b1_i_weights.reshape((-1, 1, 1)) @@ -268,12 +276,16 @@ def get_equilibrium(self) -> ArrayFloat: return mag def get_start_magnetization( - self, terms: Iterable[str], atom: str = "h" + self, + terms: Iterable[str], + atom: str = "h", ) -> ArrayFloat: ratio = XI_RATIO.get(atom, 1.0) mag = np.zeros((self.size, 1)) for term, state, (comp, vector) in product( - terms, model.states, self.vectors.items() + terms, + model.states, + self.vectors.items(), ): if comp.startswith(term) and comp.endswith(f"_{state}"): mag += self.par_values[f"p{state}"] * ratio * vector @@ -281,7 +293,8 @@ def get_start_magnetization( def keep(self, magnetization: ArrayFloat, components: Iterable[str]) -> ArrayFloat: keep = sum( - (self.vectors[name] for name in components), start=np.zeros((self.size, 1)) + (self.vectors[name] for name in components), + start=np.zeros((self.size, 1)), ) keep[keep > 0] = 1.0 return keep * magnetization diff --git a/chemex/nmr/rates.py b/chemex/nmr/rates.py index 76235f97..4d94eff2 100644 --- a/chemex/nmr/rates.py +++ b/chemex/nmr/rates.py @@ -34,7 +34,7 @@ class RatesIS: phi_i: ArrayFloat phi_s: ArrayFloat - def __init__(self): + def __init__(self) -> None: self.gh = GAMMA["h"] # Dipolar factors @@ -70,7 +70,7 @@ def __call__(self, h_frq: float, tauc: float, s2: float) -> dict[str, float]: tauc, s2, np.array( - [0.0, wi, ws, wh, wi - ws, wi + ws, wi - wh, wi + wh, ws - wh, ws + wh] + [0.0, wi, ws, wh, wi - ws, wi + ws, wi - wh, wi + wh, ws - wh, ws + wh], ), ) @@ -147,7 +147,11 @@ class RateNH(RatesIS): phi_s = np.deg2rad([10.0, 80.0, 90.0]) def __call__( - self, h_frq: float, tauc: float, s2: float, khh: float = 0.0 + self, + h_frq: float, + tauc: float, + s2: float, + khh: float = 0.0, ) -> dict[str, float]: rates = super().__call__(h_frq, tauc, s2) if khh == 0: @@ -181,7 +185,11 @@ class RateHN(RatesIS): phi_s = np.deg2rad([109.6, 90.0, 19.6]) def __call__( - self, h_frq: float, tauc: float, s2: float, khh: float = 0.0 + self, + h_frq: float, + tauc: float, + s2: float, + khh: float = 0.0, ) -> dict[str, float]: rates = super().__call__(h_frq, tauc, s2) if khh == 0: @@ -277,7 +285,7 @@ def get_model_free_expressions(basis: Basis, conditions: Conditions) -> dict[str conditions : Conditions The conditions for the fitting. - Returns + Returns: ------- A dictionary of rate names and their corresponding expressions. diff --git a/chemex/nmr/spectrometer.py b/chemex/nmr/spectrometer.py index 6db0957e..9ab0e23f 100644 --- a/chemex/nmr/spectrometer.py +++ b/chemex/nmr/spectrometer.py @@ -24,10 +24,11 @@ def calculate_propagators( - liouv: ArrayFloat, delays: float | Iterable[float], dephasing: bool = False + liouv: ArrayFloat, + delays: float | Iterable[float], + dephasing: bool = False, ) -> ArrayFloat: - """ - Calculate the propagators for the given delays. + """Calculate the propagators for the given delays. Parameters ---------- @@ -38,12 +39,11 @@ def calculate_propagators( dephasing : bool, optional Whether to apply dephasing, by default False - Returns + Returns: ------- ArrayFloat The propagators """ - # Ensure delays is a 1D NumPy array delays = np.asarray(delays).flatten() @@ -58,7 +58,9 @@ def calculate_propagators( if dephasing: # If dephasing is requested, adjust eigenvalues eigenvalues = np.where( - abs(eigenvalues.imag) < SMALL_VALUE, eigenvalues, eigenvalues * 1e9 + abs(eigenvalues.imag) < SMALL_VALUE, + eigenvalues, + eigenvalues * 1e9, ) # Calculate the exponentiated eigenvalues for each delay @@ -256,7 +258,9 @@ def get_equilibrium(self) -> ArrayFloat: return self.liouvillian.get_equilibrium() def get_start_magnetization( - self, terms: Iterable[str], atom: str = "h" + self, + terms: Iterable[str], + atom: str = "h", ) -> ArrayFloat: return self.liouvillian.get_start_magnetization(terms=terms, atom=atom) @@ -314,7 +318,10 @@ def pulse_s( return calculate_propagators(liouv, times) def pulse_is( - self, times: float | Iterable[float], phase_i: float, phase_s: float + self, + times: float | Iterable[float], + phase_i: float, + phase_s: float, ) -> ArrayFloat: dephased = self.b1_i_inh_scale == np.inf liouv = ( @@ -327,7 +334,10 @@ def pulse_is( return calculate_propagators(liouv, times, dephased) def shaped_pulse_i( - self, pw: float, amplitudes: Sequence[float], phases: Iterable[float] + self, + pw: float, + amplitudes: Sequence[float], + phases: Iterable[float], ) -> ArrayFloat: time = pw / len(amplitudes) pairs = list(zip(amplitudes, phases, strict=True)) @@ -393,7 +403,8 @@ def p9024090_nh(self, reverse: bool = False) -> ArrayFloat: pw240i, pw9024090i = np.array([8.0, 14.0]) * self._pw90_i / 3.0 pw240s, pw9024090s = np.array([8.0, 14.0]) * self._pw90_s / 3.0 t0, t1, t2, t3 = 0.5 * np.diff( - np.sort([pw240i, pw240s, pw9024090i, pw9024090s]), prepend=0.0 + np.sort([pw240i, pw240s, pw9024090i, pw9024090s]), + prepend=0.0, ) p0 = self.pulse_is(2.0 * t0, 0, 0) if pw9024090i <= pw9024090s: @@ -425,7 +436,7 @@ def p9024090_nh_2(self) -> ArrayFloat: def calculate_shifts(self) -> ArrayFloat: liouv = self.liouvillian.l_free.reshape( - (self.liouvillian.size, self.liouvillian.size) + (self.liouvillian.size, self.liouvillian.size), ) return np.linalg.eigvals(liouv).imag diff --git a/chemex/optimize/fitting.py b/chemex/optimize/fitting.py index 27ad6873..a937539d 100644 --- a/chemex/optimize/fitting.py +++ b/chemex/optimize/fitting.py @@ -43,7 +43,7 @@ def _run_statistics( path: Path, fitmethod: str | None = None, statistics: Statistics | None = None, -): +) -> None: if statistics is None: return @@ -104,7 +104,9 @@ def _fit_groups( print_group_name(message) best_lmfit_params = minimize_with_report( - group.experiments, group_lmfit_params, fitmethod + group.experiments, + group_lmfit_params, + fitmethod, ) # best_lmfit_params = minimize_hierarchical( # group.experiments, group_lmfit_params, fitmethod @@ -126,7 +128,10 @@ def _fit_groups( def run_methods( - experiments: Experiments, methods: Methods, path: Path, plot_level: str + experiments: Experiments, + methods: Methods, + path: Path, + plot_level: str, ) -> None: for index, (section, method) in enumerate(methods.items(), start=1): if section: @@ -153,11 +158,19 @@ def run_methods( if method.grid: try: run_grid( - experiments, method.grid, path_sect, plot_level, method.fitmethod + experiments, + method.grid, + path_sect, + plot_level, + method.fitmethod, ) except KeyboardInterrupt: print_calculation_stopped_error() else: _fit_groups( - experiments, path_sect, plot_level, method.fitmethod, method.statistics + experiments, + path_sect, + plot_level, + method.fitmethod, + method.statistics, ) diff --git a/chemex/optimize/gridding.py b/chemex/optimize/gridding.py index 6ba2a4f8..8f0ebb48 100644 --- a/chemex/optimize/gridding.py +++ b/chemex/optimize/gridding.py @@ -40,7 +40,9 @@ class GridResult: def _set_param_values( - params: Parameters, fnames: Iterable[str], values: tuple[float, ...] + params: Parameters, + fnames: Iterable[str], + values: tuple[float, ...], ): for fname, value in zip(fnames, values, strict=True): params[fname].value = value @@ -96,7 +98,8 @@ def run_group_grid( def _reshape_chisqr( - grid_ref: dict[str, ArrayFloat], grid_result: GridResult + grid_ref: dict[str, ArrayFloat], + grid_result: GridResult, ) -> ArrayFloat: keys = list(grid_result.grid) order = [keys.index(key) for key in grid_ref if key in keys] @@ -116,7 +119,8 @@ def _reshape_chisqr( def _get_grids( - grid: dict[str, ArrayFloat], grid_results: list[GridResult] + grid: dict[str, ArrayFloat], + grid_results: list[GridResult], ) -> list[dict[str, ArrayFloat]]: grid_params = {tuple(sorted(grid_result.grid)) for grid_result in grid_results} grid_params_tmp = grid_params.copy() @@ -127,7 +131,8 @@ def _get_grids( def combine_grids( - grid: dict[str, ArrayFloat], grid_results: list[GridResult] + grid: dict[str, ArrayFloat], + grid_results: list[GridResult], ) -> list[GridResult]: grids = _get_grids(grid, grid_results) @@ -174,7 +179,7 @@ def make_grids_nd( return grids -def plot_grid_1d(grids_1d: list[GridResult], path: Path): +def plot_grid_1d(grids_1d: list[GridResult], path: Path) -> None: """Visualize the result of the brute force grid search. The output file will display the chi-square values per parameter. @@ -198,7 +203,7 @@ def plot_grid_1d(grids_1d: list[GridResult], path: Path): plt.close() -def plot_grid_2d(grids_2d: list[GridResult], path: Path): +def plot_grid_2d(grids_2d: list[GridResult], path: Path) -> None: """Visualize the result of the brute force grid search. The output file will display the chi-square contour diff --git a/chemex/optimize/grouping.py b/chemex/optimize/grouping.py index 2a7af9ab..a27c8663 100644 --- a/chemex/optimize/grouping.py +++ b/chemex/optimize/grouping.py @@ -9,10 +9,10 @@ from chemex.parameters import database from chemex.parameters.name import ParamName -from chemex.parameters.setting import Parameters if TYPE_CHECKING: from chemex.containers.experiments import Experiments + from chemex.parameters.setting import Parameters @dataclass @@ -31,7 +31,8 @@ def ids_to_param_name(param_ids: set[str]) -> ParamName: def group_ids( - experiments: Experiments, parameters: Parameters | None = None + experiments: Experiments, + parameters: Parameters | None = None, ) -> list[tuple[ParamName, set[str]]]: if parameters is None: parameters = database.get_parameters(experiments.param_ids) @@ -94,7 +95,8 @@ def create_groups(experiments: Experiments) -> list[Group]: group_param_ids = set(database.get_parameters(param_ids)) group_experiments = experiments.get_relevant_subset(group_param_ids) group_message = group_message_template.format( - index=index, group_name=group_name + index=index, + group_name=group_name, ) groups.append(Group(group_path, group_message, group_experiments)) @@ -109,7 +111,8 @@ class ParamTree: def create_group_tree( - experiments: Experiments, parameters: Parameters | None = None + experiments: Experiments, + parameters: Parameters | None = None, ) -> ParamTree: if parameters is None: parameters = database.get_parameters(experiments.param_ids) diff --git a/chemex/optimize/helper.py b/chemex/optimize/helper.py index 24c27b89..86efb9d1 100644 --- a/chemex/optimize/helper.py +++ b/chemex/optimize/helper.py @@ -25,12 +25,13 @@ def calculate_statistics( - experiments: Experiments, params_lf: ParametersLF + experiments: Experiments, + params_lf: ParametersLF, ) -> dict[str, int | float]: residuals = experiments.residuals(params_lf) ndata = len(residuals) nvarys = len( - [param for param in params_lf.values() if param.vary and not param.expr] + [param for param in params_lf.values() if param.vary and not param.expr], ) chisqr = sum(residuals**2) redchi = chisqr / max(1, ndata - nvarys) @@ -63,7 +64,7 @@ def _write_statistics(experiments: Experiments, path: Path): f.write(f"\"reduced-chi-square\" = {stats['redchi']: .5e}\n") f.write(f"\"chi-squared test\" = {stats['pvalue']: .5e}\n") f.write( - f"\"Kolmogorov-Smirnov test\" = {stats['ks_pvalue']: .5e}\n" + f"\"Kolmogorov-Smirnov test\" = {stats['ks_pvalue']: .5e}\n", ) f.write(f"\"Akaike Information Criterion (AIC)\" = {stats['aic']: .5e}\n") f.write(f"\"Bayesian Information Criterion (BIC)\" = {stats['bic']: .5e}\n") @@ -151,7 +152,9 @@ def print_values(values: Iterable[float], chisqr: float) -> str: def print_values_stat( - params_lf: ParametersLF, fnames: Iterable[str], chisqr: float + params_lf: ParametersLF, + fnames: Iterable[str], + chisqr: float, ) -> str: body_values_list = [] for fname in fnames: diff --git a/chemex/optimize/minimizer.py b/chemex/optimize/minimizer.py index 960100ca..7370cc22 100644 --- a/chemex/optimize/minimizer.py +++ b/chemex/optimize/minimizer.py @@ -45,7 +45,7 @@ def iter_cb( ndata = len(residuals) nvarys = len( - [param for param in params.values() if param.vary and not param.expr] + [param for param in params.values() if param.vary and not param.expr], ) redchi = chisqr / max(1, ndata - nvarys) @@ -62,7 +62,9 @@ def print_footer(self, iteration: int, chisqr: float, redchi: float) -> None: def minimize( - experiments: Experiments, params: Parameters, fitmethod: str + experiments: Experiments, + params: Parameters, + fitmethod: str, ) -> Parameters: kws = { "brute": {"keep": "all"}, @@ -75,7 +77,9 @@ def minimize( def minimize_with_report( - experiments: Experiments, params: Parameters, fitmethod: str + experiments: Experiments, + params: Parameters, + fitmethod: str, ) -> Parameters: kws = { "brute": {"keep": "all"}, @@ -113,7 +117,10 @@ def residuals_hierarchical(params: Parameters, param_tree: ParamTree) -> ArrayFl for branch in param_tree.branches: branch_results = lmfit.minimize( - residuals_hierarchical, params, args=(branch,), method="leastsq" + residuals_hierarchical, + params, + args=(branch,), + method="leastsq", ) residuals_list.append(branch_results.residual) @@ -143,7 +150,10 @@ def minimize_hierarchical(experiments: Experiments, params: Parameters, fitmetho param.vary = False minimizer = Minimizer( - residuals_hierarchical, params, fcn_args=(param_tree,), iter_cb=reporter.iter_cb + residuals_hierarchical, + params, + fcn_args=(param_tree,), + iter_cb=reporter.iter_cb, ) reporter.print_header() diff --git a/chemex/parameters/database.py b/chemex/parameters/database.py index 3bd44ce4..e62f99c6 100644 --- a/chemex/parameters/database.py +++ b/chemex/parameters/database.py @@ -1,3 +1,10 @@ +"""This module offers a framework for managing NMR analysis parameters. + +It includes classes and methods for indexing, updating, and retrieving parameters, +handling parameter constraints, and integration with the lmfit library for +optimization. Additionally, it supports grid definition for parameter exploration and +ensures physical validity of J couplings. +""" from __future__ import annotations import re @@ -39,21 +46,56 @@ class ParameterIndex: + """Maintains an index of parameter names for efficient searching and retrieval. + + This class creates an index structure that allows for quick lookup of parameter + IDs based on parameter names, which is particularly useful in large datasets + with numerous parameters. + + Attributes: + _index (defaultdict[Hashable, set[str]]): Maps search keys to parameter IDs. + """ + def __init__(self) -> None: + """Initializes an empty parameter index.""" self._index: defaultdict[Hashable, set[str]] = defaultdict(set) def add(self, param_name: ParamName) -> None: + """Adds a parameter name to the index. + + Args: + param_name (ParamName): The parameter name to be indexed. + """ for search_key in param_name.search_keys: - self._index[search_key].add(param_name.id) + self._index[search_key].add(param_name.id_) def get_matching_ids(self, param_name: ParamName) -> set[str]: + """Retrieves parameter IDs matching a given parameter name. + + Args: + param_name (ParamName): Parameter name to match in the index. + + Returns: + set[str]: Set of matching parameter IDs. + """ search_keys = param_name.search_keys return set[str].intersection( - *(self._index.get(search_key, set()) for search_key in search_keys) + *(self._index.get(search_key, set()) for search_key in search_keys), ) def _convert_grid_expression_to_values(grid_expression: str) -> ArrayFloat: + """Converts grid expression to floating-point values. + + Parses grid expressions used for parameter exploration and converts them into + an array of floating-point values for further processing. + + Args: + grid_expression (str): Grid expression to be converted. + + Returns: + ArrayFloat: Array of floating-point values from the grid expression. + """ if match := re.match(_LINEAR, grid_expression): return np.linspace( float(match.group("start")), @@ -71,23 +113,52 @@ def _convert_grid_expression_to_values(grid_expression: str) -> ArrayFloat: @dataclass class ParameterCatalog: + """Manages a collection of parameter settings for NMR data analysis. + + This class is responsible for storing, updating, and retrieving various + parameter settings, including their values, expressions, and dependencies. + It also interfaces with the lmfit library for optimization purposes. + + Attributes: + _parameters (Parameters): The parameters managed by the catalog. + _index (ParameterIndex): An index for efficient parameter lookup. + """ + _parameters: Parameters = field(default_factory=dict) _index: ParameterIndex = field(default_factory=ParameterIndex) def _add(self, parameter: ParamSetting) -> None: - if parameter.id not in self._parameters: - self._parameters[parameter.id] = parameter + """Adds a single parameter to the catalog. + + Args: + parameter (ParamSetting): The parameter to be added. + """ + if parameter.id_ not in self._parameters: + self._parameters[parameter.id_] = parameter self._index.add(parameter.param_name) if parameter.vary: - self._parameters[parameter.id].vary = True - self._parameters[parameter.id].expr = "" + self._parameters[parameter.id_].vary = True + self._parameters[parameter.id_].expr = "" def add_multiple(self, parameters: Parameters) -> None: + """Adds multiple parameters to the catalog. + + Args: + parameters (Parameters): Dictionary of parameters to be added. + """ for parameter in parameters.values(): self._add(parameter) def get_parameters(self, param_ids: Iterable[str]) -> Parameters: + """Retrieves a subset of parameters based on their IDs. + + Args: + param_ids (Iterable[str]): IDs of the parameters to retrieve. + + Returns: + Parameters: Subset of parameters matching the provided IDs. + """ relevant_ids: set[str] = set() pool_ids = set(self._parameters) & set(param_ids) @@ -106,8 +177,21 @@ def get_parameters(self, param_ids: Iterable[str]) -> Parameters: } def build_lmfit_params( - self, param_ids: Iterable[str] | None = None + self, + param_ids: Iterable[str] | None = None, ) -> ParametersLF: + """Constructs lmfit Parameters from the catalog's parameters. + + This method converts the internal parameter representation to the format + required by the lmfit library for optimization. + + Args: + param_ids (Iterable[str] | None): Specific parameter IDs to include. + If None, includes all parameters. + + Returns: + ParametersLF: lmfit-compatible parameter collection. + """ if param_ids is None: param_ids = set(self._parameters) @@ -120,28 +204,59 @@ def build_lmfit_params( lmfit_params.add_many(*parameter_args) lmfit_params.update_constraints() - for id, lf_param in lmfit_params.items(): - lf_param.stderr = parameters[id].stderr + for id_, lf_param in lmfit_params.items(): + lf_param.stderr = parameters[id_].stderr return lmfit_params def update_from_lmfit_params(self, parameters: ParametersLF) -> None: + """Updates catalog parameters from lmfit Parameters. + + Args: + parameters (ParametersLF): lmfit Parameters to update from. + """ for param_id, parameter in parameters.items(): self._parameters[param_id].value = parameter.value self._parameters[param_id].stderr = parameter.stderr def get_matching_ids(self, param_name: ParamName) -> set[str]: + """Finds parameter IDs matching a specified parameter name. + + Args: + param_name (ParamName): Name of the parameter to match. + + Returns: + set[str]: Set of IDs matching the parameter name. + """ return self._index.get_matching_ids(param_name) def get_value(self, id_: str) -> float | None: + """Retrieves the value of a parameter by its ID. + + Args: + id_ (str): The ID of the parameter. + + Returns: + float | None: The value of the parameter, or None if not found. + """ return self._parameters[id_].value def set_values(self, par_values: dict[str, float]) -> None: + """Sets the values of specified parameters. + + Args: + par_values (dict[str, float]): Dictionary of parameter IDs and values. + """ for id_, value in par_values.items(): if id_ in self._parameters: self._parameters[id_].value = value def set_defaults(self, defaults: DefaultListType) -> None: + """Sets default settings for a group of parameters. + + Args: + defaults (DefaultListType): Defaults to apply. + """ id_pool = set(self._parameters) for name_to_set, setting in reversed(defaults): matching_ids = self.get_matching_ids(name_to_set) & id_pool @@ -150,11 +265,28 @@ def set_defaults(self, defaults: DefaultListType) -> None: self._parameters[matching_id].set(setting) def _count_per_section(self, param_ids: set[str]) -> Counter[str]: + """Counts parameters per section for a given set of IDs. + + Args: + param_ids (set[str]): Set of parameter IDs to count. + + Returns: + Counter[str]: Counts of parameters per section. + """ return Counter( self._parameters[param_id].param_name.section for param_id in param_ids ) def set_vary(self, section_names: Sequence[str], vary: bool) -> Counter[str]: + """Sets the variability of parameters by section name. + + Args: + section_names (Sequence[str]): Names of the sections to update. + vary (bool): Whether to set parameters as variable. + + Returns: + Counter[str]: Counts of parameters updated per section. + """ parameters = self._parameters ids_modified: set[str] = set() @@ -176,14 +308,31 @@ def set_vary(self, section_names: Sequence[str], vary: bool) -> Counter[str]: return self._count_per_section(ids_modified) def fix_all(self) -> None: + """Fixes all parameters, preventing them from varying during fitting.""" for parameter in self._parameters.values(): parameter.vary = False parameter.expr = "" def _get_ids_left(self, expression: str) -> set[str]: + """Extracts parameter IDs from the left side of an expression. + + Args: + expression (str): The expression to parse. + + Returns: + set[str]: Set of parameter IDs extracted. + """ return self.get_matching_ids(ParamName.from_section(expression)) def _get_ids_right(self, expression: str) -> dict[str, set[str]]: + """Extracts parameter IDs from the right side of an expression. + + Args: + expression (str): The expression to parse. + + Returns: + dict[str, set[str]]: Mapping of section names to parameter IDs. + """ ids_right: dict[str, set[str]] = {} for match in re.finditer(_PARAM_NAME, expression): param_name = ParamName.from_section(match.group(1)) @@ -191,6 +340,15 @@ def _get_ids_right(self, expression: str) -> dict[str, set[str]]: return ids_right def _set_expression(self, expression: str, ids_pool: set[str]) -> set[str]: + """Sets expressions for parameters based on an input expression. + + Args: + expression (str): The expression to apply. + ids_pool (set[str]): Set of parameter IDs to consider. + + Returns: + set[str]: Set of parameter IDs updated. + """ left, right, *something_else = expression.split("=") if something_else: @@ -211,6 +369,14 @@ def _set_expression(self, expression: str, ids_pool: set[str]) -> set[str]: return ids_left def set_expressions(self, expression_list: Sequence[str]) -> Counter[str]: + """Applies a list of expressions to parameters. + + Args: + expression_list (Sequence[str]): Expressions to apply. + + Returns: + Counter[str]: Counts of parameters updated per section. + """ ids_modified: set[str] = set() ids_pool = set(self._parameters) @@ -222,6 +388,14 @@ def set_expressions(self, expression_list: Sequence[str]) -> Counter[str]: return self._count_per_section(ids_modified) def parse_grid(self, grid_entries: list[str]) -> dict[str, ArrayFloat]: + """Parses grid definitions and sets up parameters accordingly. + + Args: + grid_entries (list[str]): List of grid definitions. + + Returns: + dict[str, ArrayFloat]: Mapping of parameter IDs to grid values. + """ ids_pool = set(self._parameters) grid_values: dict[str, ArrayFloat] = {} @@ -247,7 +421,7 @@ def parse_grid(self, grid_entries: list[str]) -> dict[str, ArrayFloat]: return grid_values def check_params(self): - """Check whether the J couplings have the right sign.""" + """Checks and warns about the physical validity of J couplings.""" positive_jnh = False negative_jch = False for setting in self._parameters.values(): @@ -265,46 +439,114 @@ def check_params(self): print_warning_negative_jch() def sort(self) -> None: + """Sorts the parameters in the catalog by their names.""" sorted_items = sorted( - self._parameters.items(), key=lambda item: item[1].param_name + self._parameters.items(), + key=lambda item: item[1].param_name, ) self._parameters = dict(sorted_items) @dataclass class ParamManager: + """Manages a collection of ParameterCatalogs for different fitting models. + + This class acts as an interface to multiple ParameterCatalogs, allowing + for easy management of parameters across different fitting models used + in NMR data analysis. + + Attributes: + _database (ParameterCatalog): The primary parameter catalog. + _database_mf (ParameterCatalog): The model-free parameter catalog. + """ + _database: ParameterCatalog _database_mf: ParameterCatalog @property def database(self) -> ParameterCatalog: + """Returns the appropriate parameter catalog based on the model. + + Returns: + ParameterCatalog: The active parameter catalog. + """ return self._database_mf if model.model_free else self._database def add_multiple(self, parameters: Parameters) -> None: + """Adds multiple parameters to the primary catalog. + + Args: + parameters (Parameters): Parameters to be added. + """ self._database.add_multiple(parameters) def add_multiple_mf(self, parameters: Parameters) -> None: + """Adds multiple parameters to the model-free catalog. + + Args: + parameters (Parameters): Parameters to be added. + """ self._database_mf.add_multiple(parameters) def get_parameters(self, param_ids: Iterable[str]) -> Parameters: + """Retrieves parameters from the active catalog by IDs. + + Args: + param_ids (Iterable[str]): IDs of the parameters to retrieve. + + Returns: + Parameters: Retrieved parameters. + """ return self.database.get_parameters(param_ids) def get_value(self, param_id: str) -> float | None: + """Gets the value of a parameter by its ID from the active catalog. + + Args: + param_id (str): ID of the parameter. + + Returns: + float | None: The value of the parameter or None if not found. + """ return self.database.get_value(param_id) def build_lmfit_params(self, param_ids: Iterable[str]) -> ParametersLF: + """Builds lmfit Parameters from the active catalog. + + Args: + param_ids (Iterable[str]): IDs of parameters to include. + + Returns: + ParametersLF: lmfit-compatible parameters. + """ return self.database.build_lmfit_params(param_ids) def sort(self) -> None: + """Sorts parameters in the active catalog.""" self.database.sort() def update_from_parameters(self, parameters: ParametersLF) -> None: + """Updates the active catalog from lmfit Parameters. + + Args: + parameters (ParametersLF): lmfit Parameters to update from. + """ self.database.update_from_lmfit_params(parameters) def set_values(self, par_values: dict[str, float]) -> None: + """Sets the values of specific parameters in the active catalog. + + Args: + par_values (dict[str, float]): Parameter values to set. + """ return self.database.set_values(par_values) def set_defaults(self, defaults: DefaultListType) -> None: + """Sets defaults for parameters in both catalogs. + + Args: + defaults (DefaultListType): Default settings to apply. + """ self._database_mf.set_defaults(defaults) if model.model_free: @@ -318,15 +560,41 @@ def set_defaults(self, defaults: DefaultListType) -> None: self.database.check_params() def set_vary(self, section_names: Sequence[str], vary: bool) -> Counter[str]: + """Sets variability of parameters in the active catalog by section name. + + Args: + section_names (Sequence[str]): Section names to update. + vary (bool): Whether parameters should vary. + + Returns: + Counter[str]: Counts of updated parameters per section. + """ return self.database.set_vary(section_names, vary) def fix_all(self) -> None: + """Fixes all parameters in the active catalog, preventing them from varying.""" self.database.fix_all() def set_expressions(self, expression_list: Sequence[str]) -> Counter[str]: + """Applies expressions to parameters in the active catalog. + + Args: + expression_list (Sequence[str]): Expressions to apply. + + Returns: + Counter[str]: Counts of updated parameters per section. + """ return self.database.set_expressions(expression_list) def parse_grid(self, grid_entries: list[str]) -> dict[str, ArrayFloat]: + """Parses grid definitions and sets up parameters in the active catalog. + + Args: + grid_entries (list[str]): Grid definitions to parse. + + Returns: + dict[str, ArrayFloat]: Parameters mapped to grid values. + """ return self.database.parse_grid(grid_entries) @@ -349,8 +617,13 @@ def parse_grid(self, grid_entries: list[str]) -> dict[str, ArrayFloat]: def set_parameter_status(method: Method): - """Set whether or not to vary a fitting parameter or to use a mathematical - expression. + """Sets parameter status based on a given method configuration. + + This function configures parameters to vary, be fixed, or follow certain + expressions based on the provided method configuration. + + Args: + method (Method): Method configuration to apply. """ matches_con = set_param_expressions(method.constraints) matches_fix = set_param_vary(method.fix, vary=False) diff --git a/chemex/parameters/factory.py b/chemex/parameters/factory.py index 3199a5c6..f9868c67 100644 --- a/chemex/parameters/factory.py +++ b/chemex/parameters/factory.py @@ -23,7 +23,8 @@ @cache def _build_settings( - basis: Basis, conditions: Conditions + basis: Basis, + conditions: Conditions, ) -> tuple[LocalSettings, LocalSettings]: settings_spins, settings_spins_mf = build_spin_param_settings(basis, conditions) settings_kinetics = model_factory.create(model.name, conditions) @@ -32,7 +33,11 @@ def _build_settings( return settings, settings_mf -def _set_to_fit(parameters: Parameters, name_map: dict[str, str], fitted: list[str]): +def _set_to_fit( + parameters: Parameters, + name_map: dict[str, str], + fitted: list[str], +) -> None: pool = set(name_map) for fitted_name in fitted: selection = {name for name in pool if name.startswith(fitted_name)} @@ -44,7 +49,9 @@ def _set_to_fit(parameters: Parameters, name_map: dict[str, str], fitted: list[s def _build_parameters( - settings: LocalSettings, spin_system: SpinSystem, conditions: Conditions + settings: LocalSettings, + spin_system: SpinSystem, + conditions: Conditions, ) -> tuple[dict[str, str], Parameters]: param_names = { local_name: setting.name_setting.get_param_name(spin_system, conditions) @@ -52,7 +59,7 @@ def _build_parameters( } name_map = { - local_name: param_name.id for local_name, param_name in param_names.items() + local_name: param_name.id_ for local_name, param_name in param_names.items() } parameters: Parameters = {} @@ -77,11 +84,15 @@ def create_parameters(config: ConfigType, liouvillian: LiouvillianIS) -> dict[st settings, settings_mf = _build_settings(liouvillian.basis, config.conditions) name_map, parameters = _build_parameters( - settings, liouvillian.spin_system, config.conditions + settings, + liouvillian.spin_system, + config.conditions, ) name_map_mf, parameters_mf = _build_parameters( - settings_mf, liouvillian.spin_system, config.conditions + settings_mf, + liouvillian.spin_system, + config.conditions, ) _set_to_fit(parameters, name_map, config.to_be_fitted.rates) diff --git a/chemex/parameters/name.py b/chemex/parameters/name.py index 9b2326e2..33389032 100644 --- a/chemex/parameters/name.py +++ b/chemex/parameters/name.py @@ -4,7 +4,7 @@ from dataclasses import dataclass, field from functools import cached_property from re import Pattern -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, TypeVar from rapidfuzz.process import extractOne @@ -14,6 +14,8 @@ if TYPE_CHECKING: from collections.abc import Hashable, Iterable +Self = TypeVar("Self", bound="ParamName") + _EXPAND = {"-": "_", "+": "_", ".": "_"} _FLOAT = r"[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?" @@ -73,7 +75,7 @@ class ParamName: conditions: Conditions = field(default_factory=Conditions.model_construct) search_keys: set[Hashable] = field(init=False, compare=False) - def __post_init__(self): + def __post_init__(self) -> None: self.name = self.name.strip().upper() self.conditions = self.conditions.rounded() self.search_keys = ( @@ -81,14 +83,14 @@ def __post_init__(self): ) @classmethod - def from_section(cls, section: str = "") -> ParamName: + def from_section(cls: type[Self], section: str = "") -> Self: parsed = _parse(_RE_SECTION, section.strip(' []"')) name = parsed.get("name") if name is None: name = "" spin_system = SpinSystem(parsed.get("spin_system")) conditions = Conditions.model_validate(parsed) - return ParamName(name, spin_system, conditions) + return cls(name, spin_system, conditions) @cached_property def section(self) -> str: @@ -109,10 +111,10 @@ def folder(self) -> str: return "_".join(parts).strip("_").upper() @cached_property - def id(self) -> str: + def id_(self) -> str: return f"__{_expand(self.folder)}" - def match(self, other: ParamName) -> bool: + def match(self: Self, other: Self) -> bool: if self.name and self.name not in other.name: return False if not self.spin_system.match(other.spin_system): @@ -122,14 +124,16 @@ def match(self, other: ParamName) -> bool: return True def get_closest_id(self, ids: Iterable[str]) -> str: - best_match, _, _ = extractOne(self.id, ids) + best_match, _, _ = extractOne(self.id_, ids) return best_match - def __and__(self, other: ParamName) -> ParamName: + def __and__(self: Self, other: object) -> Self: + if not isinstance(other, type(self)): + return NotImplemented name = self.name if self.name == other.name else "" spin_system = self.spin_system & other.spin_system conditions = self.conditions & other.conditions - return ParamName(name, spin_system, conditions) + return type(self)(name, spin_system, conditions) def __bool__(self) -> bool: return bool(self.name) or bool(self.spin_system) or bool(self.conditions) diff --git a/chemex/parameters/setting.py b/chemex/parameters/setting.py index de70c798..caf9d4f1 100644 --- a/chemex/parameters/setting.py +++ b/chemex/parameters/setting.py @@ -24,14 +24,18 @@ class NameSetting: spin_system_part: Literal["i", "s", "is", "g", ""] = "" conditions_part: tuple[str, ...] = field(default_factory=tuple) - def get_param_name(self, spin_system: SpinSystem, conditions: Conditions): + def get_param_name( + self, + spin_system: SpinSystem, + conditions: Conditions, + ) -> ParamName: param_spin_system = spin_system.build_sub_spin_system(self.spin_system_part) param_conditions = conditions.select_conditions(self.conditions_part) return ParamName(self.name, param_spin_system, param_conditions) class ExpressionSetting: - def __init__(self, re_dependencies: Pattern[str]): + def __init__(self, re_dependencies: Pattern[str]) -> None: self.re_dependencies = re_dependencies self.__expr: str = "" self.__dependencies: set[str] = set() @@ -119,12 +123,12 @@ def dependencies(self) -> set[str]: return self.__expr.dependencies @property - def id(self) -> str: - return self.param_name.id + def id_(self) -> str: + return self.param_name.id_ @property def args(self) -> tuple[str, float | None, bool | None, float, float, str]: - return self.id, self.value, self.vary, self.min, self.max, self.expr + return self.id_, self.value, self.vary, self.min, self.max, self.expr def set(self, default_setting: DefaultSetting) -> None: self.value = default_setting.value diff --git a/chemex/parameters/spins.py b/chemex/parameters/spins.py index cbe25a78..fb64aadb 100644 --- a/chemex/parameters/spins.py +++ b/chemex/parameters/spins.py @@ -14,7 +14,9 @@ def _update_expr_for_proton_exchange( - settings: dict[str, ParamLocalSetting], state: str, basis: Basis + settings: dict[str, ParamLocalSetting], + state: str, + basis: Basis, ) -> None: # As 1HN sites exchange with water, the "expr" should be modified accordingly # for spin system including an amide proton @@ -28,7 +30,9 @@ def _update_expr_for_proton_exchange( def _add_temp_coef_param_settings( - settings: dict[str, ParamLocalSetting], state: str, conditions: Conditions + settings: dict[str, ParamLocalSetting], + state: str, + conditions: Conditions, ) -> None: settings[f"dwm_i_a{state}"] = ParamLocalSetting( name_setting=NameSetting(f"dwm_a{state}", "i"), @@ -68,7 +72,9 @@ def _add_temp_coef_param_settings( def _add_dw_param_settings( - settings: dict[str, ParamLocalSetting], state: str, conditions: Conditions + settings: dict[str, ParamLocalSetting], + state: str, + conditions: Conditions, ) -> None: settings[f"dw_i_a{state}"] = ParamLocalSetting( name_setting=NameSetting(f"dw_a{state}", "i", ("temperature",)), @@ -98,7 +104,9 @@ def _set_equal_to_a(settings: dict[str, ParamLocalSetting]) -> None: def create_base_param_settings( - basis: Basis, state: str, conditions: Conditions + basis: Basis, + state: str, + conditions: Conditions, ) -> dict[str, ParamLocalSetting]: ext = basis.extension settings = { @@ -113,39 +121,50 @@ def create_base_param_settings( min=0.0, ), f"khh_{state}": ParamLocalSetting( - name_setting=NameSetting(f"khh_{state}", "g", ("temperature",)), value=0.0 + name_setting=NameSetting(f"khh_{state}", "g", ("temperature",)), + value=0.0, ), f"r2_i_{state}": ParamLocalSetting( name_setting=NameSetting( - f"r2{ext}_{state}", "i", ("temperature", "h_larmor_frq") + f"r2{ext}_{state}", + "i", + ("temperature", "h_larmor_frq"), ), value=10.0, min=0.0, ), f"r2_s_{state}": ParamLocalSetting( name_setting=NameSetting( - f"r2_{state}", "s", ("temperature", "h_larmor_frq") + f"r2_{state}", + "s", + ("temperature", "h_larmor_frq"), ), value=10.0, min=0.0, ), f"r1_i_{state}": ParamLocalSetting( name_setting=NameSetting( - f"r1{ext}_{state}", "i", ("temperature", "h_larmor_frq") + f"r1{ext}_{state}", + "i", + ("temperature", "h_larmor_frq"), ), value=1.5, min=0.0, ), f"r1_s_{state}": ParamLocalSetting( name_setting=NameSetting( - f"r1_{state}", "s", ("temperature", "h_larmor_frq") + f"r1_{state}", + "s", + ("temperature", "h_larmor_frq"), ), value=1.5, min=0.0, ), f"r2a_i_{state}": ParamLocalSetting( name_setting=NameSetting( - f"r2a{ext}_{state}", "i", ("temperature", "h_larmor_frq") + f"r2a{ext}_{state}", + "i", + ("temperature", "h_larmor_frq"), ), value=12.0, min=0.0, @@ -153,7 +172,9 @@ def create_base_param_settings( ), f"r2a_s_{state}": ParamLocalSetting( name_setting=NameSetting( - f"r2a_{state}", "s", ("temperature", "h_larmor_frq") + f"r2a_{state}", + "s", + ("temperature", "h_larmor_frq"), ), value=12.0, min=0.0, @@ -161,14 +182,18 @@ def create_base_param_settings( ), f"r2mq_is_{state}": ParamLocalSetting( name_setting=NameSetting( - f"r2mq_{state}", "is", ("temperature", "h_larmor_frq") + f"r2mq_{state}", + "is", + ("temperature", "h_larmor_frq"), ), value=15.0, min=0.0, ), f"r1a_is_{state}": ParamLocalSetting( name_setting=NameSetting( - f"r1a{ext}_{state}", "is", ("temperature", "h_larmor_frq") + f"r1a{ext}_{state}", + "is", + ("temperature", "h_larmor_frq"), ), value=4.0, min=0.0, @@ -176,52 +201,67 @@ def create_base_param_settings( ), f"etaxy_i_{state}": ParamLocalSetting( name_setting=NameSetting( - f"etaxy{ext}_{state}", "i", ("temperature", "h_larmor_frq") + f"etaxy{ext}_{state}", + "i", + ("temperature", "h_larmor_frq"), ), value=0.0, ), f"etaxy_s_{state}": ParamLocalSetting( name_setting=NameSetting( - f"etaxy_{state}", "s", ("temperature", "h_larmor_frq") + f"etaxy_{state}", + "s", + ("temperature", "h_larmor_frq"), ), value=0.0, ), f"etaz_i_{state}": ParamLocalSetting( name_setting=NameSetting( - f"etaz{ext}_{state}", "i", ("temperature", "h_larmor_frq") + f"etaz{ext}_{state}", + "i", + ("temperature", "h_larmor_frq"), ), value=0.0, ), f"etaz_s_{state}": ParamLocalSetting( name_setting=NameSetting( - f"etaz_{state}", "s", ("temperature", "h_larmor_frq") + f"etaz_{state}", + "s", + ("temperature", "h_larmor_frq"), ), value=0.0, ), f"sigma_is_{state}": ParamLocalSetting( name_setting=NameSetting( - f"sigma_{state}", "is", ("temperature", "h_larmor_frq") + f"sigma_{state}", + "is", + ("temperature", "h_larmor_frq"), ), value=0.0, ), f"mu_is_{state}": ParamLocalSetting( name_setting=NameSetting( - f"mu_{state}", "is", ("temperature", "h_larmor_frq") + f"mu_{state}", + "is", + ("temperature", "h_larmor_frq"), ), value=0.0, ), f"cs_i_{state}": ParamLocalSetting( - name_setting=NameSetting(f"cs_{state}", "i", ("temperature",)), value=0.0 + name_setting=NameSetting(f"cs_{state}", "i", ("temperature",)), + value=0.0, ), f"cs_s_{state}": ParamLocalSetting( - name_setting=NameSetting(f"cs_{state}", "s", ("temperature",)), value=0.0 + name_setting=NameSetting(f"cs_{state}", "s", ("temperature",)), + value=0.0, ), f"j_is_{state}": ParamLocalSetting( name_setting=NameSetting(f"j_{state}", "is"), value=J_COUPLINGS.get(basis.spin_system, 0.0), ), f"d_{state}": ParamLocalSetting( - name_setting=NameSetting(f"d_{state}", "", ("temperature",)), value=0.0 + name_setting=NameSetting(f"d_{state}", "", ("temperature",)), + value=0.0, ), } @@ -235,7 +275,9 @@ def create_base_param_settings( def _build_model_free_settings( - settings: LocalSettings, basis: Basis, conditions: Conditions + settings: LocalSettings, + basis: Basis, + conditions: Conditions, ) -> LocalSettings: model_free_expressions = get_model_free_expressions(basis, conditions) settings_mf = deepcopy(settings) @@ -247,7 +289,8 @@ def _build_model_free_settings( def _select_relevant_settings( - all_settings: LocalSettings, basis: Basis + all_settings: LocalSettings, + basis: Basis, ) -> LocalSettings: pool = set(all_settings) & set(basis.matrices) selection: set[str] = set() @@ -260,7 +303,8 @@ def _select_relevant_settings( def build_spin_param_settings( - basis: Basis, conditions: Conditions + basis: Basis, + conditions: Conditions, ) -> tuple[LocalSettings, LocalSettings]: all_settings: LocalSettings = {} for state in model.states: diff --git a/chemex/parameters/userfunctions.py b/chemex/parameters/userfunctions.py index 53a19b99..5b2c47f5 100644 --- a/chemex/parameters/userfunctions.py +++ b/chemex/parameters/userfunctions.py @@ -1,4 +1,5 @@ """Pace where user functions used by lmfit are stored.""" + from __future__ import annotations from collections.abc import Callable diff --git a/chemex/plotters/cest.py b/chemex/plotters/cest.py index 73305bf4..5346c52d 100644 --- a/chemex/plotters/cest.py +++ b/chemex/plotters/cest.py @@ -81,7 +81,10 @@ def add_resonance_positions( kwargs2 = {"color": _GREY400, "linewidth": 0.75, "zorder": -1} cs_shifted = circular_shift.centre(cs_values, centre) for a_cs, a_cs_shifted, lstyle in zip( - cs_values, cs_shifted, _LSTYLES, strict=False + cs_values, + cs_shifted, + _LSTYLES, + strict=False, ): ax1.axvline(a_cs_shifted, linestyle=lstyle, **kwargs2) ax2.axvline(a_cs_shifted, linestyle=lstyle, **kwargs2) @@ -158,7 +161,8 @@ def create_plot_data_calc(profile: Profile) -> Data: data_for_calculation = Data(exp=filler, err=filler, metadata=offsets_plot) scale = profile.data.scale / np.mean(data.exp[refs]) data_for_calculation.calc = scale * profile.pulse_sequence.calculate( - spectrometer, data_for_calculation + spectrometer, + data_for_calculation, ) ppms = spectrometer.offsets_to_ppms(offsets_plot) @@ -175,12 +179,12 @@ def get_state_positions(spectrometer: Spectrometer) -> ArrayFloat: spectrometer.par_values[name] for name in names if name in spectrometer.par_values - ] + ], ) class CestPlotter(Generic[T]): - def __init__(self, filename: Path, config: T, **_extra: Any): + def __init__(self, filename: Path, config: T, **_extra: Any) -> None: self.filename = filename self.config = config self.printer: PlotPrinter = data_plot_printers["cest"] @@ -197,7 +201,12 @@ def _plot_profile( dip_positions = get_state_positions(spectrometer) circular_shift = CircularShift(spectrometer, sw) plot_dcest( - pdf, str(profile.name), data_exp, data_calc, dip_positions, circular_shift + pdf, + str(profile.spin_system), + data_exp, + data_calc, + dip_positions, + circular_shift, ) def plot(self, path: Path, profiles: list[Profile]) -> None: @@ -216,8 +225,12 @@ def plot(self, path: Path, profiles: list[Profile]) -> None: data_exp = create_plot_data_exp(profile) data_calc = create_plot_data_calc(profile) self._plot_profile(file_pdf, profile, data_exp, data_calc) - file_exp.write(self.printer.print_exp(str(profile.name), data_exp)) - file_calc.write(self.printer.print_calc(str(profile.name), data_calc)) + file_exp.write( + self.printer.print_exp(str(profile.spin_system), data_exp) + ) + file_calc.write( + self.printer.print_calc(str(profile.spin_system), data_calc) + ) def plot_simulation(self, path: Path, profiles: list[Profile]) -> None: basename = path / self.filename.name @@ -233,4 +246,6 @@ def plot_simulation(self, path: Path, profiles: list[Profile]) -> None: data_exp = create_plot_data_exp(profile) data_calc = create_plot_data_calc(profile) self._plot_profile(file_pdf, profile, data_exp, data_calc) - file_sim.write(self.printer.print_calc(str(profile.name), data_calc)) + file_sim.write( + self.printer.print_calc(str(profile.spin_system), data_calc) + ) diff --git a/chemex/plotters/cpmg.py b/chemex/plotters/cpmg.py index 2b4a6d90..4791afce 100644 --- a/chemex/plotters/cpmg.py +++ b/chemex/plotters/cpmg.py @@ -46,7 +46,9 @@ def plot_cpmg(file_pdf: PdfPages, name: str, data_exp: Data, data_calc: Data): def intensities_to_rates( - intensities: ArrayFloat, intensities0: ArrayFloat, time_t2: float + intensities: ArrayFloat, + intensities0: ArrayFloat, + time_t2: float, ) -> ArrayFloat: normalized_intensities = intensities / np.mean(intensities0, axis=-1, keepdims=True) @@ -85,7 +87,9 @@ def calculate_errorbars(data: Data, rates: ArrayFloat, time_t2: float) -> ArrayF intensities0_ensemble = intensities0 + intensities0_err * randn0 rates_ensemble: ArrayFloat = intensities_to_rates( - intensities_ensemble, intensities0_ensemble, time_t2 + intensities_ensemble, + intensities0_ensemble, + time_t2, ) # Set infinity rates to high values as `np.percentile` does not take infinity @@ -137,7 +141,8 @@ def create_plot_data_calc(profile: Profile, config: CpmgExperimentConfig) -> Dat data_for_calculation = Data(exp=filler, err=filler, metadata=ncycs) intensities = profile.data.scale * profile.pulse_sequence.calculate( - spectrometer, data_for_calculation + spectrometer, + data_for_calculation, ) nu_cpmgs = ncycs_to_nu_cpmgs(ncycs, time_t2) @@ -148,7 +153,7 @@ def create_plot_data_calc(profile: Profile, config: CpmgExperimentConfig) -> Dat class CpmgPlotter(Generic[T]): - def __init__(self, filename: Path, config: T, **_extra: Any): + def __init__(self, filename: Path, config: T, **_extra: Any) -> None: self.filename = filename self.config = config self.printer: PlotPrinter = data_plot_printers["cpmg"] @@ -168,9 +173,13 @@ def plot(self, path: Path, profiles: list[Profile]) -> None: for profile in sorted(profiles): data_exp = create_plot_data_exp(profile, self.config) data_calc = create_plot_data_calc(profile, self.config) - plot_cpmg(file_pdf, str(profile.name), data_exp, data_calc) - file_exp.write(self.printer.print_exp(str(profile.name), data_exp)) - file_calc.write(self.printer.print_calc(str(profile.name), data_calc)) + plot_cpmg(file_pdf, str(profile.spin_system), data_exp, data_calc) + file_exp.write( + self.printer.print_exp(str(profile.spin_system), data_exp) + ) + file_calc.write( + self.printer.print_calc(str(profile.spin_system), data_calc) + ) def plot_simulation(self, path: Path, profiles: list[Profile]) -> None: basename = path / self.filename.name @@ -185,5 +194,7 @@ def plot_simulation(self, path: Path, profiles: list[Profile]) -> None: for profile in sorted(profiles): data_exp = create_plot_data_exp(profile, self.config) data_calc = create_plot_data_calc(profile, self.config) - plot_cpmg(file_pdf, str(profile.name), data_exp, data_calc) - file_sim.write(self.printer.print_calc(str(profile.name), data_calc)) + plot_cpmg(file_pdf, str(profile.spin_system), data_exp, data_calc) + file_sim.write( + self.printer.print_calc(str(profile.spin_system), data_calc) + ) diff --git a/chemex/plotters/relaxation.py b/chemex/plotters/relaxation.py index 1dc8968f..bfd05381 100644 --- a/chemex/plotters/relaxation.py +++ b/chemex/plotters/relaxation.py @@ -63,7 +63,7 @@ def create_plot_data_calc(profile: Profile) -> Data: class RelaxationPlotter: - def __init__(self, filename: Path, **_extra: Any): + def __init__(self, filename: Path, **_extra: Any) -> None: self.filename = filename self.printer: PlotPrinter = data_plot_printers["relaxation"] @@ -82,9 +82,13 @@ def plot(self, path: Path, profiles: list[Profile]) -> None: for profile in sorted(profiles): data_exp = create_plot_data_exp(profile) data_calc = create_plot_data_calc(profile) - plot_relaxation(file_pdf, str(profile.name), data_exp, data_calc) - file_exp.write(self.printer.print_exp(str(profile.name), data_exp)) - file_calc.write(self.printer.print_calc(str(profile.name), data_calc)) + plot_relaxation(file_pdf, str(profile.spin_system), data_exp, data_calc) + file_exp.write( + self.printer.print_exp(str(profile.spin_system), data_exp) + ) + file_calc.write( + self.printer.print_calc(str(profile.spin_system), data_calc) + ) def plot_simulation(self, path: Path, profiles: list[Profile]) -> None: basename = path / self.filename.name @@ -99,5 +103,7 @@ def plot_simulation(self, path: Path, profiles: list[Profile]) -> None: for profile in sorted(profiles): data_exp = create_plot_data_exp(profile) data_calc = create_plot_data_calc(profile) - plot_relaxation(file_pdf, str(profile.name), data_exp, data_calc) - file_sim.write(self.printer.print_calc(str(profile.name), data_calc)) + plot_relaxation(file_pdf, str(profile.spin_system), data_exp, data_calc) + file_sim.write( + self.printer.print_calc(str(profile.spin_system), data_calc) + ) diff --git a/chemex/plotters/shift.py b/chemex/plotters/shift.py index cd943d2b..94671051 100644 --- a/chemex/plotters/shift.py +++ b/chemex/plotters/shift.py @@ -42,7 +42,7 @@ def create_plot_data(profiles: list[Profile]) -> Data: class ShiftPlotter: - def __init__(self, filename: Path, **_extra: Any): + def __init__(self, filename: Path, **_extra: Any) -> None: self.filename = filename self.plot_simulation = self.plot diff --git a/chemex/printers/data.py b/chemex/printers/data.py index 7491f824..ff878c26 100644 --- a/chemex/printers/data.py +++ b/chemex/printers/data.py @@ -25,7 +25,7 @@ class ShiftPrinter: f"# {'NAME':>16s} {'SHIFT (EXP)':>17s}" f" {'ERROR (EXP)':>17s} {'SHIFT (CALC)':>17s}\n" ), - ] + ], ) def print(self, name: str, data: Data) -> str: @@ -51,13 +51,18 @@ def print(self, name: str, data: Data) -> str: ] for metadata, exp, err, calc, mask in zip( - data.metadata, data.exp, data.err, data.calc, data.mask, strict=True + data.metadata, + data.exp, + data.err, + data.calc, + data.mask, + strict=True, ): start = " " if mask else "#" end = "" if mask else " # NOT USED IN THE FIT" output.append( f"{start} {metadata: {self.first_column_fmt}} {exp: 17.8e}" - f" {err: 17.8e} {calc: 17.8e}{end}" + f" {err: 17.8e} {calc: 17.8e}{end}", ) return "\n".join(output) + "\n\n" @@ -78,3 +83,33 @@ class CpmgPrinter(ProfilePrinter): class RelaxationPrinter(ProfilePrinter): first_column_name: str = "TIME (S)" first_column_fmt: str = "12.2f" + + +@dataclass +class EXSYPrinter(ProfilePrinter): + first_column_name: str = "TIME (S)" + first_column_fmt: str = "12.6f" + header = "" + + def print(self, name: str, data: Data) -> str: + output = [ + f"[{name}]", + f"# {self.first_column_name:>12s} {'STATE1':>12s} {'STATE2':>12s} {'INTENSITY (EXP)':>17s} {'ERROR (EXP)':>17s} {'INTENSITY (CALC)':>17s}", + ] + + for metadata, exp, err, calc, mask in zip( + data.metadata, + data.exp, + data.err, + data.calc, + data.mask, + ): + start = " " if mask else "#" + end = "" if mask else " # NOT USED IN THE FIT" + time = metadata["times"] + state1 = metadata["states1"] + state2 = metadata["states1"] + output.append( + f"{start} {time: {self.first_column_fmt}} {state1} {state2} {exp: 17.8e} {err: 17.8e} {calc: 17.8e}{end}", + ) + return "\n".join(output) + "\n\n" diff --git a/chemex/printers/parameters.py b/chemex/printers/parameters.py index 628d208f..3156c961 100644 --- a/chemex/printers/parameters.py +++ b/chemex/printers/parameters.py @@ -64,7 +64,8 @@ def _format_fixed(param: ParamSetting) -> str: def _params_to_strings( - parameters: GlobalLocalParameters, status: str + parameters: GlobalLocalParameters, + status: str, ) -> dict[str, dict[str, str]]: result: defaultdict[str, dict[str, str]] = defaultdict(dict) @@ -138,7 +139,9 @@ def classify_parameters(experiments: Experiments) -> ClassifiedParameters: } return ClassifiedParameters( - classify_global(fitted), classify_global(fixed), classify_global(constrained) + classify_global(fitted), + classify_global(fixed), + classify_global(constrained), ) diff --git a/chemex/printers/plot.py b/chemex/printers/plot.py index d4ed42ee..605b2f4d 100644 --- a/chemex/printers/plot.py +++ b/chemex/printers/plot.py @@ -30,13 +30,17 @@ def print_exp(self, name: str, data: Data) -> str: ] for metadata, exp, err, mask in zip( - data.metadata, data.exp, data.err, data.mask, strict=True + data.metadata, + data.exp, + data.err, + data.mask, + strict=True, ): start = " " if mask else "#" end = "" if mask else " # NOT USED IN THE FIT" output.append( f"{start} {metadata: {self.first_column_fmt}} {exp: 17.8e}" - f" {err[0]: 17.8e}{end}" + f" {err[0]: 17.8e}{end}", ) return "\n".join(output) + "\n\n" @@ -67,13 +71,17 @@ def print_exp(self, name: str, data: Data) -> str: ] for metadata, exp, err, mask in zip( - data.metadata, data.exp, data.err, data.mask, strict=True + data.metadata, + data.exp, + data.err, + data.mask, + strict=True, ): start = " " if mask else "#" end = "" if mask else " # NOT USED IN THE FIT" output.append( f"{start} {metadata: {self.first_column_fmt}} {exp: 17.8e}" - f" {err[0]: 17.8e} {err[1]: 17.8e}{end}" + f" {err[0]: 17.8e} {err[1]: 17.8e}{end}", ) return "\n".join(output) + "\n\n" @@ -89,5 +97,5 @@ def print_calc(self, name: str, data: Data) -> str: data_plot_printers: dict[str, PlotPrinter] = { "cest": DataPlotPrinter("OFFSET (PPM)", "12.2f"), "cpmg": CpmgDataPlotPrinter(), - "relaxation": DataPlotPrinter("TIME (S)", "12.2f"), + "relaxation": DataPlotPrinter("TIME (S)", "12.6f"), } diff --git a/chemex/uncertainty.py b/chemex/uncertainty.py index b3d7db5c..be093023 100644 --- a/chemex/uncertainty.py +++ b/chemex/uncertainty.py @@ -1,3 +1,4 @@ +"""The module provides functions for estimating the noise variance in data.""" from __future__ import annotations import contextlib @@ -15,19 +16,28 @@ def _variance_from_duplicates(data: Data) -> float: - """Estimate the variance of duplicate points. + """Estimates variance from duplicate data points in a dataset. - Estimate the uncertainty using the pooled standard deviation. - Reference: https://goldbook.iupac.org/html/P/P04758.html + This function calculates the variance using the pooled standard deviation method. + It groups the data points by their metadata and computes the variance for each + group. If no duplicates are found, the average of the experimental error values is + returned. - If no duplicates are found, the average of the experimental error - values is returned + Args: + data (Data): The data containing experimental values and associated metadata. + Returns: + float: The estimated variance of the dataset. + + Reference: + IUPAC Gold Book definition of pooled standard deviation. + URL: https://goldbook.iupac.org/html/P/P04758.html """ groups: defaultdict[Any, list[float]] = defaultdict(list) for x, y in zip(data.metadata, data.exp, strict=True): groups[x].append(y) - variances, weights = [], [] + variances: list[float] = [] + weights: list[float] = [] for group in groups.values(): group_size = len(group) if group_size > 1: @@ -39,11 +49,22 @@ def _variance_from_duplicates(data: Data) -> float: def _variance_from_scatter(data: Data) -> float: - """Estimate the uncertainty in the CEST profile. + """Estimates the uncertainty in the CEST profile or similar data. + + The function uses numerical methods to estimate the variance. It applies finite + difference approximation and interpolates the sorted experimental data to estimate + the standard deviation at different percentages of the data. The final variance is + calculated as the median of these estimates, adjusted for the size of the data. + + Args: + data (Data): The data containing experimental values. - Adapted from: - https://www.mathworks.com/matlabcentral/fileexchange/16683-estimatenoise + Returns: + float: The estimated variance of the dataset. + Reference: + MATLAB Central File Exchange, 'EstimateNoise' function. + URL: https://www.mathworks.com/matlabcentral/fileexchange/16683-estimatenoise """ fda = [ [1, -1], @@ -63,7 +84,7 @@ def _variance_from_scatter(data: Data) -> float: if ntrim <= 1: continue xaxis = (0.5 + np.arange(1, ntrim + 1)) / (ntrim + 0.5) - sigmas = [] + sigmas: list[float] = [] function = interpolate.interp1d(xaxis, noisedata, "linear") for a_perc, a_z in zip(percents, percent_points, strict=True): with contextlib.suppress(ValueError): From fe635867e59745465e5585d535bb32fabf0e8af1 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Tue, 28 Nov 2023 11:22:34 +0100 Subject: [PATCH 14/18] Forbid unknown options in method files --- chemex/configuration/methods.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/chemex/configuration/methods.py b/chemex/configuration/methods.py index 5bd35d48..236ffc5a 100644 --- a/chemex/configuration/methods.py +++ b/chemex/configuration/methods.py @@ -35,7 +35,7 @@ class Selection: class Method(BaseModelLowerCase): - model_config = ConfigDict(str_to_lower=True) + model_config = ConfigDict(str_to_lower=True, extra="forbid") fitmethod: str = "leastsq" include: SelectionType = None exclude: SelectionType = None From 96eb67a157b98b62d4a25a44bb90f2a57e773a78 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Tue, 28 Nov 2023 11:23:25 +0100 Subject: [PATCH 15/18] Refactor "spin_system.py" into a package --- chemex/parameters/spin_system.py | 371 ------------------- chemex/parameters/spin_system/__init__.py | 3 + chemex/parameters/spin_system/atom.py | 72 ++++ chemex/parameters/spin_system/constants.py | 50 +++ chemex/parameters/spin_system/group.py | 131 +++++++ chemex/parameters/spin_system/nucleus.py | 55 +++ chemex/parameters/spin_system/spin.py | 62 ++++ chemex/parameters/spin_system/spin_system.py | 179 +++++++++ chemex/parameters/spin_system/utilities.py | 32 ++ 9 files changed, 584 insertions(+), 371 deletions(-) delete mode 100644 chemex/parameters/spin_system.py create mode 100644 chemex/parameters/spin_system/__init__.py create mode 100644 chemex/parameters/spin_system/atom.py create mode 100644 chemex/parameters/spin_system/constants.py create mode 100644 chemex/parameters/spin_system/group.py create mode 100644 chemex/parameters/spin_system/nucleus.py create mode 100644 chemex/parameters/spin_system/spin.py create mode 100644 chemex/parameters/spin_system/spin_system.py create mode 100644 chemex/parameters/spin_system/utilities.py diff --git a/chemex/parameters/spin_system.py b/chemex/parameters/spin_system.py deleted file mode 100644 index d3e3c92f..00000000 --- a/chemex/parameters/spin_system.py +++ /dev/null @@ -1,371 +0,0 @@ -from __future__ import annotations - -from dataclasses import dataclass, field -from enum import Enum, auto -from functools import cache, cached_property, total_ordering -from itertools import chain, combinations -from re import search -from typing import TYPE_CHECKING, Annotated, Any, Literal - -from pydantic import PlainValidator - -if TYPE_CHECKING: - from collections.abc import Hashable, Iterable, Sequence - - from chemex.nmr.basis import Basis - - -SPIN_ALIASES = "isx" - - -class Nucleus(Enum): - """Define all the different types of atoms.""" - - H1 = auto() - N15 = auto() - C13 = auto() - X = auto() - - -# Conversion dictionary from atom letter to corresponding Nucleus -STR_TO_NUCLEUS: dict[str, Nucleus] = { - "H": Nucleus.H1, - "Q": Nucleus.H1, - "M": Nucleus.H1, - "N": Nucleus.N15, - "C": Nucleus.C13, - "X": Nucleus.X, -} - -# Conversion dictionary from 3-letter to 1-letter amino-acid convention -AAA_TO_A = { - "ALA": "A", - "ARG": "R", - "ASN": "N", - "ASP": "D", - "CYS": "C", - "GLN": "Q", - "GLU": "E", - "GLY": "G", - "HIS": "H", - "ILE": "I", - "LEU": "L", - "LYS": "K", - "MET": "M", - "PHE": "F", - "PRO": "P", - "SER": "S", - "THR": "T", - "TRP": "W", - "TYR": "Y", - "VAL": "V", -} - - -# Conversion dictionary to correct different ways to spell nuclei -CORRECT_ATOM_NAME = {"HN": "H", "C'": "C", "CO": "C"} - -# fmt: off -STANDARD_ATOM_NAMES_PROTEIN = { - "C", "CA", "CB", "CD", "CD1", "CD2", "CE", "CE1", "CE2", "CE3", "CG", "CG1", "CG2", - "CH2", "CQD", "CQE", "CQG", "CZ", "CZ2", "CZ3", "H", "H2", "H3", "HA", "HA2", - "HA3", "HB", "HB1", "HB2", "HB3", "HD", "HD1", "HD11", "HD12", "HD13", "HD2", - "HD21", "HD22", "HD23", "HD3", "HE", "HE1", "HE2", "HE21", "HE22", "HE3", "HG", - "HG1", "HG11", "HG12", "HG13", "HG2", "HG21", "HG22", "HG23", "HG3", "HH", "HH1", - "HH11", "HH12", "HH2", "HH21", "HH22", "HZ", "HZ1", "HZ2", "HZ3", "MB", "MD", "MD1", - "MD2", "ME", "MG", "MG1", "MG2", "MZ", "N", "ND1", "ND2", "NE", "NE1", "NE2", "NH", - "NH1", "NH2", "NQH", "NZ", "QA", "QB", "QD", "QD2", "QE", "QE2", "QG", "QG1", "QH1", - "QH2", "QMD", "QMG", "QQH", "QR", "QZ", -} - -STANDARD_ATOM_NAMES_DNA_RNA = { - "C1'", "C2", "C2'", "C3'", "C4", "C4'", "C5", "C5'", "C6", "C7", "C8", - "H1", "H1'", "H2", "H2'", "H2'1", "H2'2", "H21", "H22", "H3", "H3'", "H4'", "H41", - "H42", "H5", "H5'1", "H5'2", "H6", "H61", "H62", "H71", "H72", "H73", "H8", - "M7", "N1", "N2", "N3", "N4", "N6", "N7", "N9" -} -# fmt: on -STANDARD_ATOM_NAMES = STANDARD_ATOM_NAMES_PROTEIN | STANDARD_ATOM_NAMES_DNA_RNA - - -@dataclass(order=True) -class Atom: - name: str - nucleus: Nucleus = field(init=False, compare=False) - search_keys: set[Hashable] = field(init=False, default_factory=set, compare=False) - - def __post_init__(self): - name = self.name.strip().upper() - self.name = CORRECT_ATOM_NAME.get(name, name) - self.nucleus = STR_TO_NUCLEUS.get(self.name[:1], Nucleus.X) - self.search_keys.update({self, self.nucleus}) - - def match(self, other: Atom) -> bool: - return other.name.startswith(self.name) - - def __hash__(self) -> int: - return hash(self.name) - - def __bool__(self) -> bool: - return bool(self.name) - - def __str__(self): - return self.name - - -@total_ordering -class Group: - NO_NUMBER: int = -100000000 - - def __init__(self, name: str) -> None: - self.symbol, self.number, self.suffix = self.parse_group(name.strip().upper()) - self.symbol = AAA_TO_A.get(self.symbol, self.symbol) - self.search_keys: set[Hashable] = {self} if self else set() - - def parse_group(self, name: str) -> tuple[str, int, str]: - if found := search("[0-9]+", name.strip().upper()): - return name[: found.start()], int(found.group()), name[found.end() :] - return name, self.NO_NUMBER, "" - - @property - def name(self) -> str: - number = "" if self.number == self.NO_NUMBER else self.number - return f"{self.symbol}{number}{self.suffix}" - - def match(self, other: Group) -> bool: - symbol = other.symbol == self.symbol or not self.symbol - number = self.number in (other.number, self.NO_NUMBER) - suffix = other.suffix == self.suffix or not self.suffix - return number and symbol and suffix - - def __lt__(self, other: object) -> bool: - if not isinstance(other, Group): - return NotImplemented - return self.number < other.number - - def __eq__(self, other: object) -> bool: - if not isinstance(other, Group): - return NotImplemented - return self.name == other.name - - def __hash__(self) -> int: - return hash(self.name) - - def __bool__(self) -> bool: - return bool(self.name) - - def __str__(self) -> str: - return self.name - - -@total_ordering -class Spin: - def __init__(self, name: str, group_for_completion: Group | None = None) -> None: - self.group, self.atom = self.split_group_atom(name.strip().upper()) - if not self.group and group_for_completion: - self.group = group_for_completion - self.search_keys = self.group.search_keys | self.atom.search_keys - - @staticmethod - def split_group_atom(name: str) -> tuple[Group, Atom]: - if name == "?": - return Group(""), Atom("") - found_digit = search("[0-9]", name) - first_digit = found_digit.start() if found_digit else 0 - found_atom = search("[HCNQM]", name[first_digit:]) - if not found_atom: - if name in STANDARD_ATOM_NAMES: - return Group(""), Atom(name) - return Group(name), Atom("") - atom_index = first_digit + found_atom.start() - return Group(name[:atom_index]), Atom(name[atom_index:]) - - @property - def name(self) -> str: - return f"{self.group}{self.atom}" - - def match(self, other: Spin): - return self.group.match(other.group) and self.atom.match(other.atom) - - def __lt__(self, other: Spin) -> bool: - self_tuple = (self.atom.nucleus.name, self.group, self.atom) - other_tuple = (other.atom.nucleus.name, other.group, other.atom) - return self_tuple < other_tuple - - def __eq__(self, other: object) -> bool: - if not isinstance(other, Spin): - return NotImplemented - return self.name == other.name - - def __hash__(self) -> int: - return hash(self.name) - - def __bool__(self) -> bool: - return bool(self.name) - - def __repr__(self) -> str: - return self.name - - def __str__(self) -> str: - return self.name - - -def powerset(iterable: Iterable[Any]) -> Iterable[Any]: - "powerset([1,2,3]) --> (1,) (2,) (3,) (1,2) (1,3) (2,3) (1,2,3)." - s = list(iterable) - return chain.from_iterable(combinations(s, r) for r in range(1, len(s) + 1)) - - -@total_ordering -class SpinSystem: - @staticmethod - @cache - def _parse_spin_system(name: str) -> dict[str, Spin]: - if not name: - return {} - split = name.split("-") - spins: dict[str, Spin] = {} - last_group = None - for short_name, name_spin in zip(SPIN_ALIASES, split, strict=False): - spin = Spin(name_spin, last_group) - spins[short_name] = spin - last_group = spin.group - return spins - - @staticmethod - def _spins2name(spins: Iterable[Spin]) -> str: - spin_names: list[str] = [] - last_group: Group = Group("") - for spin in spins: - spin_name = str(spin.atom) if spin.group == last_group else str(spin) - spin_names.append(spin_name) - last_group = spin.group - return "-".join(spin_names) - - def __init__(self, name: str | int | None = None): - if name is None: - name = "" - if isinstance(name, int): - name = str(name) - self.spins = self._parse_spin_system(name.strip().upper()) - self.name = self._spins2name(self.spins.values()) - self.search_keys: set[Hashable] = set() - self.search_keys = self.search_keys.union( - *(spin.search_keys for spin in self.spins.values()) - ) - - def __deepcopy__(self, memo: dict[Any, Any]) -> SpinSystem: - return SpinSystem(self.name) - - @cached_property - def names(self) -> dict[str, str]: - result: dict[str, str] = {} - for alias_set in powerset(SPIN_ALIASES): - if set(alias_set).issubset(self.spins): - key = "".join(alias_set) - name = self._spins2name(self.spins[alias] for alias in alias_set) - result[key] = name - return result - - @cached_property - def groups(self) -> dict[str, Group]: - return {alias: spin.group for alias, spin in self.spins.items()} - - @cached_property - def symbols(self) -> dict[str, str]: - return {alias: group.symbol for alias, group in self.groups.items()} - - @cached_property - def numbers(self) -> dict[str, int]: - return {alias: group.number for alias, group in self.groups.items()} - - @cached_property - def atoms(self) -> dict[str, Atom]: - return {alias: spin.atom for alias, spin in self.spins.items()} - - @cached_property - def nuclei(self) -> dict[str, Nucleus]: - return {alias: atom.nucleus for alias, atom in self.atoms.items()} - - def match(self, other: SpinSystem) -> bool: - spin_pairs = zip(self.spins.values(), other.spins.values(), strict=False) - return all(spin.match(other_spin) for spin, other_spin in spin_pairs) - - def part_of(self, selection: Sequence[SpinSystem] | str) -> bool: - if isinstance(selection, str): - return selection.lower() in ("all", "*") - return any(item.match(self) for item in selection) - - def correct(self, basis: Basis) -> SpinSystem: - spins: list[Spin] = [] - last_spin = Spin("") - for letter, atom in basis.atoms.items(): - spin = Spin(self.spins.get(letter, last_spin).name) - if not spin.atom.name.startswith(atom.upper()): - spin.atom = Atom(f"{atom}{spin.atom.name[1:]}") - last_spin = spin - spins.append(spin) - return SpinSystem(self._spins2name(spins)) - - def build_sub_spin_system( - self, spin_system_part: Literal["i", "s", "is", "g", ""] - ) -> SpinSystem: - if spin_system_part == "g": - return SpinSystem(str(self.groups.get("i", ""))) - if spin_system_part == "i": - return SpinSystem(str(self.spins.get("i", ""))) - if spin_system_part == "s": - return SpinSystem(str(self.spins.get("s", ""))) - if spin_system_part == "is": - return self - return SpinSystem() - - def __and__(self, other: Any) -> SpinSystem: - if not isinstance(other, SpinSystem): - return NotImplemented - if self == other: - return SpinSystem(self.name) - if spins := set(self.spins.values()) & set(other.spins.values()): - return SpinSystem("-".join(spin.name for spin in spins)) - groups = set(self.groups.values()) & set(other.groups.values()) - if len(groups) == 1: - return SpinSystem("-".join(group.name for group in groups)) - return SpinSystem("") - - def __lt__(self, other: object) -> bool: - if not isinstance(other, SpinSystem): - return NotImplemented - return tuple(self.spins.values()) < tuple(other.spins.values()) - - def __eq__(self, other: object) -> bool: - if not isinstance(other, SpinSystem): - return NotImplemented - return self.name == other.name - - def __hash__(self) -> int: - return hash(self.name) - - def __bool__(self) -> bool: - return bool(self.name) - - def __str__(self) -> str: - return self.name - - -# We now create an `Annotated` wrapper that we'll use as the annotation for -# fields on `BaseModel` -PydanticSpinSystem = Annotated[SpinSystem, PlainValidator(lambda x: SpinSystem(x))] - - -# if __name__ == "__main__": -# print(SpinSystem("G23N-G23HN"), SpinSystem("GLY023N-HN"), SpinSystem("g23N-hN")) -# print(SpinSystem("G23N-G23HN") == SpinSystem("GLY023N-HN")) -# print(SpinSystem("G23N-G23HN").match(SpinSystem("GLY023N-HN"))) -# print(SpinSystem("G23N-G23HN") & SpinSystem("G23C")) -# print(SpinSystem("") == SpinSystem()) -# group = Group("L99") -# spin = Spin("HD1", group) -# print(f"spin = {spin}, spin.group = {spin.group}, spin.atom = {spin.atom}") -# print(SpinSystem("GLY023N-HN").search_keys) -# print(SpinSystem("GLY023N-HN").names) -# print(SpinSystem("G23C1'").names) diff --git a/chemex/parameters/spin_system/__init__.py b/chemex/parameters/spin_system/__init__.py new file mode 100644 index 00000000..2acc1fa5 --- /dev/null +++ b/chemex/parameters/spin_system/__init__.py @@ -0,0 +1,3 @@ +from .spin_system import Group, PydanticSpinSystem, SpinSystem + +__all__ = ["SpinSystem", "PydanticSpinSystem", "Group"] diff --git a/chemex/parameters/spin_system/atom.py b/chemex/parameters/spin_system/atom.py new file mode 100644 index 00000000..1e313881 --- /dev/null +++ b/chemex/parameters/spin_system/atom.py @@ -0,0 +1,72 @@ +"""The atom module defines the Atom class, used to identify atoms.""" + +from __future__ import annotations + +from dataclasses import dataclass, field +from typing import TYPE_CHECKING + +from .constants import CORRECT_ATOM_NAME +from .nucleus import Nucleus, str2nucleus + +if TYPE_CHECKING: + from collections.abc import Hashable + + +@dataclass(order=True) +class Atom: + """Represents an atom in a molecular structure. + + This class encapsulates details about an atom, including its name, + associated nucleus type, and search keys for matching and identification. + + Attributes: + name (str): The name of the atom. + nucleus (Nucleus): The type of nucleus associated with the atom, determined automatically. + search_keys (set[Hashable]): Set of keys used for searching or matching the atom. + """ + + name: str + nucleus: Nucleus = field(init=False, compare=False) + search_keys: set[Hashable] = field(init=False, default_factory=set, compare=False) + + def __post_init__(self) -> None: + """Initializes the Atom instance, correcting the atom name and determining the nucleus type.""" + name = self.name.strip().upper() + self.name = CORRECT_ATOM_NAME.get(name, name) + self.nucleus = str2nucleus(self.name[:1]) + self.search_keys.update({self, self.nucleus}) + + def match(self, other: Atom) -> bool: + """Checks if this atom matches another atom based on the name. + + Args: + other (Atom): The other atom to compare with. + + Returns: + bool: True if the other atom's name starts with the name of this atom, False otherwise. + """ + return other.name.startswith(self.name) + + def __hash__(self) -> int: + """Generates a hash value for an Atom instance. + + Returns: + int: The hash value of the atom. + """ + return hash(self.name) + + def __bool__(self) -> bool: + """Determines the boolean value of the Atom instance. + + Returns: + bool: True if the atom has a valid name, False otherwise. + """ + return bool(self.name) + + def __str__(self) -> str: + """Returns the string representation of the Atom instance. + + Returns: + str: The name of the atom. + """ + return self.name diff --git a/chemex/parameters/spin_system/constants.py b/chemex/parameters/spin_system/constants.py new file mode 100644 index 00000000..e6cd06d2 --- /dev/null +++ b/chemex/parameters/spin_system/constants.py @@ -0,0 +1,50 @@ +# Conversion dictionary from 3-letter to 1-letter amino-acid convention +AAA_TO_A = { + "ALA": "A", + "ARG": "R", + "ASN": "N", + "ASP": "D", + "CYS": "C", + "GLN": "Q", + "GLU": "E", + "GLY": "G", + "HIS": "H", + "ILE": "I", + "LEU": "L", + "LYS": "K", + "MET": "M", + "PHE": "F", + "PRO": "P", + "SER": "S", + "THR": "T", + "TRP": "W", + "TYR": "Y", + "VAL": "V", +} + + +# Conversion dictionary to correct different ways to spell nuclei +CORRECT_ATOM_NAME = {"HN": "H", "C'": "C", "CO": "C"} + +# fmt: off +STANDARD_ATOM_NAMES_PROTEIN = { + "C", "CA", "CB", "CD", "CD1", "CD2", "CE", "CE1", "CE2", "CE3", "CG", "CG1", "CG2", + "CH2", "CQD", "CQE", "CQG", "CZ", "CZ2", "CZ3", "H", "H2", "H3", "HA", "HA2", + "HA3", "HB", "HB1", "HB2", "HB3", "HD", "HD1", "HD11", "HD12", "HD13", "HD2", + "HD21", "HD22", "HD23", "HD3", "HE", "HE1", "HE2", "HE21", "HE22", "HE3", "HG", + "HG1", "HG11", "HG12", "HG13", "HG2", "HG21", "HG22", "HG23", "HG3", "HH", "HH1", + "HH11", "HH12", "HH2", "HH21", "HH22", "HZ", "HZ1", "HZ2", "HZ3", "MB", "MD", "MD1", + "MD2", "ME", "MG", "MG1", "MG2", "MZ", "N", "ND1", "ND2", "NE", "NE1", "NE2", "NH", + "NH1", "NH2", "NQH", "NZ", "QA", "QB", "QD", "QD2", "QE", "QE2", "QG", "QG1", "QH1", + "QH2", "QMD", "QMG", "QQH", "QR", "QZ", +} + +STANDARD_ATOM_NAMES_DNA_RNA = { + "C1'", "C2", "C2'", "C3'", "C4", "C4'", "C5", "C5'", "C6", "C7", "C8", + "H1", "H1'", "H2", "H2'", "H2'1", "H2'2", "H21", "H22", "H3", "H3'", "H4'", "H41", + "H42", "H5", "H5'1", "H5'2", "H6", "H61", "H62", "H71", "H72", "H73", "H8", + "M7", "N1", "N2", "N3", "N4", "N6", "N7", "N9", +} +# fmt: on + +STANDARD_ATOM_NAMES = STANDARD_ATOM_NAMES_PROTEIN | STANDARD_ATOM_NAMES_DNA_RNA diff --git a/chemex/parameters/spin_system/group.py b/chemex/parameters/spin_system/group.py new file mode 100644 index 00000000..655b644e --- /dev/null +++ b/chemex/parameters/spin_system/group.py @@ -0,0 +1,131 @@ +from __future__ import annotations + +from functools import total_ordering +from re import search +from typing import TYPE_CHECKING + +from .constants import AAA_TO_A + +if TYPE_CHECKING: + from collections.abc import Hashable + + +NO_NUMBER = -100000000 + + +@total_ordering +class Group: + """Represents a molecular group in a spin system. + + This class encapsulates the information about an amino acid residue or nucleic + acid base, including its symbol, sequence number, and suffix for identifying + different states. It provides methods for parsing group names and comparing group + objects. + + Attributes: + symbol (str): The symbol of the group. + number (int): The number associated with the group, if any. + suffix (str): Any suffix associated with the group name. + search_keys (set[Hashable]): A set of keys used for searching or matching the + group. + """ + + def __init__(self, name: str) -> None: + """Initializes a Group object with a given name. + + The constructor parses the input name into symbol, number, and suffix + components. + + Args: + name (str): The name of the group to be parsed. + """ + self.symbol, self.number, self.suffix = self.parse_group(name.strip().upper()) + self.symbol = AAA_TO_A.get(self.symbol, self.symbol) + self.search_keys: set[Hashable] = {self} if self else set() + + def parse_group(self, name: str) -> tuple[str, int, str]: + """Parses the group name into symbol, number, and suffix. + + Args: + name (str): The name of the group to be parsed. + + Returns: + tuple[str, int, str]: A tuple containing the symbol, number, and suffix. + """ + if found := search("[0-9]+", name.strip().upper()): + return name[: found.start()], int(found.group()), name[found.end() :] + return name, NO_NUMBER, "" + + @property + def name(self) -> str: + """Represents the full name of the group. + + Returns: + str: The full name of the group, combining symbol, number, and suffix. + """ + number = "" if self.number == NO_NUMBER else self.number + return f"{self.symbol}{number}{self.suffix}" + + def match(self, other: Group) -> bool: + """Determines if this group matches another group. + + Args: + other (Group): Another group to compare with. + + Returns: + bool: True if the groups match, False otherwise. + """ + symbol = other.symbol == self.symbol or not self.symbol + number = self.number in (other.number, NO_NUMBER) + suffix = other.suffix == self.suffix or not self.suffix + return number and symbol and suffix + + def __lt__(self, other: object) -> bool: + """Less than comparison for ordering of Group objects. + + Args: + other (object): Another object to compare with. + + Returns: + bool: True if this group is considered less than the other, False otherwise. + """ + if not isinstance(other, type(self)): + return NotImplemented + return self.number < other.number + + def __eq__(self, other: object) -> bool: + """Equality comparison for Group objects. + + Args: + other (object): Another object to compare with. + + Returns: + bool: True if the groups are equal, False otherwise. + """ + if not isinstance(other, type(self)): + return NotImplemented + return self.name == other.name + + def __hash__(self) -> int: + """Generates a hash value for a Group object. + + Returns: + int: The hash value of the group. + """ + return hash(self.name) + + def __bool__(self) -> bool: + """Boolean representation of the Group object. + + Returns: + bool: True if the group has a valid name, False otherwise. + """ + return bool(self.name) + + def __str__(self) -> str: + """String representation of the Group object. + + Returns: + str: The full name of the group. + """ + return self.name diff --git a/chemex/parameters/spin_system/nucleus.py b/chemex/parameters/spin_system/nucleus.py new file mode 100644 index 00000000..a2b493b6 --- /dev/null +++ b/chemex/parameters/spin_system/nucleus.py @@ -0,0 +1,55 @@ +from enum import Enum, auto + + +class Nucleus(Enum): + """Enumeration of different types of atomic nuclei. + + This Enum class represents different types of atomic nuclei commonly + used in NMR spectroscopy. + + Attributes: + H1: Represents Hydrogen-1 nucleus. + N15: Represents Nitrogen-15 nucleus. + C13: Represents Carbon-13 nucleus. + X: Placeholder for unknown or unspecified nucleus type. + """ + + H1 = auto() + N15 = auto() + C13 = auto() + X = auto() + + +# Dictionary mapping atom letter abbreviations to corresponding Nucleus enum values. +STR_TO_NUCLEUS: dict[str, Nucleus] = { + "H": Nucleus.H1, + "Q": Nucleus.H1, # Q, M are aliases for Hydrogen-1 + "M": Nucleus.H1, + "N": Nucleus.N15, + "C": Nucleus.C13, + "X": Nucleus.X, +} + + +def str2nucleus(atom_letter: str) -> Nucleus: + """Converts a single-letter atom name to the corresponding Nucleus enum. + + This function maps a single-letter abbreviation for an atom (e.g., 'H', 'C') + to the corresponding Nucleus enumeration member. If the atom letter is not + recognized, it defaults to 'X', representing an unknown or unspecified nucleus. + + Args: + atom_letter (str): A single-letter abbreviation of an atom. + + Returns: + Nucleus: The corresponding Nucleus enumeration member. + + Examples: + >>> str2nucleus('H') + + >>> str2nucleus('C') + + >>> str2nucleus('Z') # Not recognized + + """ + return STR_TO_NUCLEUS.get(atom_letter, Nucleus.X) diff --git a/chemex/parameters/spin_system/spin.py b/chemex/parameters/spin_system/spin.py new file mode 100644 index 00000000..32687dd4 --- /dev/null +++ b/chemex/parameters/spin_system/spin.py @@ -0,0 +1,62 @@ +from __future__ import annotations + +from functools import total_ordering +from re import search + +from chemex.parameters.spin_system.atom import Atom +from chemex.parameters.spin_system.constants import STANDARD_ATOM_NAMES +from chemex.parameters.spin_system.group import Group + + +@total_ordering +class Spin: + def __init__(self, name: str, group_for_completion: Group | None = None) -> None: + self.group, self.atom = self.split_group_atom(name.strip().upper()) + if not self.group and group_for_completion: + self.group = group_for_completion + self.search_keys = self.group.search_keys | self.atom.search_keys + + @staticmethod + def split_group_atom(name: str) -> tuple[Group, Atom]: + if name == "?": + return Group(""), Atom("") + found_digit = search("[0-9]", name) + first_digit = found_digit.start() if found_digit else 0 + found_atom = search("[HCNQM]", name[first_digit:]) + if not found_atom: + if name in STANDARD_ATOM_NAMES: + return Group(""), Atom(name) + return Group(name), Atom("") + atom_index = first_digit + found_atom.start() + return Group(name[:atom_index]), Atom(name[atom_index:]) + + @property + def name(self) -> str: + return f"{self.group}{self.atom}" + + def match(self, other: Spin) -> bool: + return self.group.match(other.group) and self.atom.match(other.atom) + + def __lt__(self, other: object) -> bool: + if not isinstance(other, type(self)): + return NotImplemented + self_tuple = (self.atom.nucleus.name, self.group, self.atom) + other_tuple = (other.atom.nucleus.name, other.group, other.atom) + return self_tuple < other_tuple + + def __eq__(self, other: object) -> bool: + if not isinstance(other, type(self)): + return NotImplemented + return self.name == other.name + + def __hash__(self) -> int: + return hash(self.name) + + def __bool__(self) -> bool: + return bool(self.name) + + def __repr__(self) -> str: + return self.name + + def __str__(self) -> str: + return self.name diff --git a/chemex/parameters/spin_system/spin_system.py b/chemex/parameters/spin_system/spin_system.py new file mode 100644 index 00000000..91d1f74d --- /dev/null +++ b/chemex/parameters/spin_system/spin_system.py @@ -0,0 +1,179 @@ +from __future__ import annotations + +from functools import cache, cached_property, total_ordering +from typing import TYPE_CHECKING, Annotated, Any, Literal, TypeVar + +from pydantic import PlainValidator + +from .atom import Atom +from .group import Group +from .spin import Spin +from .utilities import powerset + +if TYPE_CHECKING: + from collections.abc import Hashable, Iterable, Sequence + + from chemex.nmr.basis import Basis + + from .nucleus import Nucleus + + +Self = TypeVar("Self", bound="SpinSystem") + +SPIN_ALIASES = "isx" + + +@total_ordering +class SpinSystem: + @staticmethod + @cache + def _parse_spin_system(name: str) -> dict[str, Spin]: + if not name: + return {} + split = name.split("-") + spins: dict[str, Spin] = {} + last_group = None + for short_name, name_spin in zip(SPIN_ALIASES, split, strict=False): + spin = Spin(name_spin, last_group) + spins[short_name] = spin + last_group = spin.group + return spins + + @staticmethod + def _spins2name(spins: Iterable[Spin]) -> str: + spin_names: list[str] = [] + last_group: Group = Group("") + for spin in spins: + spin_name = str(spin.atom) if spin.group == last_group else str(spin) + spin_names.append(spin_name) + last_group = spin.group + return "-".join(spin_names) + + def __init__(self, name: str | int | None = None) -> None: + if name is None: + name = "" + if isinstance(name, int): + name = str(name) + self.spins = self._parse_spin_system(name.strip().upper()) + self.name = self._spins2name(self.spins.values()) + self.search_keys: set[Hashable] = set() + self.search_keys = self.search_keys.union( + *(spin.search_keys for spin in self.spins.values()), + ) + + def __deepcopy__(self: Self, memo: dict[Any, Any]) -> Self: + return type(self)(self.name) + + @cached_property + def names(self) -> dict[str, str]: + result: dict[str, str] = {} + for alias_set in powerset(SPIN_ALIASES): + if set(alias_set).issubset(self.spins): + key = "".join(alias_set) + name = self._spins2name(self.spins[alias] for alias in alias_set) + result[key] = name + return result + + @cached_property + def groups(self) -> dict[str, Group]: + return {alias: spin.group for alias, spin in self.spins.items()} + + @cached_property + def symbols(self) -> dict[str, str]: + return {alias: group.symbol for alias, group in self.groups.items()} + + @cached_property + def numbers(self) -> dict[str, int]: + return {alias: group.number for alias, group in self.groups.items()} + + @cached_property + def atoms(self) -> dict[str, Atom]: + return {alias: spin.atom for alias, spin in self.spins.items()} + + @cached_property + def nuclei(self) -> dict[str, Nucleus]: + return {alias: atom.nucleus for alias, atom in self.atoms.items()} + + def match(self: Self, other: Self) -> bool: + spin_pairs = zip(self.spins.values(), other.spins.values(), strict=False) + return all(spin.match(other_spin) for spin, other_spin in spin_pairs) + + def part_of(self: Self, selection: Sequence[Self] | str) -> bool: + if isinstance(selection, str): + return selection.lower() in ("all", "*") + return any(item.match(self) for item in selection) + + def correct(self: Self, basis: Basis) -> Self: + spins: list[Spin] = [] + last_spin = Spin("") + for letter, atom in basis.atoms.items(): + spin = Spin(self.spins.get(letter, last_spin).name) + if not spin.atom.name.startswith(atom.upper()): + spin.atom = Atom(f"{atom}{spin.atom.name[1:]}") + last_spin = spin + spins.append(spin) + return type(self)(self._spins2name(spins)) + + def build_sub_spin_system( + self: Self, + spin_system_part: Literal["i", "s", "is", "g", ""], + ) -> Self: + if spin_system_part == "g": + return type(self)(str(self.groups.get("i", ""))) + if spin_system_part == "i": + return type(self)(str(self.spins.get("i", ""))) + if spin_system_part == "s": + return type(self)(str(self.spins.get("s", ""))) + if spin_system_part == "is": + return self + return type(self)() + + def __and__(self: Self, other: object) -> Self: + if not isinstance(other, type(self)): + return NotImplemented + if self == other: + return type(self)(self.name) + if spins := set(self.spins.values()) & set(other.spins.values()): + return type(self)("-".join(spin.name for spin in spins)) + groups = set(self.groups.values()) & set(other.groups.values()) + if len(groups) == 1: + return type(self)("-".join(group.name for group in groups)) + return type(self)("") + + def __lt__(self, other: object) -> bool: + if not isinstance(other, type(self)): + return NotImplemented + return tuple(self.spins.values()) < tuple(other.spins.values()) + + def __eq__(self, other: object) -> bool: + if not isinstance(other, type(self)): + return NotImplemented + return self.name == other.name + + def __hash__(self) -> int: + return hash(self.name) + + def __bool__(self) -> bool: + return bool(self.name) + + def __str__(self) -> str: + return self.name + + +# We now create an `Annotated` wrapper that we'll use as the annotation for +# fields on `BaseModel` +PydanticSpinSystem = Annotated[SpinSystem, PlainValidator(lambda x: SpinSystem(x))] + + +# if __name__ == "__main__": +# print(SpinSystem("G23N-G23HN"), SpinSystem("GLY023N-HN"), SpinSystem("g23N-hN")) +# print(SpinSystem("G23N-G23HN") == SpinSystem("GLY023N-HN")) +# print(SpinSystem("G23N-G23HN").match(SpinSystem("GLY023N-HN"))) +# print(SpinSystem("G23N-G23HN") & SpinSystem("G23C")) +# print(SpinSystem("") == SpinSystem()) +# group = Group("L99") +# spin = Spin("HD1", group) +# print(f"spin = {spin}, spin.group = {spin.group}, spin.atom = {spin.atom}") +# print(SpinSystem("GLY023N-HN").search_keys) +# print(SpinSystem("GLY023N-HN").names) +# print(SpinSystem("G23C1'").names) diff --git a/chemex/parameters/spin_system/utilities.py b/chemex/parameters/spin_system/utilities.py new file mode 100644 index 00000000..96b2c7d2 --- /dev/null +++ b/chemex/parameters/spin_system/utilities.py @@ -0,0 +1,32 @@ +from collections.abc import Iterable +from itertools import chain, combinations +from typing import TypeVar + +T = TypeVar("T") + + +def powerset(iterable: Iterable[T]) -> Iterable[tuple[T, ...]]: + """Generates all possible non-empty subsets of the given iterable. + + This function returns the power set of the input iterable, excluding the empty set. + The subsets are returned as tuples. The order of subsets follows the order of + elements in the input iterable. + + Args: + iterable (Iterable[Any]): An iterable for which to generate the power set. + + Returns: + Iterable[Any]: An iterable of tuples, each representing a non-empty subset of + the input iterable. + + Examples: + >>> powerset([1, 2, 3]) + (1,) (2,) (3,) (1, 2) (1, 3) (2, 3) (1, 2, 3) + + Note: + This implementation uses `itertools.chain` and `itertools.combinations`, and is + efficient for small to medium-sized iterables. + + """ + s = list(iterable) + return chain.from_iterable(combinations(s, r) for r in range(1, len(s) + 1)) From d74ff780f4e9113ca8956f7e8e0a3e236287b4ec Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Tue, 28 Nov 2023 11:24:53 +0100 Subject: [PATCH 16/18] Refactor "pick_cest.py" into a package --- chemex/tools/pick_cest.py | 290 -------------------------- chemex/tools/pick_cest/__init__.py | 3 + chemex/tools/pick_cest/buttons.py | 215 +++++++++++++++++++ chemex/tools/pick_cest/cest_picker.py | 121 +++++++++++ chemex/tools/pick_cest/curve.py | 40 ++++ chemex/tools/plot_param.py | 11 +- 6 files changed, 387 insertions(+), 293 deletions(-) delete mode 100644 chemex/tools/pick_cest.py create mode 100644 chemex/tools/pick_cest/__init__.py create mode 100644 chemex/tools/pick_cest/buttons.py create mode 100644 chemex/tools/pick_cest/cest_picker.py create mode 100644 chemex/tools/pick_cest/curve.py diff --git a/chemex/tools/pick_cest.py b/chemex/tools/pick_cest.py deleted file mode 100644 index cff9f44e..00000000 --- a/chemex/tools/pick_cest.py +++ /dev/null @@ -1,290 +0,0 @@ -from __future__ import annotations - -import contextlib -import sys -from typing import TYPE_CHECKING - -import matplotlib.pyplot as plt -import numpy as np -from matplotlib.widgets import Button, Cursor, Slider -from scipy.interpolate import CubicSpline - -from chemex.configuration.methods import Selection -from chemex.experiments.builder import build_experiments -from chemex.experiments.loader import register_experiments -from chemex.models import model -from chemex.parameters.spin_system import Nucleus, SpinSystem -from chemex.plotters.cest import create_plot_data_exp - -if TYPE_CHECKING: - from argparse import Namespace - from pathlib import Path - - from chemex.containers.experiments import Experiments - from chemex.containers.profile import Profile - -KWARGS = {"color": "0.74", "linewidth": 1.0} -LSTYLE = {"a": "-", "b": ":"} -TEXT_Y = {"a": 0.8, "b": 0.75} - - -class Curve: - def __init__(self, profile: Profile, sw: float | None = None): - data = create_plot_data_exp(profile) - settings = getattr(profile.pulse_sequence, "settings", None) - - delta_ppm = 0.0 - if settings is not None: - spectrometer = profile.spectrometer - cos_n = getattr(settings, "cos_n", None) - sw = getattr(settings, "sw", None) - if cos_n is not None and cos_n % 2 == 0 and sw is not None: - shifts_ppm = spectrometer.offsets_to_ppms(np.array([sw / 2.0, 0.0])) - delta_ppm = shifts_ppm[0] - shifts_ppm[1] - - ppms = data.metadata - delta_ppm - xmin, xmax = min(ppms), max(ppms) - self.xrange = xmax - xmin - self.xcentre = 0.5 * (xmin + xmax) - self.x = ppms - self.y = data.exp - _, indices = np.unique(ppms, return_index=True) - x = ppms[indices] - y = data.exp[indices] - if sw is not None: - y[0] = y[-1] = 0.5 * (y[0] + y[-1]) - self.spline = CubicSpline(x, y, bc_type="periodic", extrapolate="periodic") - else: - self.spline = CubicSpline(x, y) - - def get_xrange(self, sw: float | None = None): - if sw is None: - sw = 1.0 - return self.xcentre + sw * self.xrange * np.array([-0.5, 0.5]) - - -class Buttons: - def __init__(self, experiments: Experiments, path: Path, sw: float | None) -> None: - self.data: dict[SpinSystem, list[Curve]] = {} - names: set[SpinSystem] = set() - - for experiment in experiments: - for profile in experiment: - name = SpinSystem(profile.name.names["i"]) - names.add(name) - self.data.setdefault(name, []).append(Curve(profile, sw)) - - self.names = sorted(names) - self.out = path - - self.name = None - self.curves = None - self.cs_a, self.cs_b = {}, {} - self.lines = [] - self.cid = None - self.sw = sw - - self.fig, self.axis = plt.subplots(figsize=(12, 5)) - self.fig.subplots_adjust(left=0.07, bottom=0.1, right=0.8, top=0.9) - - self.cursor = Cursor(self.axis, horizOn=False, useblit=True) - - self.index = -1 - self.next(None) - - def _clear_lines(self): - while self.lines: - self.lines.pop().remove() - - def _clear_axis(self): - self._clear_lines() - self.axis.clear() - - def _show_labels(self): - self.axis.set_title(str(self.name).upper()) - atom = SpinSystem(str(self.name)).atoms["i"] - if atom.nucleus == Nucleus.N15: - self.axis.set_xlabel(r"$^{15}$N (ppm)") - elif atom.nucleus == Nucleus.C13: - self.axis.set_xlabel(r"$^{13}$C (ppm)") - elif atom.nucleus == Nucleus.H1: - self.axis.set_xlabel(r"$^{1}$H (ppm)") - else: - self.axis.set_xlabel(r"Chemical shift (ppm)") - self.axis.set_ylabel("$I/I_0$") - - def _plot_profiles(self): - if self.curves is None: - return - xranges = np.concatenate([curve.get_xrange(self.sw) for curve in self.curves]) - grid = np.linspace(min(xranges), max(xranges), 1000) - - for index, curve in enumerate(self.curves): - color = f"C{index}" - self.axis.plot(curve.x, curve.y, ".", color=color) - self.axis.plot(grid, curve.spline(grid), "--", color=color, alpha=0.66) - self.axis.invert_xaxis() - self._show_labels() - self.fig.canvas.draw_idle() - - def _get_click_position(self, event=None): - return event.xdata if event and event.inaxes == self.axis else None - - def _add_line(self, position, state): - text_ = rf"$\varpi_{state}$ = {position:.3f} ppm" - text = self.fig.text(0.82, TEXT_Y[state], text_) - line = self.axis.axvline(position, linestyle=LSTYLE[state], **KWARGS) - self.lines.extend([line, text]) - - def _add_text_dw(self, dw_ab): - text_ = rf"$\Delta\varpi_{{ab}}$ = {dw_ab:.3f} ppm" - text = self.fig.text(0.82, 0.7, text_) - self.lines.append(text) - - def _save(self): - self.out.mkdir(parents=True, exist_ok=True) - - fname1 = self.out / "cs_a.toml" - fname2 = self.out / "dw_ab.toml" - - with contextlib.ExitStack() as stack: - file1 = stack.enter_context(fname1.open("w")) - file2 = stack.enter_context(fname2.open("w")) - file1.write("[CS_A]\n") - file2.write("[DW_AB]\n") - - for name in self.names: - cs_a = self.cs_a.get(name) - cs_b = self.cs_b.get(name) - - if cs_a is None: - continue - - file1.write(f"{str(name).upper():10s} = {cs_a:8.3f}\n") - - if cs_b is not None: - dw_ab = cs_b - cs_a - file2.write(f"{str(name).upper():10s} = {dw_ab:8.3f}\n") - - def _plot_lines(self, event=None): - cs_a = self.cs_a.get(self.name) - cs_b = self.cs_b.get(self.name) - - xdata = self._get_click_position(event) - - if xdata is not None: - if cs_a is None: - cs_a = xdata - else: - cs_b = xdata - - self._clear_lines() - - if cs_a is not None: - self._add_line(cs_a, "a") - - if cs_b is not None: - dw_ab = cs_b - cs_a - self._add_line(cs_b, "b") - self._add_text_dw(dw_ab) - - self.cs_a[self.name] = cs_a - self.cs_b[self.name] = cs_b - - self._save() - - self.fig.canvas.draw_idle() - self.fig.canvas.flush_events() - - def _plot(self, _event=None): - self.cid = self.fig.canvas.mpl_connect("button_press_event", self._plot_lines) - self._clear_axis() - self._plot_lines() - self._plot_profiles() - self.fig.canvas.draw_idle() - - def _shift(self, step): - self.index += step - self.index %= len(self.names) - self.name = self.names[self.index] - self.curves = self.data[self.name] - self._clear_axis() - self._plot() - - def next(self, _event=None): - """Go to next residue.""" - self._shift(+1) - - def previous(self, _event=None): - """Go to previous residue.""" - self._shift(-1) - - def swap(self, _event=None): - """Swap peak peak positions for major/minor states.""" - name = self.name - if self.cs_b[name] is not None: - self.cs_a[name], self.cs_b[name] = self.cs_b[name], self.cs_a[name] - self._plot_lines() - - def clear(self, _event=None): - name = self.name - self.cs_a[name], self.cs_b[name] = None, None - self._plot_lines() - - def set_sw(self, text): - with contextlib.suppress(ValueError): - self.sw = float(text) - - self._clear_axis() - self._plot() - - -def pick_cest(args: Namespace): - """Pick peak positions in CEST profiles.""" - register_experiments() - - # Read experimental setup and data - model.set_model("2st") - - # Read experimental setup and data - no_selection = Selection(include=None, exclude=None) - experiments = build_experiments(args.experiments, no_selection) - - sw = None - - for experiment in experiments: - if not experiment.name.startswith(("cest", "dcest", "coscest")): - sys.exit( - f"\nError: '{experiment.name}' experiment not supported. " - "The command 'chemex pick_cest' only works with CEST experiments.\n" - ) - if experiment.name.startswith("dcest") or experiment.name.startswith("coscest"): - sw = 4.0 - - callback = Buttons(experiments, args.output, sw) - - if sw is not None: - axsw = plt.axes((0.855, 0.425, 0.1, 0.02)) - sw_slider = Slider( - ax=axsw, label="Scale", valmin=1.0, valmax=10.0, valfmt="%3.1f", valinit=sw - ) - # bsw = Textbox(axsw, "Number of SWs:", initial="3.0", label_pad=0.15) - sw_slider.on_changed(callback.set_sw) - - axprevious = plt.axes((0.825, 0.3, 0.075, 0.075)) - bprevious = Button(axprevious, "Previous") - bprevious.on_clicked(callback.previous) - - axnext = plt.axes((0.9, 0.3, 0.075, 0.075)) - bnext = Button(axnext, "Next") - bnext.on_clicked(callback.next) - - axswap = plt.axes((0.825, 0.2, 0.15, 0.075)) - bswap = Button(axswap, "Swap") - bswap.on_clicked(callback.swap) - - axclear = plt.axes((0.825, 0.1, 0.15, 0.075)) - bclear = Button(axclear, "Clear") - bclear.on_clicked(callback.clear) - - plt.show() diff --git a/chemex/tools/pick_cest/__init__.py b/chemex/tools/pick_cest/__init__.py new file mode 100644 index 00000000..d4c87d4d --- /dev/null +++ b/chemex/tools/pick_cest/__init__.py @@ -0,0 +1,3 @@ +from .cest_picker import pick_cest + +__all__ = ["pick_cest"] diff --git a/chemex/tools/pick_cest/buttons.py b/chemex/tools/pick_cest/buttons.py new file mode 100644 index 00000000..9bd696e8 --- /dev/null +++ b/chemex/tools/pick_cest/buttons.py @@ -0,0 +1,215 @@ +import contextlib +from pathlib import Path +from typing import Literal + +import numpy as np +from matplotlib.artist import Artist +from matplotlib.axes import Axes +from matplotlib.backend_bases import Event, LocationEvent +from matplotlib.figure import Figure +from matplotlib.widgets import Cursor + +from chemex.containers.experiments import Experiments +from chemex.parameters.spin_system import SpinSystem +from chemex.parameters.spin_system.nucleus import Nucleus + +from .curve import Curve + +LSTYLE = {"a": "-", "b": ":"} +TEXT_Y = {"a": 0.8, "b": 0.75} +XLABELS = { + Nucleus.N15: r"$^{15}$N (ppm)", + Nucleus.C13: r"$^{13}$C (ppm)", + Nucleus.H1: r"$^{1}$H (ppm)", + Nucleus.X: r"Chemical shift (ppm)", +} + + +class Buttons: + def __init__( + self, + figure: Figure, + axis: Axes, + experiments: Experiments, + path: Path, + sw: float | None, + ) -> None: + self.fig = figure + self.axis = axis + self.data: dict[SpinSystem, list[Curve]] = {} + spin_systems: set[SpinSystem] = set() + + for experiment in experiments: + for profile in experiment: + spin_system = profile.spin_system + spin_systems.add(spin_system) + self.data.setdefault(spin_system, []).append(Curve(profile, sw)) + + self.spin_systems = sorted(spin_systems) + self.out = path + + self.spin_system = SpinSystem("") + self.curves: list[Curve] = [] + self.cs_a: dict[SpinSystem, float | None] = {} + self.cs_b: dict[SpinSystem, float | None] = {} + self.artists: list[Artist] = [] + self.sw = sw + + self.cursor = Cursor(self.axis, horizOn=False, useblit=True) + + self.index = -1 + self.next() + + def _clear_artists(self) -> None: + while self.artists: + self.artists.pop().remove() + + def _clear_axis(self) -> None: + self._clear_artists() + self.axis.clear() + + def _show_labels(self) -> None: + self.axis.set_title(str(self.spin_system)) + self.axis.set_xlabel(XLABELS[self.spin_system.nuclei["i"]]) + self.axis.set_ylabel("$I/I_0$") + + def _plot_profiles(self) -> None: + if not self.curves: + return + xranges = np.concatenate([curve.get_xrange(self.sw) for curve in self.curves]) + grid = np.linspace(min(xranges), max(xranges), 1000) + + for index, curve in enumerate(self.curves): + color = f"C{index}" + self.axis.plot(curve.x, curve.y, ".", color=color) + self.axis.plot(grid, curve.spline(grid), "--", color=color, alpha=0.66) + + self.axis.invert_xaxis() + self._show_labels() + self.fig.canvas.draw_idle() + + def _get_click_position(self, event: Event) -> float | None: + if not isinstance(event, LocationEvent): + return None + if event.inaxes != self.axis: + return None + return event.xdata + + def _add_line(self, position: float, state: Literal["a", "b"]): + text_ = rf"$\varpi_{state}$ = {position:.3f} ppm" + text = self.fig.text(0.82, TEXT_Y[state], text_) + line = self.axis.axvline( + x=position, + linestyle=LSTYLE[state], + color="0.74", + linewidth=1.0, + ) + self.artists.extend([line, text]) + + def _add_text_dw(self, dw_ab: float) -> None: + text_ = rf"$\Delta\varpi_{{ab}}$ = {dw_ab:.3f} ppm" + text = self.fig.text(0.82, 0.7, text_) + self.artists.append(text) + + def _save(self): + self.out.mkdir(parents=True, exist_ok=True) + + fname1 = self.out / "cs_a.toml" + fname2 = self.out / "dw_ab.toml" + + with contextlib.ExitStack() as stack: + file1 = stack.enter_context(fname1.open("w")) + file2 = stack.enter_context(fname2.open("w")) + file1.write("[CS_A]\n") + file2.write("[DW_AB]\n") + + for name in self.spin_systems: + cs_a = self.cs_a.get(name) + cs_b = self.cs_b.get(name) + + if cs_a is None: + continue + + file1.write(f"{str(name).upper():10s} = {cs_a:8.3f}\n") + + if cs_b is not None: + dw_ab = cs_b - cs_a + file2.write(f"{str(name).upper():10s} = {dw_ab:8.3f}\n") + + def set_cs(self, event: Event) -> None: + """Set the chemical shift.""" + xdata = self._get_click_position(event) + if xdata is None: + return + + key = self.spin_system + + if self.cs_a.get(key) is None or self.cs_b.get(key) is not None: + self.cs_a[key] = xdata + self.cs_b[key] = None + else: + self.cs_b[key] = xdata + + self._plot_lines() + + def _plot_lines(self) -> None: + key = self.spin_system + cs_a = self.cs_a.get(key) + cs_b = self.cs_b.get(key) + + self._clear_artists() + + if cs_a is not None: + self._add_line(cs_a, "a") + + if cs_b is not None: + self._add_line(cs_b, "b") + + if cs_a is not None and cs_b is not None: + self._add_text_dw(cs_b - cs_a) + + self._save() + + self.fig.canvas.draw_idle() + self.fig.canvas.flush_events() + + def _plot(self, event: Event | None = None) -> None: + self._clear_axis() + self._plot_lines() + self._plot_profiles() + self.fig.canvas.draw_idle() + + def _shift(self, step: int): + self.index += step + self.index %= len(self.spin_systems) + self.spin_system = self.spin_systems[self.index] + self.curves = self.data[self.spin_system] + self._clear_axis() + self._plot() + + def next(self, _event: Event | None = None) -> None: + """Go to next residue.""" + self._shift(+1) + + def previous(self, _event: Event) -> None: + """Go to previous residue.""" + self._shift(-1) + + def swap(self, event: Event) -> None: + """Swap peak peak positions for major/minor states.""" + name = self.spin_system + if self.cs_b[name] is not None: + self.cs_a[name], self.cs_b[name] = self.cs_b[name], self.cs_a[name] + self._plot_lines() + + def clear(self, event: Event) -> None: + name = self.spin_system + self.cs_a[name], self.cs_b[name] = None, None + self._plot_lines() + + def set_sw(self, sw: float) -> None: + with contextlib.suppress(ValueError): + self.sw = sw + + self._clear_axis() + self._plot() diff --git a/chemex/tools/pick_cest/cest_picker.py b/chemex/tools/pick_cest/cest_picker.py new file mode 100644 index 00000000..b95ffd8e --- /dev/null +++ b/chemex/tools/pick_cest/cest_picker.py @@ -0,0 +1,121 @@ +import sys +from argparse import Namespace +from collections.abc import Callable +from typing import Any + +from matplotlib import pyplot as plt +from matplotlib.axes import Axes +from matplotlib.backend_bases import Event +from matplotlib.figure import Figure +from matplotlib.widgets import Button, Slider + +from chemex.configuration.methods import Selection +from chemex.containers.experiment import Experiment +from chemex.containers.experiments import Experiments +from chemex.experiments.builder import build_experiments +from chemex.experiments.loader import register_experiments +from chemex.models import model +from chemex.tools.pick_cest.buttons import Buttons + +FigureSizeType = tuple[float, float] +AdjustParamsType = tuple[float, float, float, float] +PositionType = tuple[float, float, float, float] + +FIGURE_SIZE = (12.0, 5.0) +ADJUST_PARAMS = (0.07, 0.1, 0.8, 0.9) +POSITION_SCALE = (0.855, 0.425, 0.1, 0.02) +POSITION_PREVIOUS = (0.825, 0.3, 0.075, 0.075) +POSITION_NEXT = (0.9, 0.3, 0.075, 0.075) +POSITION_SWAP = (0.825, 0.2, 0.15, 0.075) +POSITION_CLEAR = (0.825, 0.1, 0.15, 0.075) + + +def create_figure( + size: FigureSizeType = FIGURE_SIZE, + adjust_params: AdjustParamsType = ADJUST_PARAMS, +) -> tuple[Figure, Axes]: + """Creates and returns a matplotlib figure and axes.""" + fig, axes = plt.subplots() + fig.set_size_inches(*size) + fig.subplots_adjust(*adjust_params) + return fig, axes + + +def is_cest_experiment(experiment: Experiment) -> bool: + """Checks if an experiment is a CEST experiment.""" + return experiment.name.startswith(("cest", "dcest", "coscest")) + + +def initialize_cest(args: Namespace) -> Experiments: + """Initializes CEST experiments.""" + register_experiments() + model.set_model("2st") + return build_experiments(args.experiments, Selection(include=None, exclude=None)) + + +def create_slider( + fig: Figure, + position: PositionType, + label: str, + val_range: tuple[float, float], + initial_value: float, + on_change: Callable[[float], None], +) -> Slider: + """Creates and returns a matplotlib slider.""" + ax = fig.add_axes(position) + slider = Slider(ax, label, *val_range, valfmt="%3.1f", valinit=initial_value) + slider.on_changed(on_change) + return slider + + +def create_button( + fig: Figure, + position: PositionType, + label: str, + on_click: Callable[[Event], Any], +) -> Button: + """Creates and returns a matplotlib button.""" + ax = fig.add_axes(position) + button = Button(ax, label) + button.on_clicked(on_click) + return button + + +def pick_cest(args: Namespace) -> None: + """Pick peak positions in CEST profiles.""" + experiments = initialize_cest(args) + sw = None + + for experiment in experiments: + if not is_cest_experiment(experiment): + sys.exit( + f"\nError: '{experiment.name}' experiment not supported. " + "The command 'chemex pick_cest' only works with CEST experiments.\n", + ) + if experiment.name.startswith(("dcest", "coscest")): + sw = 4.0 + + fig, axes = create_figure() + + callback = Buttons(fig, axes, experiments, args.output, sw) + + if sw is not None: + # For the Slider to remain responsive you must keep a reference to it. + _slider = create_slider( + fig, + POSITION_SCALE, + "Scale", + (1.0, 10.0), + sw, + callback.set_sw, + ) + + # For the button to remain responsive you must keep a reference to it. + _button1 = create_button(fig, POSITION_PREVIOUS, "Previous", callback.previous) + _button2 = create_button(fig, POSITION_NEXT, "Next", callback.next) + _button3 = create_button(fig, POSITION_SWAP, "Swap", callback.swap) + _button4 = create_button(fig, POSITION_CLEAR, "Clear", callback.clear) + + fig.canvas.mpl_connect("button_press_event", callback.set_cs) + + plt.show() diff --git a/chemex/tools/pick_cest/curve.py b/chemex/tools/pick_cest/curve.py new file mode 100644 index 00000000..036df763 --- /dev/null +++ b/chemex/tools/pick_cest/curve.py @@ -0,0 +1,40 @@ +import numpy as np +from scipy.interpolate import CubicSpline + +from chemex.containers.profile import Profile +from chemex.plotters.cest import create_plot_data_exp + + +class Curve: + def __init__(self, profile: Profile, sw: float | None = None) -> None: + data = create_plot_data_exp(profile) + settings = getattr(profile.pulse_sequence, "settings", None) + + delta_ppm = 0.0 + if settings is not None: + spectrometer = profile.spectrometer + cos_n = getattr(settings, "cos_n", None) + sw = getattr(settings, "sw", None) + if cos_n is not None and cos_n % 2 == 0 and sw is not None: + shifts_ppm = spectrometer.offsets_to_ppms(np.array([sw / 2.0, 0.0])) + delta_ppm = shifts_ppm[0] - shifts_ppm[1] + + ppms = data.metadata - delta_ppm + xmin, xmax = min(ppms), max(ppms) + self.xrange = xmax - xmin + self.xcentre = 0.5 * (xmin + xmax) + self.x = ppms + self.y = data.exp + _, indices = np.unique(ppms, return_index=True) + x = ppms[indices] + y = data.exp[indices] + if sw is not None: + y[0] = y[-1] = 0.5 * (y[0] + y[-1]) + self.spline = CubicSpline(x, y, bc_type="periodic", extrapolate="periodic") + else: + self.spline = CubicSpline(x, y) + + def get_xrange(self, sw: float | None = None): + if sw is None: + sw = 1.0 + return self.xcentre + sw * self.xrange * np.array([-0.5, 0.5]) diff --git a/chemex/tools/plot_param.py b/chemex/tools/plot_param.py index 19f775c0..a3daaf6f 100644 --- a/chemex/tools/plot_param.py +++ b/chemex/tools/plot_param.py @@ -14,14 +14,14 @@ from argparse import Namespace -def plot_param(args: Namespace): +def plot_param(args: Namespace) -> None: """Plot values of a parameter versus residue number.""" params = configparser.ConfigParser() if len(args.parameters) > 1: sys.exit( "\nError: Multiple parameter files were given. 'chemex plot_param' " - "should only be run with a single parameter file.\n" + "should only be run with a single parameter file.\n", ) params.read(str(args.parameters.pop())) @@ -53,7 +53,12 @@ def plot_param(args: Namespace): for section, (residues, values, errors) in curves.items(): axis.errorbar( - residues, values, yerr=errors, label=section, fmt=".", barsabove=True + residues, + values, + yerr=errors, + label=section, + fmt=".", + barsabove=True, ) plt.legend() From 99a52ccda23e10a5de5c2ab3d336e314264f8bb9 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Tue, 28 Nov 2023 15:21:31 +0100 Subject: [PATCH 17/18] Add 1H EXSY experiment --- chemex/containers/dataset.py | 30 ++++- chemex/experiments/catalog/noesyfpgpph19.py | 97 +++++++++++++ chemex/plotters/exsy.py | 142 ++++++++++++++++++++ 3 files changed, 268 insertions(+), 1 deletion(-) create mode 100644 chemex/experiments/catalog/noesyfpgpph19.py create mode 100644 chemex/plotters/exsy.py diff --git a/chemex/containers/dataset.py b/chemex/containers/dataset.py index 83eebd1f..7b8beb69 100644 --- a/chemex/containers/dataset.py +++ b/chemex/containers/dataset.py @@ -36,7 +36,35 @@ def load_relaxation_dataset(base_path: Path, settings: RelaxationConfig) -> Data err=raw_data["err"], metadata=raw_data["metadata"], ), - ) + ), + ) + + return dataset + + +def load_exsy_dataset(base_path: Path, settings: RelaxationConfig) -> Dataset: + data_path = normalize_path(base_path, settings.data.path) + dtype = [ + ("times", "f8"), + ("states1", "U1"), + ("states2", "U1"), + ("exp", "f8"), + ("err", "f8"), + ] + + dataset: Dataset = [] + for spin_system, filepaths in settings.data.profiles.items(): + for filepath in filepaths: + raw_data = np.loadtxt(data_path / filepath, dtype=dtype) + dataset.append( + ( + spin_system, + Data( + exp=raw_data["exp"], + err=raw_data["err"], + metadata=raw_data[["times", "states1", "states2"]], + ), + ), ) return dataset diff --git a/chemex/experiments/catalog/noesyfpgpph19.py b/chemex/experiments/catalog/noesyfpgpph19.py new file mode 100644 index 00000000..1b0b1295 --- /dev/null +++ b/chemex/experiments/catalog/noesyfpgpph19.py @@ -0,0 +1,97 @@ +from __future__ import annotations + +from dataclasses import dataclass +from typing import TYPE_CHECKING, Literal + +import numpy as np +from numpy.typing import NDArray + +from chemex.configuration.data import RelaxationDataSettings +from chemex.configuration.experiment import ( + ExperimentConfig, + RelaxationSettings, + ToBeFitted, +) +from chemex.containers.dataset import load_exsy_dataset +from chemex.experiments.factories import Creators, factories +from chemex.filterers import PlanesFilterer +from chemex.nmr.basis import Basis +from chemex.nmr.liouvillian import LiouvillianIS +from chemex.nmr.spectrometer import Spectrometer +from chemex.plotters.exsy import EXSYPlotter +from chemex.printers.data import EXSYPrinter + +if TYPE_CHECKING: + from chemex.containers.data import Data + from chemex.parameters.spin_system import SpinSystem + +# Type definitions +NDArrayFloat = NDArray[np.float_] +NDArrayBool = NDArray[np.bool_] + + +EXPERIMENT_NAME = "noesyfpgpph19" + + +class Noesyfpgpph19Settings(RelaxationSettings): + name: Literal["noesyfpgpph19"] + + +class Noesyfpgpph19Config( + ExperimentConfig[Noesyfpgpph19Settings, RelaxationDataSettings], +): + @property + def to_be_fitted(self) -> ToBeFitted: + return ToBeFitted(rates=["r1_i"], model_free=["tauc", "s2"]) + + +def build_spectrometer( + config: Noesyfpgpph19Config, + spin_system: SpinSystem, +) -> Spectrometer: + conditions = config.conditions + + basis = Basis(type="iz", spin_system="hn") + liouvillian = LiouvillianIS(spin_system, basis, conditions) + + return Spectrometer(liouvillian) + + +@dataclass +class Noesyfpgpph19Sequence: + settings: Noesyfpgpph19Settings + + def calculate(self, spectrometer: Spectrometer, data: Data) -> np.ndarray: + times = data.metadata["times"] + states1 = data.metadata["states1"] + states2 = data.metadata["states2"] + + # Getting the starting magnetization + equilibrium = spectrometer.get_equilibrium() + + # Calculate delay propagators + delays = spectrometer.delays(times) + + intensities = [] + for state1, state2, delay in zip(states1, states2, delays): + start = spectrometer.keep(equilibrium, [f"iz_{state1}"]) + spectrometer.detection = f"[iz_{state2}]" + intensities.append(spectrometer.detect(delay @ start)) + + return np.array(intensities) + + def is_reference(self, metadata: NDArrayFloat) -> NDArrayBool: + return np.full_like(metadata, False, dtype=np.bool_) + + +def register() -> None: + creators = Creators( + config_creator=Noesyfpgpph19Config, + spectrometer_creator=build_spectrometer, + sequence_creator=Noesyfpgpph19Sequence, + dataset_creator=load_exsy_dataset, + filterer_creator=PlanesFilterer, + printer_creator=EXSYPrinter, + plotter_creator=EXSYPlotter, + ) + factories.register(type=EXPERIMENT_NAME, creators=creators) diff --git a/chemex/plotters/exsy.py b/chemex/plotters/exsy.py new file mode 100644 index 00000000..b41e9d4b --- /dev/null +++ b/chemex/plotters/exsy.py @@ -0,0 +1,142 @@ +from __future__ import annotations + +from collections import defaultdict +from contextlib import ExitStack +from itertools import product +from typing import TYPE_CHECKING, Any + +import numpy as np +from matplotlib.backends.backend_pdf import PdfPages + +from chemex.containers.data import Data +from chemex.messages import print_plot_filename +from chemex.plotters.plot import get_grid, plot_profile +from chemex.printers.plot import PlotPrinter, data_plot_printers + +if TYPE_CHECKING: + from pathlib import Path + + from chemex.containers.profile import Profile + + +def plot_exsy(file_pdf: PdfPages, name: str, data_exp: Data, data_calc: Data): + fig = plot_profile(name, data_exp, data_calc) + ax2 = fig.axes[1] + ax2.set_xlabel(r"Time (s)") + ax2.set_ylabel(r"Intensity") + ax2.set_xlim(0.0, max(data_exp.metadata) + min(data_calc.metadata)) + file_pdf.savefig(fig) + + +def create_plot_data_exp(profile: Profile) -> dict[tuple[str, str], Data]: + data = profile.data + + intensity0 = data.exp[np.argmax(abs(data.exp))] + + data_values = defaultdict(list) + for metadata, exp, calc, err, mask in zip( + data.metadata, + data.exp, + data.calc, + data.err, + data.mask, + strict=True, + ): + states = tuple(metadata[["states1", "states2"]]) + data_values[states].append((metadata["times"], exp, calc, err, mask)) + + data_exp_dict = {} + dtype = [ + ("times", "f8"), + ("exp", "f8"), + ("calc", "f8"), + ("err", "f8"), + ("mask", "?"), + ] + for states, values in data_values.items(): + values_array = np.array(values, dtype=dtype) + values_array["exp"] /= intensity0 + values_array["calc"] /= intensity0 + errors = values_array["err"] / abs(intensity0) + errorbars = np.array([-errors, errors]).transpose() + + data_exp = Data( + exp=values_array["exp"], + err=errorbars, + metadata=values_array["times"], + ) + data_exp.calc = values_array["calc"] + data_exp.mask = values_array["mask"] + data_exp.sort() + + data_exp_dict[states] = data_exp + + return data_exp_dict + + +def create_plot_data_calc(profile: Profile) -> dict[tuple[str, str], Data]: + spectrometer = profile.spectrometer + data = profile.data + + times = get_grid(data.metadata["times"], 100, 0.0) + states = np.unique(data.metadata[["states1", "states2"]]) + metadata_list = [ + (time, state1, state2) for time, (state1, state2) in product(times, states) + ] + dtype = [("times", "f8"), ("states1", "U1"), ("states2", "U1")] + metadata = np.array(metadata_list, dtype=dtype) + + filler = np.zeros_like(metadata["times"]) + data_fit = Data(exp=filler, err=filler, metadata=metadata) + + intensity0 = data.exp[np.argmax(abs(data.exp))] + scale = profile.data.scale / intensity0 + data_fit.calc = scale * profile.pulse_sequence.calculate(spectrometer, data_fit) + + data_values = defaultdict(list) + for metadata, calc in zip(data_fit.metadata, data_fit.calc): + states = tuple(metadata[["states1", "states2"]]) + data_values[states].append((metadata["times"], calc)) + + data_calc_dict = {} + dtype = [("times", "f8"), ("calc", "f8")] + for states, values in data_values.items(): + values_array = np.array(values, dtype=dtype) + filler = np.zeros_like(values_array["calc"]) + + data_calc = Data(exp=filler, err=filler, metadata=values_array["times"]) + data_calc.calc = values_array["calc"] + data_calc.sort() + + data_calc_dict[states] = data_calc + + return data_calc_dict + + +class EXSYPlotter: + def __init__(self, filename: Path, **_extra: Any) -> None: + self.filename = filename + self.printer: PlotPrinter = data_plot_printers["relaxation"] + + def plot(self, path: Path, profiles: list[Profile]) -> None: + basename = path / self.filename.name + name_pdf = basename.with_suffix(".pdf") + name_exp = basename.with_suffix(".exp") + name_fit = basename.with_suffix(".fit") + + print_plot_filename(name_pdf) + + with ExitStack() as stack: + file_pdf = stack.enter_context(PdfPages(str(name_pdf))) + file_calc = stack.enter_context(name_fit.open("w")) + file_exp = stack.enter_context(name_exp.open("w")) + for profile in sorted(profiles): + data_exp_dict = create_plot_data_exp(profile) + data_calc_dict = create_plot_data_calc(profile) + for states in data_exp_dict: + data_exp = data_exp_dict[states] + data_calc = data_calc_dict[states] + name = f"{profile.spin_system!s}_{''.join(states)}" + plot_exsy(file_pdf, name, data_exp, data_calc) + file_exp.write(self.printer.print_exp(name, data_exp)) + file_calc.write(self.printer.print_calc(name, data_calc)) From ab752282ec85528813541e9ab8c55704e6291864 Mon Sep 17 00:00:00 2001 From: Guillaume Bouvignies Date: Mon, 4 Dec 2023 15:32:57 +0100 Subject: [PATCH 18/18] Update the documentation to Docusaurus 3.0 --- website/docs/examples/binding.md | 2 +- website/docs/examples/{index.md => index.mdx} | 0 website/docs/experiments/cest/cest_13c.md | 40 +- website/docs/experiments/cest/cest_15n.md | 20 +- website/docs/experiments/cest/cest_15n_cw.md | 6 +- website/docs/experiments/cest/cest_15n_tr.md | 8 +- website/docs/experiments/cest/cest_1hn_ap.md | 8 +- .../docs/experiments/cest/cest_1hn_ip_ap.md | 12 +- .../experiments/cest/cest_ch3_1h_ip_ap.md | 8 +- .../experiments/cest/{index.md => index.mdx} | 0 website/docs/experiments/cpmg/cpmg_13c_ip.md | 10 +- website/docs/experiments/cpmg/cpmg_13co_ap.md | 6 +- website/docs/experiments/cpmg/cpmg_15n_ip.md | 8 +- .../docs/experiments/cpmg/cpmg_15n_ip_0013.md | 8 +- website/docs/experiments/cpmg/cpmg_15n_tr.md | 20 +- .../docs/experiments/cpmg/cpmg_15n_tr_0013.md | 10 +- website/docs/experiments/cpmg/cpmg_1hn_ap.md | 6 +- .../docs/experiments/cpmg/cpmg_1hn_ap_0013.md | 6 +- .../docs/experiments/cpmg/cpmg_ch3_13c_h2c.md | 8 +- .../docs/experiments/cpmg/cpmg_ch3_1h_dq.md | 8 +- .../docs/experiments/cpmg/cpmg_ch3_1h_sq.md | 8 +- .../docs/experiments/cpmg/cpmg_ch3_1h_tq.md | 22 +- .../experiments/cpmg/cpmg_ch3_1h_tq_diff.md | 8 +- website/docs/experiments/cpmg/cpmg_ch3_mq.md | 8 +- .../docs/experiments/cpmg/cpmg_chd2_1h_ap.md | 8 +- .../docs/experiments/cpmg/cpmg_hn_dq_zq.md | 6 +- .../experiments/cpmg/{index.md => index.mdx} | 0 .../experiments/dcest/coscest_1hn_ip_ap.md | 6 +- website/docs/experiments/dcest/dcest_13c.md | 8 +- website/docs/experiments/dcest/dcest_15n.md | 22 +- .../experiments/dcest/{index.md => index.mdx} | 0 .../docs/experiments/{index.md => index.mdx} | 0 .../relaxation/{index.md => index.mdx} | 0 .../experiments/relaxation/relaxation_hznz.md | 8 +- .../experiments/relaxation/relaxation_nz.md | 6 +- .../experiments/shift/{index.md => index.mdx} | 0 website/docs/getting_started.md | 89 - website/docs/introduction.md | 17 + ...onal_modules.md => additional_modules.mdx} | 2 +- website/docs/user_guide/fitting/chemex_fit.md | 73 +- .../fitting/{data_files.md => data_files.mdx} | 0 .../user_guide/fitting/experiment_files.md | 109 +- .../fitting/{index.md => index.mdx} | 2 +- .../docs/user_guide/fitting/method_files.md | 56 +- .../fitting/{outputs.md => outputs.mdx} | 0 .../user_guide/fitting/parameter_files.md | 2 +- .../docs/user_guide/{index.md => index.mdx} | 0 website/docs/user_guide/introduction.md | 51 - website/docs/user_guide/running_chemex.md | 29 +- website/docs/welcome_to_chemex.md | 61 + website/docusaurus.config.js | 17 +- website/package-lock.json | 35527 +++++----------- website/package.json | 41 +- website/src/pages/index.js | 2 +- 54 files changed, 12081 insertions(+), 24301 deletions(-) rename website/docs/examples/{index.md => index.mdx} (100%) rename website/docs/experiments/cest/{index.md => index.mdx} (100%) rename website/docs/experiments/cpmg/{index.md => index.mdx} (100%) rename website/docs/experiments/dcest/{index.md => index.mdx} (100%) rename website/docs/experiments/{index.md => index.mdx} (100%) rename website/docs/experiments/relaxation/{index.md => index.mdx} (100%) rename website/docs/experiments/shift/{index.md => index.mdx} (100%) delete mode 100644 website/docs/getting_started.md create mode 100644 website/docs/introduction.md rename website/docs/user_guide/{additional_modules.md => additional_modules.mdx} (99%) rename website/docs/user_guide/fitting/{data_files.md => data_files.mdx} (100%) rename website/docs/user_guide/fitting/{index.md => index.mdx} (93%) rename website/docs/user_guide/fitting/{outputs.md => outputs.mdx} (100%) rename website/docs/user_guide/{index.md => index.mdx} (100%) delete mode 100644 website/docs/user_guide/introduction.md create mode 100644 website/docs/welcome_to_chemex.md diff --git a/website/docs/examples/binding.md b/website/docs/examples/binding.md index 7a39b83b..dd756e50 100644 --- a/website/docs/examples/binding.md +++ b/website/docs/examples/binding.md @@ -32,7 +32,7 @@ step, the major purpose is to obtain residue-specific parameters. Further analysis of the fitting results can be carried out with the aid of additional functions in ChemEx (refer to -[`Plotting best-fit parameters`](user_guide/additional_modules.md#plotting-best-fit-parameters) +[`Plotting best-fit parameters`](user_guide/additional_modules.mdx#plotting-best-fit-parameters) subsection). During the whole fitting process Kd is fixed to the value obtained from ITC experiments, more details about this example can be found in the reference.[^1] diff --git a/website/docs/examples/index.md b/website/docs/examples/index.mdx similarity index 100% rename from website/docs/examples/index.md rename to website/docs/examples/index.mdx diff --git a/website/docs/experiments/cest/cest_13c.md b/website/docs/experiments/cest/cest_13c.md index 7f1dec81..5ef2fdc7 100644 --- a/website/docs/experiments/cest/cest_13c.md +++ b/website/docs/experiments/cest/cest_13c.md @@ -17,32 +17,32 @@ CEST block. This keeps the spin system purely in-phase throughout, and is calculated using the (3n)×(3n), single-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), - Ix(b), Iy(b), Iz(b), ... } + \{ Ix(a), Iy(a), Iz(a), + Ix(b), Iy(b), Iz(b), ... \} ## References -- P. Vallurupalli, G. Bouvignies, and L.E. Kay. _ChemBioChem_ **14**, 1709-1713 - (2014) -- G. Bouvignies, P. Vallurupalli, and L.E. Kay. _J. Mol. Biol._ **426**, 763-774 - (2014) -- P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ **52**, 4156-4159 - (2013) -- D.F. Hansen, G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **55**, 279-289 - (2013) -- G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **53**, 303-310 (2012) -- E. Rennella, R. Huang, A. Velyvis, and L.E. Kay. _J. Biomol. NMR_ **63**, - 187-199 (2015) +- P. Vallurupalli, G. Bouvignies, and L.E. Kay. _ChemBioChem_ **14**, 1709-1713 + (2014) +- G. Bouvignies, P. Vallurupalli, and L.E. Kay. _J. Mol. Biol._ **426**, 763-774 + (2014) +- P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ **52**, 4156-4159 + (2013) +- D.F. Hansen, G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **55**, 279-289 + (2013) +- G. Bouvignies, and L.E. Kay. _J. Biomol. NMR_ **53**, 303-310 (2012) +- E. Rennella, R. Huang, A. Velyvis, and L.E. Kay. _J. Biomol. NMR_ **63**, + 187-199 (2015) ## Example -- An example for studying side-chain methyl groups in selectively ¹³C-labeled - sample is available - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C/). -- An example for studying - [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is - available - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C_LABEL_CN/). +- An example for studying side-chain methyl groups in selectively ¹³C-labeled + sample is available + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C/). +- An example for studying + [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is + available + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_13C_LABEL_CN/). ## Sample configuration file diff --git a/website/docs/experiments/cest/cest_15n.md b/website/docs/experiments/cest/cest_15n.md index b797fc24..59d6b495 100644 --- a/website/docs/experiments/cest/cest_15n.md +++ b/website/docs/experiments/cest/cest_15n.md @@ -17,22 +17,22 @@ CEST block. This keeps the spin system purely in-phase throughout, and is calculated using the (3n)×(3n), single-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), - Ix(b), Iy(b), Iz(b), ... } + \{ Ix(a), Iy(a), Iz(a), + Ix(b), Iy(b), Iz(b), ... \} ## Reference -- P. Vallurupalli, G. Bouvignies, and L.E. Kay. _J. Am. Chem. Soc._ **134**, - 8148-8161 (2012) +- P. Vallurupalli, G. Bouvignies, and L.E. Kay. _J. Am. Chem. Soc._ **134**, + 8148-8161 (2012) ## Examples -- An example for studying ¹⁵N-labeled sample is available - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N/). -- An example for studying - [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is - available - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N_LABEL_CN/). +- An example for studying ¹⁵N-labeled sample is available + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N/). +- An example for studying + [uniformly ¹³C, ¹⁵N-labeled sample](../../examples/cest_13c_15n.md) is + available + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CEST_15N_LABEL_CN/). ## Sample configuration file diff --git a/website/docs/experiments/cest/cest_15n_cw.md b/website/docs/experiments/cest/cest_15n_cw.md index edfe0b6e..e2773a22 100644 --- a/website/docs/experiments/cest/cest_15n_cw.md +++ b/website/docs/experiments/cest/cest_15n_cw.md @@ -16,14 +16,14 @@ Analyzes chemical exchange in the presence of ¹H CW decoupling during the CEST block. Magnetization evolution is calculated using the (15n)×(15n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), Sx(a), IxSx(a), IySx(a), IzSx(a), + \{ Ix(a), Iy(a), Iz(a), Sx(a), IxSx(a), IySx(a), IzSx(a), Sy(a), IxSy(a), IySy(a), IzSy(a), Sz(a), IxSz(a), IySz(a), IzSz(a), Ix(b), Iy(b), Iz(b), Sx(b), IxSx(b), IySx(b), IzSx(b), - Sy(b), IxSy(b), IySy(b), IzSy(b), Sz(b), IxSz(b), IySz(b), IzSz(b), ... } + Sy(b), IxSy(b), IySy(b), IzSy(b), Sz(b), IxSz(b), IySz(b), IzSz(b), ... \} ## Reference -- G. Bouvignies, and L.E. Kay. _J. Phys. Chem. B_ **116**, 14311-14317 (2012) +- G. Bouvignies, and L.E. Kay. _J. Phys. Chem. B_ **116**, 14311-14317 (2012) ## Example diff --git a/website/docs/experiments/cest/cest_15n_tr.md b/website/docs/experiments/cest/cest_15n_tr.md index a9d4469b..3d33acf3 100644 --- a/website/docs/experiments/cest/cest_15n_tr.md +++ b/website/docs/experiments/cest/cest_15n_tr.md @@ -16,13 +16,13 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), - Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... } + \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), + Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \} ## Reference -- D. Long, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci. USA_ **111**, - 8820-8825 (2014) +- D. Long, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci. USA_ **111**, + 8820-8825 (2014) ## Example diff --git a/website/docs/experiments/cest/cest_1hn_ap.md b/website/docs/experiments/cest/cest_1hn_ap.md index d6f8b925..7bfbebbb 100644 --- a/website/docs/experiments/cest/cest_1hn_ap.md +++ b/website/docs/experiments/cest/cest_1hn_ap.md @@ -16,13 +16,13 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), - Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... } + \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), + Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \} ## Reference -- A. Sekhar, R. Rosenzweig, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci. - USA_ **113**, E2794-E2801 (2016) +- A. Sekhar, R. Rosenzweig, G. Bouvignies, and L.E. Kay. _Proc. Natl. Acad. Sci. + USA_ **113**, E2794-E2801 (2016) ## Example diff --git a/website/docs/experiments/cest/cest_1hn_ip_ap.md b/website/docs/experiments/cest/cest_1hn_ip_ap.md index f187ccc4..7e4b4ef6 100644 --- a/website/docs/experiments/cest/cest_1hn_ip_ap.md +++ b/website/docs/experiments/cest/cest_1hn_ip_ap.md @@ -16,15 +16,15 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), - Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... } + \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), + Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \} ## References -- T. Yuwen, A. Sekhar, and L.E. Kay. _Angew. Chem. Int. Ed._ **56**, 6122-6125 - (2017) -- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **67**, 295-307 (2017) -- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018) +- T. Yuwen, A. Sekhar, and L.E. Kay. _Angew. Chem. Int. Ed._ **56**, 6122-6125 + (2017) +- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **67**, 295-307 (2017) +- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018) ## Example diff --git a/website/docs/experiments/cest/cest_ch3_1h_ip_ap.md b/website/docs/experiments/cest/cest_ch3_1h_ip_ap.md index 69e12171..89cc0d1d 100644 --- a/website/docs/experiments/cest/cest_ch3_1h_ip_ap.md +++ b/website/docs/experiments/cest/cest_ch3_1h_ip_ap.md @@ -16,8 +16,8 @@ Analyzes chemical exchange during the CEST block. Magnetization evolution is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), - Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... } + \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), + Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \} :::note @@ -27,8 +27,8 @@ The same module works for both ¹³CH₃- and ¹³CHD₂-labeled methyl groups. ## References -- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **68**, 215-224 (2017) -- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018) +- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **68**, 215-224 (2017) +- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **70**, 93-102 (2018) ## Example diff --git a/website/docs/experiments/cest/index.md b/website/docs/experiments/cest/index.mdx similarity index 100% rename from website/docs/experiments/cest/index.md rename to website/docs/experiments/cest/index.mdx diff --git a/website/docs/experiments/cpmg/cpmg_13c_ip.md b/website/docs/experiments/cpmg/cpmg_13c_ip.md index 388acb22..f910c896 100644 --- a/website/docs/experiments/cpmg/cpmg_13c_ip.md +++ b/website/docs/experiments/cpmg/cpmg_13c_ip.md @@ -17,8 +17,8 @@ during the CPMG block. This keeps the spin system purely in-phase throughout, and is calculated using the (3n)×(3n), single-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), - Ix(b), Iy(b), Iz(b), ... } + \{ Ix(a), Iy(a), Iz(a), + Ix(b), Iy(b), Iz(b), ... \} The CW decoupling on ¹H is assumed to be strong enough (> 15 kHz) such that perfect ¹H decoupling can be achieved. In the case of CHD2 experiment, CW @@ -26,9 +26,9 @@ decoupling on 2H should be applied properly. ## References -- D.F. Hansen, P. Vallurupalli, Lundström, Neudecker, and L.E. Kay. _J. Am. - Chem. Soc._ **130**, 2667-2675 (2008) -- E. Rennella, Schuetz, and L.E. Kay. _J. Biomol. NMR_ **65**, 59-64 (2016) +- D.F. Hansen, P. Vallurupalli, Lundström, Neudecker, and L.E. Kay. _J. Am. + Chem. Soc._ **130**, 2667-2675 (2008) +- E. Rennella, Schuetz, and L.E. Kay. _J. Biomol. NMR_ **65**, 59-64 (2016) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_13co_ap.md b/website/docs/experiments/cpmg/cpmg_13co_ap.md index d10cffcc..c2426d0a 100644 --- a/website/docs/experiments/cpmg/cpmg_13co_ap.md +++ b/website/docs/experiments/cpmg/cpmg_13co_ap.md @@ -17,8 +17,8 @@ magnetization throughout the CPMG block. This results in lower intrinsic relaxation rates and therefore better sensitivity. The calculations use a (6n)×(6n), two-spin matrix, where n is the number of states: - { COx(a), COy(a), COz(a), 2COxNz(a), 2COyNz(a), 2COzNz(a), - COx(b), COy(b), COz(b), 2COxNz(b), 2COyNz(b), 2COzNz(b), ... } + \{ COx(a), COy(a), COz(a), 2COxNz(a), 2COyNz(a), 2COzNz(a), + COx(b), COy(b), COz(b), 2COxNz(b), 2COyNz(b), 2COzNz(b), ... \} Because of the length of the shaped pulses used during the CPMG blocks, off-resonance effects are taken into account only for the 90-degree pulses that @@ -29,7 +29,7 @@ the "refocusing" flag, with such option ncyc_cp should be set as even. # Reference: -- Lundström, D.F. Hansen, and L.E. Kay. _J. Biomol. NMR_ **42**, 35-47 (2008) +- Lundström, D.F. Hansen, and L.E. Kay. _J. Biomol. NMR_ **42**, 35-47 (2008) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_15n_ip.md b/website/docs/experiments/cpmg/cpmg_15n_ip.md index c0eac554..57b0092e 100644 --- a/website/docs/experiments/cpmg/cpmg_15n_ip.md +++ b/website/docs/experiments/cpmg/cpmg_15n_ip.md @@ -17,16 +17,16 @@ during the CPMG block. This keeps the spin system purely in-phase throughout, and is calculated using the (3n)×(3n), single-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), - Ix(b), Iy(b), Iz(b), ... } + \{ Ix(a), Iy(a), Iz(a), + Ix(b), Iy(b), Iz(b), ... \} The CW decoupling on ¹H is assumed to be strong enough (> 15 kHz) such that perfect ¹H decoupling can be achieved. ## Reference -- D.F. Hansen, P. Vallurupalli, and L.E. Kay. **J. Phys. Chem. B** **112**, - 5898-5904 (2008) +- D.F. Hansen, P. Vallurupalli, and L.E. Kay. **J. Phys. Chem. B** **112**, + 5898-5904 (2008) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_15n_ip_0013.md b/website/docs/experiments/cpmg/cpmg_15n_ip_0013.md index 48d72341..89df028a 100644 --- a/website/docs/experiments/cpmg/cpmg_15n_ip_0013.md +++ b/website/docs/experiments/cpmg/cpmg_15n_ip_0013.md @@ -17,8 +17,8 @@ during the CPMG block. This keeps the spin system purely in-phase throughout, and is calculated using the (3n)×(3n), single-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), - Ix(b), Iy(b), Iz(b), ... } + \{ Ix(a), Iy(a), Iz(a), + Ix(b), Iy(b), Iz(b), ... \} This version is modified such that CPMG pulses are applied with [0013] phase cycle as shown in Daiwen's paper. The CW decoupling on ¹H is assumed to be @@ -26,8 +26,8 @@ strong enough (> 15 kHz) such that perfect ¹H decoupling can be achieved. ## Reference -- B. Jiang, B. Yu, X. Zhang, M. Liu, and D. Yang. _J. Magn. Reson._ **257**, 1-7 - (2015) +- B. Jiang, B. Yu, X. Zhang, M. Liu, and D. Yang. _J. Magn. Reson._ **257**, 1-7 + (2015) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_15n_tr.md b/website/docs/experiments/cpmg/cpmg_15n_tr.md index 5eca2b07..c4e58f38 100644 --- a/website/docs/experiments/cpmg/cpmg_15n_tr.md +++ b/website/docs/experiments/cpmg/cpmg_15n_tr.md @@ -18,22 +18,22 @@ exchange dynamics. Resulting magnetization intensity after the CPMG block is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Nx(a), Ny(a), Nz(a), 2HzNx(a), 2HzNy(a), 2HzNz(a), - Nx(b), Ny(b), Nz(b), 2HzNx(b), 2HzNy(b), 2HzNz(b), ... } + \{ Nx(a), Ny(a), Nz(a), 2HzNx(a), 2HzNy(a), 2HzNz(a), + Nx(b), Ny(b), Nz(b), 2HzNx(b), 2HzNy(b), 2HzNz(b), ... \} ## Reference -- P. Vallurupalli, D.F. Hansen, E. Stollar, E. Meirovitch, and L.E. Kay. _Proc. - Natl. Acad. Sci. USA_ **104**, 18473-18477 (2007) +- P. Vallurupalli, D.F. Hansen, E. Stollar, E. Meirovitch, and L.E. Kay. _Proc. + Natl. Acad. Sci. USA_ **104**, 18473-18477 (2007) ## Examples -- An example use of the module is given - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CPMG_15N_TR/). -- An example use of the module in the context of - [RDC measurement of a protein minor, short-lived state](../../examples/trosy_cpmg_rdc.md) - can be found - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Combinations/N15_NH_RDC/). +- An example use of the module is given + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CPMG_15N_TR/). +- An example use of the module in the context of + [RDC measurement of a protein minor, short-lived state](../../examples/trosy_cpmg_rdc.md) + can be found + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Combinations/N15_NH_RDC/). ## Sample configuration file diff --git a/website/docs/experiments/cpmg/cpmg_15n_tr_0013.md b/website/docs/experiments/cpmg/cpmg_15n_tr_0013.md index 3dd1301c..83501796 100644 --- a/website/docs/experiments/cpmg/cpmg_15n_tr_0013.md +++ b/website/docs/experiments/cpmg/cpmg_15n_tr_0013.md @@ -18,17 +18,17 @@ exchange dynamics. Resulting magnetization intensity after the CPMG block is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Nx(a), Ny(a), Nz(a), 2HzNx(a), 2HzNy(a), 2HzNz(a), - Nx(b), Ny(b), Nz(b), 2HzNx(b), 2HzNy(b), 2HzNz(b), ... } + \{ Nx(a), Ny(a), Nz(a), 2HzNx(a), 2HzNy(a), 2HzNz(a), + Nx(b), Ny(b), Nz(b), 2HzNx(b), 2HzNy(b), 2HzNz(b), ... \} This version is modified such that CPMG pulses are applied with [0013] phase cycle as used in ¹⁵N pure in-phase experiments. ## References -- Jiang, Yu, Zhang, Liu, and Yang. J Magn Reson **257**, 1-7 (2015) -- P. Vallurupalli, D.F. Hansen, E. Stollar, E. Meirovitch, and L.E. Kay. _Proc. - Natl. Acad. Sci. USA_ **104**, 18473-18477 (2007) +- Jiang, Yu, Zhang, Liu, and Yang. J Magn Reson **257**, 1-7 (2015) +- P. Vallurupalli, D.F. Hansen, E. Stollar, E. Meirovitch, and L.E. Kay. _Proc. + Natl. Acad. Sci. USA_ **104**, 18473-18477 (2007) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_1hn_ap.md b/website/docs/experiments/cpmg/cpmg_1hn_ap.md index dacd5b22..c0f77ff5 100644 --- a/website/docs/experiments/cpmg/cpmg_1hn_ap.md +++ b/website/docs/experiments/cpmg/cpmg_1hn_ap.md @@ -17,14 +17,14 @@ magnetization throughout the CPMG block. This results in lower intrinsic relaxation rates and therefore better sensitivity. The calculations use a (6n)×(6n), two-spin matrix, where n is the number of states: - { Hx(a), Hy(a), Hz(a), 2HxNz(a), 2HyNz(a), 2HzNz(a), - Hx(b), Hy(b), Hz(b), 2HxNz(b), 2HyNz(b), 2HzNz(b), ... } + \{ Hx(a), Hy(a), Hz(a), 2HxNz(a), 2HyNz(a), 2HzNz(a), + Hx(b), Hy(b), Hz(b), 2HxNz(b), 2HyNz(b), 2HzNz(b), ... \} ## Reference Adapted from: -- Ishima, and Torshia. _J. Biomol. NMR_ **25**, 243-248 (2003) +- Ishima, and Torshia. _J. Biomol. NMR_ **25**, 243-248 (2003) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_1hn_ap_0013.md b/website/docs/experiments/cpmg/cpmg_1hn_ap_0013.md index cfbb0db1..d9da4c13 100644 --- a/website/docs/experiments/cpmg/cpmg_1hn_ap_0013.md +++ b/website/docs/experiments/cpmg/cpmg_1hn_ap_0013.md @@ -17,15 +17,15 @@ magnetization throughout the CPMG block. This results in lower intrinsic relaxation rates and therefore better sensitivity. The calculations use the (6n)×(6n), two-spin matrix, where n is the number of states: - { Hx(a), Hy(a), Hz(a), 2HxNz(a), 2HyNz(a), 2HzNz(a), - Hx(b), Hy(b), Hz(b), 2HxNz(b), 2HyNz(b), 2HzNz(b), ... } + \{ Hx(a), Hy(a), Hz(a), 2HxNz(a), 2HyNz(a), 2HzNz(a), + Hx(b), Hy(b), Hz(b), 2HxNz(b), 2HyNz(b), 2HzNz(b), ... \} This version is modified such that CPMG pulses are applied with [0013] phase cycle to help better overcome off-resonance effects. ## Reference -- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **73**, 641-650 (2019) +- T. Yuwen, and L.E. Kay. _J. Biomol. NMR_ **73**, 641-650 (2019) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_ch3_13c_h2c.md b/website/docs/experiments/cpmg/cpmg_ch3_13c_h2c.md index 2b53e12f..70e44db4 100644 --- a/website/docs/experiments/cpmg/cpmg_ch3_13c_h2c.md +++ b/website/docs/experiments/cpmg/cpmg_ch3_13c_h2c.md @@ -19,13 +19,13 @@ even ncyc should be recorded. Resulting magnetization intensity after the CPMG block is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), - Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... } + \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), + Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \} ## Reference -- P. Lundström, P. Vallurupalli, T.M. Religa, F.W. Dahlquist, and L.E. Kay. _J. - Biomol. NMR_ **38**, 79-88 (2007) +- P. Lundström, P. Vallurupalli, T.M. Religa, F.W. Dahlquist, and L.E. Kay. _J. + Biomol. NMR_ **38**, 79-88 (2007) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_ch3_1h_dq.md b/website/docs/experiments/cpmg/cpmg_ch3_1h_dq.md index 70a473b3..eed10a30 100644 --- a/website/docs/experiments/cpmg/cpmg_ch3_1h_dq.md +++ b/website/docs/experiments/cpmg/cpmg_ch3_1h_dq.md @@ -18,13 +18,13 @@ initially anti-phase and is read out as anti-phase. The calculation uses a simplified scheme that includes only (6n)×(6n) basis set, two-spin matrix, where n is the number of states: - { 2HDQxCz(a), 2HDQyCz(a), 2HzCz(a), HDQx(a), HDQy(a), Hz(a), - 2HDQxCz(b), 2HDQyCz(b), 2HzCz(b), HDQx(b), HDQy(b), Hz(b), ... } + \{ 2HDQxCz(a), 2HDQyCz(a), 2HzCz(a), HDQx(a), HDQy(a), Hz(a), + 2HDQxCz(b), 2HDQyCz(b), 2HzCz(b), HDQx(b), HDQy(b), Hz(b), ... \} ## Reference -- Gopalan, T. Yuwen, L.E. Kay, and P. Vallurupalli. _J. Biomol. NMR_ **72**, - 79-91 (2018) +- Gopalan, T. Yuwen, L.E. Kay, and P. Vallurupalli. _J. Biomol. NMR_ **72**, + 79-91 (2018) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_ch3_1h_sq.md b/website/docs/experiments/cpmg/cpmg_ch3_1h_sq.md index 4d6e7b76..e856ab2b 100644 --- a/website/docs/experiments/cpmg/cpmg_ch3_1h_sq.md +++ b/website/docs/experiments/cpmg/cpmg_ch3_1h_sq.md @@ -18,13 +18,13 @@ initially anti-phase and is read out as anti-phase prior to ¹H detection. Resulting magnetization intensity after the CPMG block is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), - Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... } + \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), + Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \} ## Reference -- T. Yuwen, R. Huang, P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ - **58**, 6250-6254 (2019) +- T. Yuwen, R. Huang, P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ + **58**, 6250-6254 (2019) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_ch3_1h_tq.md b/website/docs/experiments/cpmg/cpmg_ch3_1h_tq.md index 3e467e60..b5c544e5 100644 --- a/website/docs/experiments/cpmg/cpmg_ch3_1h_tq.md +++ b/website/docs/experiments/cpmg/cpmg_ch3_1h_tq.md @@ -18,23 +18,23 @@ initially anti-phase and is read out as anti-phase. The calculation uses a simplified scheme that includes only (6n)×(6n) basis set, two-spin matrix, where n is the number of states: - { 2HTQxCz(a), 2HTQyCz(a), 2HzCz(a), HTQx(a), HTQy(a), Hz(a), - 2HTQxCz(b), 2HTQyCz(b), 2HzCz(b), HTQx(b), HTQy(b), Hz(b), ... } + \{ 2HTQxCz(a), 2HTQyCz(a), 2HzCz(a), HTQx(a), HTQy(a), Hz(a), + 2HTQxCz(b), 2HTQyCz(b), 2HzCz(b), HTQx(b), HTQy(b), Hz(b), ... \} ## Reference -- T. Yuwen, P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ (2016) 55, - 11490-11494 +- T. Yuwen, P. Vallurupalli, and L.E. Kay. _Angew. Chem. Int. Ed._ (2016) 55, + 11490-11494 ## Examples -- An example use of the module is given - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CPMG_CH3_1H_SQ/). -- An example, where joint fit of - [methyl ¹H double quantum CPMG (cpmg_ch3_1h_dq)](cpmg_ch3_1h_dq.md) and - [methyl ¹H triple quantum CPMG (cpmg_ch3_1h_tq)](cpmg_ch3_1h_tq.md) - experiments is performed, is available - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Combinations/CPMG_CH3_1H_DQ_TQ/). +- An example use of the module is given + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/CPMG_CH3_1H_SQ/). +- An example, where joint fit of + [methyl ¹H double quantum CPMG (cpmg_ch3_1h_dq)](cpmg_ch3_1h_dq.md) and + [methyl ¹H triple quantum CPMG (cpmg_ch3_1h_tq)](cpmg_ch3_1h_tq.md) + experiments is performed, is available + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Combinations/CPMG_CH3_1H_DQ_TQ/). ## Sample configuration file diff --git a/website/docs/experiments/cpmg/cpmg_ch3_1h_tq_diff.md b/website/docs/experiments/cpmg/cpmg_ch3_1h_tq_diff.md index f14feba5..af7fa11b 100644 --- a/website/docs/experiments/cpmg/cpmg_ch3_1h_tq_diff.md +++ b/website/docs/experiments/cpmg/cpmg_ch3_1h_tq_diff.md @@ -21,13 +21,13 @@ Magnetization is initially anti-phase and is read out as anti-phase. The calculation uses a simplified scheme that includes only (6n)×(6n) basis set, two-spin matrix, where n is the number of states: - { 2HTQxCz(a), 2HTQyCz(a), 2HzCz(a), HTQx(a), HTQy(a), Hz(a), - 2HTQxCz(b), 2HTQyCz(b), 2HzCz(b), HTQx(b), HTQy(b), Hz(b), ... } + \{ 2HTQxCz(a), 2HTQyCz(a), 2HzCz(a), HTQx(a), HTQy(a), Hz(a), + 2HTQxCz(b), 2HTQyCz(b), 2HzCz(b), HTQx(b), HTQy(b), Hz(b), ... \} ## Reference -- T. Yuwen, A. Sekhar, A.J. Baldwin, P. Vallurupalli, and L.E. Kay. _Angew. - Chem. Int. Ed._ (2018) 57, 16777-16780 +- T. Yuwen, A. Sekhar, A.J. Baldwin, P. Vallurupalli, and L.E. Kay. _Angew. + Chem. Int. Ed._ (2018) 57, 16777-16780 ## Example diff --git a/website/docs/experiments/cpmg/cpmg_ch3_mq.md b/website/docs/experiments/cpmg/cpmg_ch3_mq.md index 282f665d..36abc6da 100644 --- a/website/docs/experiments/cpmg/cpmg_ch3_mq.md +++ b/website/docs/experiments/cpmg/cpmg_ch3_mq.md @@ -17,8 +17,8 @@ Analyzes HyCx methyl group multiple quantum CPMG measured on site-specific magnetization intensity after the CPMG block is calculated using the (4n)×(4n), two-spin matrix, where n is the number of states: - { HxCx(a), HyCx(a), HxCy(a), HyCy(a), - HxCx(b), HyCx(b), HxCy(b), HyCy(b), ... } + \{ HxCx(a), HyCx(a), HxCy(a), HyCy(a), + HxCx(b), HyCx(b), HxCy(b), HyCy(b), ... \} This is a simplified basis set, which assumes ¹³C is on-resonance (i.e., off-resonance effects are not taken into account). @@ -29,8 +29,8 @@ found in the reference and can be run with either small_protein_flag = "y" or ## Reference -- D.M. Korzhnev, K. Kloiber, V. Kanelis, V. Tugarinov and L.E. Kay _J. Am. Chem. - Soc._ **126**, 3964-3973 (2004) +- D.M. Korzhnev, K. Kloiber, V. Kanelis, V. Tugarinov and L.E. Kay _J. Am. Chem. + Soc._ **126**, 3964-3973 (2004) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_chd2_1h_ap.md b/website/docs/experiments/cpmg/cpmg_chd2_1h_ap.md index f4a3420e..fbfff47a 100644 --- a/website/docs/experiments/cpmg/cpmg_chd2_1h_ap.md +++ b/website/docs/experiments/cpmg/cpmg_chd2_1h_ap.md @@ -18,13 +18,13 @@ initially anti-phase and is read out as anti-phase prior to ¹³C evolution. Resulting magnetization intensity after the CPMG block is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), - Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... } + \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), + Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \} ## Reference -- A.J. Baldwin, T.M. Religa, D.F. Hansen, G. Bouvignies, and L.E. Kay. _J. Am. - Chem. Soc._ **132**, 10992-10995 (2010) +- A.J. Baldwin, T.M. Religa, D.F. Hansen, G. Bouvignies, and L.E. Kay. _J. Am. + Chem. Soc._ **132**, 10992-10995 (2010) ## Example diff --git a/website/docs/experiments/cpmg/cpmg_hn_dq_zq.md b/website/docs/experiments/cpmg/cpmg_hn_dq_zq.md index 6ad1d55f..ae38a438 100644 --- a/website/docs/experiments/cpmg/cpmg_hn_dq_zq.md +++ b/website/docs/experiments/cpmg/cpmg_hn_dq_zq.md @@ -17,17 +17,17 @@ simultaneously. The spin system is maintained as DQ or ZQ during Trelax, and is calculated using the (15n)×(15n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), Sx(a), IxSx(a), IySx(a), IzSx(a), + \{ Ix(a), Iy(a), Iz(a), Sx(a), IxSx(a), IySx(a), IzSx(a), Sy(a), IxSy(a), IySy(a), IzSy(a), Sz(a), IxSz(a), IySz(a), IzSz(a), Ix(b), Iy(b), Iz(b), Sx(b), IxSx(b), IySx(b), IzSx(b), - Sy(b), IxSy(b), IySy(b), IzSy(b), Sz(b), IxSz(b), IySz(b), IzSz(b), ... } + Sy(b), IxSy(b), IySy(b), IzSy(b), Sz(b), IxSz(b), IySz(b), IzSz(b), ... \} The phase cycle of CPMG pulses is chosen based on νCPMG as described in the reference, which is a mixture of constant-phase and XY-family phase cycles. ## References -- Orekhov, Korzhnev, and L.E. Kay _J. Am. Chem. Soc._ **126**, 1886-1891 (2004) +- Orekhov, Korzhnev, and L.E. Kay _J. Am. Chem. Soc._ **126**, 1886-1891 (2004) ## Sample configuration file diff --git a/website/docs/experiments/cpmg/index.md b/website/docs/experiments/cpmg/index.mdx similarity index 100% rename from website/docs/experiments/cpmg/index.md rename to website/docs/experiments/cpmg/index.mdx diff --git a/website/docs/experiments/dcest/coscest_1hn_ip_ap.md b/website/docs/experiments/dcest/coscest_1hn_ip_ap.md index 82a7aede..9af85d50 100644 --- a/website/docs/experiments/dcest/coscest_1hn_ip_ap.md +++ b/website/docs/experiments/dcest/coscest_1hn_ip_ap.md @@ -16,12 +16,12 @@ Analyzes chemical exchange during the COS-CEST block. Magnetization evolution is calculated using the (6n)×(6n), two-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), - Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... } + \{ Ix(a), Iy(a), Iz(a), IxSz(a), IySz(a), IzSz(a), + Ix(b), Iy(b), Iz(b), IxSz(b), IySz(b), IzSz(b), ... \} ## References -- T. Yuwen, G. Bouvignies, and L.E. Kay. _J. Mag. Reson._ **292**, 1-7 (2018) +- T. Yuwen, G. Bouvignies, and L.E. Kay. _J. Mag. Reson._ **292**, 1-7 (2018) ## Example diff --git a/website/docs/experiments/dcest/dcest_13c.md b/website/docs/experiments/dcest/dcest_13c.md index ea1c371d..a34c04a1 100644 --- a/website/docs/experiments/dcest/dcest_13c.md +++ b/website/docs/experiments/dcest/dcest_13c.md @@ -17,13 +17,13 @@ D-CEST block. This keeps the spin system purely in-phase throughout, and is calculated using the (3n)×(3n), single-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), - Ix(b), Iy(b), Iz(b), ... } + \{ Ix(a), Iy(a), Iz(a), + Ix(b), Iy(b), Iz(b), ... \} ## References -- T. Yuwen, L.E. Kay, and G. Bouvignies. _ChemPhysChem_ **19**, 1707-1710 (2018) -- T. Yuwen, G. Bouvignies, and L.E. Kay. _J. Mag. Reson._ **292**, 1-7 (2018) +- T. Yuwen, L.E. Kay, and G. Bouvignies. _ChemPhysChem_ **19**, 1707-1710 (2018) +- T. Yuwen, G. Bouvignies, and L.E. Kay. _J. Mag. Reson._ **292**, 1-7 (2018) ## Sample configuration file diff --git a/website/docs/experiments/dcest/dcest_15n.md b/website/docs/experiments/dcest/dcest_15n.md index 6145584a..3dac1144 100644 --- a/website/docs/experiments/dcest/dcest_15n.md +++ b/website/docs/experiments/dcest/dcest_15n.md @@ -17,23 +17,23 @@ D-CEST block. This keeps the spin system purely in-phase throughout, and is calculated using the (3n)×(3n), single-spin matrix, where n is the number of states: - { Ix(a), Iy(a), Iz(a), - Ix(b), Iy(b), Iz(b), ... } + \{ Ix(a), Iy(a), Iz(a), + Ix(b), Iy(b), Iz(b), ... \} ## References -- T. Yuwen, L.E. Kay, and G. Bouvignies. _ChemPhysChem_ **19**, 1707-1710 (2018) -- T. Yuwen, A. Bah, Brady, F. Ferrage, G. Bouvignies, and L.E. Kay. _J. Phys. - Chem. B_ **122**, 11206-11217 (2018) +- T. Yuwen, L.E. Kay, and G. Bouvignies. _ChemPhysChem_ **19**, 1707-1710 (2018) +- T. Yuwen, A. Bah, Brady, F. Ferrage, G. Bouvignies, and L.E. Kay. _J. Phys. + Chem. B_ **122**, 11206-11217 (2018) ## Examples -- An example for studying a two-state exchange system is given - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/DCEST_15N/). -- An example for studying a three-state exchange system is given - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/DCEST_15N_3States/). -- An example for H/D solvent exchange measurement using ¹⁵N D-CEST can be found - [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/DCEST_15N_HD_EXCH/). +- An example for studying a two-state exchange system is given + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/DCEST_15N/). +- An example for studying a three-state exchange system is given + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/DCEST_15N_3States/). +- An example for H/D solvent exchange measurement using ¹⁵N D-CEST can be found + [here](https://github.com/gbouvignies/chemex/tree/master/examples/Experiments/DCEST_15N_HD_EXCH/). ## Sample configuration file diff --git a/website/docs/experiments/dcest/index.md b/website/docs/experiments/dcest/index.mdx similarity index 100% rename from website/docs/experiments/dcest/index.md rename to website/docs/experiments/dcest/index.mdx diff --git a/website/docs/experiments/index.md b/website/docs/experiments/index.mdx similarity index 100% rename from website/docs/experiments/index.md rename to website/docs/experiments/index.mdx diff --git a/website/docs/experiments/relaxation/index.md b/website/docs/experiments/relaxation/index.mdx similarity index 100% rename from website/docs/experiments/relaxation/index.md rename to website/docs/experiments/relaxation/index.mdx diff --git a/website/docs/experiments/relaxation/relaxation_hznz.md b/website/docs/experiments/relaxation/relaxation_hznz.md index 404d9393..a93e0a71 100644 --- a/website/docs/experiments/relaxation/relaxation_hznz.md +++ b/website/docs/experiments/relaxation/relaxation_hznz.md @@ -16,13 +16,13 @@ Analyzes ¹H-¹⁵N longitudinal two-spin order relaxation experiments. Decay is calculated using the (2n)×(2n), two-spin matrix, where n is the number of states: - { Iz(a), 2IzSz(a), - Iz(b), 2IzSz(b), ... } + \{ Iz(a), 2IzSz(a), + Iz(b), 2IzSz(b), ... \} ## Reference -- D.F. Hansen, D. Yang, H. Feng, Z. Zhou, S. Wiesner, Y. Bai, and L.E. Kay. _J. - Am. Chem. Soc._ **129**, 11468-11479 (2007) +- D.F. Hansen, D. Yang, H. Feng, Z. Zhou, S. Wiesner, Y. Bai, and L.E. Kay. _J. + Am. Chem. Soc._ **129**, 11468-11479 (2007) ## Example diff --git a/website/docs/experiments/relaxation/relaxation_nz.md b/website/docs/experiments/relaxation/relaxation_nz.md index a645b698..9151bd0d 100644 --- a/website/docs/experiments/relaxation/relaxation_nz.md +++ b/website/docs/experiments/relaxation/relaxation_nz.md @@ -16,12 +16,12 @@ Analyzes ¹⁵N T1 experiments. This keeps the spin system purely in-phase throughout, and is calculated using the (1n)×(1n), single-spin matrix, where n is the number of states: - { Iz(a), Iz(b), ... } + \{ Iz(a), Iz(b), ... \} ## Reference -- L.E. Kay, L.K. Nicholson, F. Delaglio, A. Bax, and D.A. Torchia. _J. Mag. - Reson._ **97**, 359-375 (1992) +- L.E. Kay, L.K. Nicholson, F. Delaglio, A. Bax, and D.A. Torchia. _J. Mag. + Reson._ **97**, 359-375 (1992) ## Example diff --git a/website/docs/experiments/shift/index.md b/website/docs/experiments/shift/index.mdx similarity index 100% rename from website/docs/experiments/shift/index.md rename to website/docs/experiments/shift/index.mdx diff --git a/website/docs/getting_started.md b/website/docs/getting_started.md deleted file mode 100644 index 7f8b71d6..00000000 --- a/website/docs/getting_started.md +++ /dev/null @@ -1,89 +0,0 @@ ---- -sidebar_position: 1 -lastmod: 2022-04-19T20:32:18.485Z ---- - -# Getting started - -## Overview - -ChemEx is a tool for analyzing datasets from different types of NMR experiments -to study chemical exchange processes. The most commonly used experiments include -Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion and Chemical Exchange -Saturation Transfer (CEST). - -## Installation - -The only prerequisite for installing ChemEx is Python itself. If you don’t have -Python yet and want the simplest way to get started, we recommend you use the -[Anaconda](https://www.anaconda.com/distribution/) Distribution -- it includes -Python, Numpy, and many other commonly used packages for scientific computing -and data science. - -ChemEx can be installed with **conda**, with **pip**, or -[from source](https://github.com/gbouvignies/ChemEx/). - -import Tabs from '@theme/Tabs'; import TabItem from '@theme/TabItem'; - - - - -The recommended way to install ChemEx is via **conda** (which is included in all -versions of [Anaconda](https://www.anaconda.com/distribution/) and -[Miniconda](https://docs.conda.io/en/latest/miniconda.html)): - -```shell -# Best practice, use an environment rather than install in the base env -conda create -n chemex -conda activate chemex - -# If the default version of Python is less than 3.9 -conda install python=3.9 - -# ChemEx is available from the conda-forge channel -conda config --env --add channels conda-forge - -# The actual install command -conda install chemex -``` - - - - -ChemEx is also available via the -[Python Package Index](https://pypi.org/project/chemex/) using pip: - -```shell -pip install chemex -``` - -Also when using pip, it's good practice to use a virtual environment -- see -[this guide](https://dev.to/bowmanjd/python-tools-for-managing-virtual-environments-3bko#howto) -for details on using virtual environments. - -:::tip - -Due to the extensive numerical calculations during the fitting process, the -performance of ChemEx highly depends on the efficiency of numerical calculation -modules. It is highly recommended to install -[NumPy](https://numpy.org)/[SciPy](https://scipy.org) modules compiled with -Intel® Math Kernel Library (Intel® MKL), which can be obtained from -[Anaconda](https://www.anaconda.com/distribution/) or -[Intel® Distribution for Python](https://software.intel.com/en-us/distribution-for-python). -The [NumPy](https://numpy.org)/[SciPy](https://scipy.org) modules installed with -**pip** are usually not optimized and may show lower performance. - -::: - - - - -The development version can be installed directly from -[Github](https://github.com/gbouvignies/ChemEx/) via **pip**: - -```shell -pip install git+https://github.com/gbouvignies/ChemEx.git -``` - - - diff --git a/website/docs/introduction.md b/website/docs/introduction.md new file mode 100644 index 00000000..cf88d5ac --- /dev/null +++ b/website/docs/introduction.md @@ -0,0 +1,17 @@ +--- +sidebar_position: 2 +--- + +# Overview + +## Context + +Biological macromolecules such as proteins and nucleic acids are inherently flexible molecules, whose function (or malfunction) critically depends on interconversions between different conformational states. Understanding how biomolecules work therefore requires a quantitative characterization of their thermally accessible conformational landscape. The task is challenging, however, because many of the populated conformers are only transiently formed and marginally populated, so that they remain invisible to most standard biophysical techniques. Over the past two decades, nuclear magnetic resonance (NMR) has emerged as an extremely powerful tool to study these elusive states at atomic resolution. Central to this success has been the development of chemical exchange-based approaches, such as (CPMG, R$_{1ρ}$) relaxation dispersion and chemical exchange saturation transfer (CEST) experiments, with the numerical tools needed to extract the kinetic (rates) and thermodynamic (populations) parameters associated with the exchange process and the structural information (chemical shifts) of the sparsely populated, "invisible" excited states. + +![exchange_cest_cpmg_figure](/img/exchange_cest_cpmg_figure.png) + +## About ChemEx + +ChemEx is an open-source [Python](https://www.python.org) application for the analysis of NMR chemical exchange data, whose general idea is to integrate the evolution matrix of the spin-system of interest over the pulse sequence and extract the best-fit parameters by least-squares optimization. As ChemEx does not rely on analytical equations to fit the data sets, any type of experiments (e.g., D-CEST/COS-CEST) or kinetic models (e.g., 3-state exchange model) can be simulated, and most experimental details (e.g., finite pulse width, off-resonance effects, etc.) can be taken into account. ChemEx offers a wide range of pulse sequences and kinetic models to choose from. Some of its main features include multi-step fits, joint analysis of datasets from different experiments, error analysis, grid search, etc. This documentation provides an overview of these different features, along with a description of different examples illustrating their use. + +ChemEx is a pure Python package, leveraging established open-source libraries like NumPy, SciPy, Matplotlib, Rich, and pydantic. The minimization process utilizes the LMFIT module, encompassing multiple optimization algorithms available in SciPy. diff --git a/website/docs/user_guide/additional_modules.md b/website/docs/user_guide/additional_modules.mdx similarity index 99% rename from website/docs/user_guide/additional_modules.md rename to website/docs/user_guide/additional_modules.mdx index 3462adfd..e7628f81 100644 --- a/website/docs/user_guide/additional_modules.md +++ b/website/docs/user_guide/additional_modules.mdx @@ -1,5 +1,5 @@ --- -sidebar_position: 4 +sidebar_position: 3 --- # Additional modules diff --git a/website/docs/user_guide/fitting/chemex_fit.md b/website/docs/user_guide/fitting/chemex_fit.md index afc0c2a5..81d459b9 100644 --- a/website/docs/user_guide/fitting/chemex_fit.md +++ b/website/docs/user_guide/fitting/chemex_fit.md @@ -2,13 +2,11 @@ sidebar_position: 1 --- -# Starting a fit +# Starting a Fit ## Command -To initiate a fit of NMR chemical exchange dataset(s), run the command -`chemex fit` from the command-line followed by a set of options to set and -control the fitting process. +To initiate a fit of NMR chemical exchange datasets, use the `chemex fit` command in the command line. This command can be accompanied by various options to customize the fitting process: ```shell chemex fit @@ -16,64 +14,46 @@ chemex fit ## Options -The list of available options is given in the table below. More details about -the options and their associated files are given in following sections. Some of -the option names of the table are clickable, so that you can reach the related -section directly. Let's dive in. - -| Name | Description | -| --------------------------------------------------------------------- | ------------------------------------------------------------------------------ | -| [`-e`](experiment_files.md) or [`--experiments`](experiment_files.md) | Specify the files containing the experimental setup and data location. | -| [`-p`](parameter_files.md) or [`--parameters`](parameter_files.md) | Specify the files containing the initial values of fitting parameters. | -| [`-m`](method_files.md) or [`--methods`](method_files.md) | Specify the file containing the fitting method (optional). | -| [`-d`](kinetic_models.md) or [`--model`](kinetic_models.md) | Specify the kinetic model used to fit the datasets (optional, default: `2st`). | -| [`-o`](outputs.md) or [`--output`](outputs.md) | Specify the output directory (optional, default: `./Output`). | -| [`--plot {nothing,normal,all}`](method_files.md#plotting) | Plotting level (optional, default: `normal`). | -| `--include` | Residue(s) to include in the fit (optional). | -| `--exclude` | Residue(s) to exclude from the fit (optional). | +The following table lists the options for `chemex fit`. Each option's name is a link to its detailed explanation, and these options are further elaborated in subsequent sections. + +| Name | Description | +| ---- | ----------- | +| [`-e`](experiment_files.md) or [`--experiments`](experiment_files.md) | Specify files containing experimental setup and data. | +| [`-p`](parameter_files.md) or [`--parameters`](parameter_files.md) | Specify files containing initial fitting parameters. | +| [`-m`](method_files.md) or [`--methods`](method_files.md) | Indicate the fitting method file (optional). | +| [`-d`](kinetic_models.md) or [`--model`](kinetic_models.md) | Specify the kinetic model for fitting (optional, default: `2st`). | +| [`-o`](outputs.mdx) or [`--output`](outputs.mdx) | Set the output directory (optional, default: `./Output`). | +| [`--plot {nothing,normal,all}`](method_files.md#plotting) | Select the plotting level (optional, default: `normal`). | +| `--include` | Define residues to include in the fit (optional). | +| `--exclude` | Define residues to exclude from the fit (optional). | :::note -`--experiments` and `--parameters` options are mandatory. +The `--experiments` and `--parameters` options are mandatory. ::: :::tip -For arguments requiring input files (e.g., `-p`), it is possible to provide -multiple files by using the wildcard character (i.e., `*`), instead of -specifying the name of each file individually. +For file-input arguments (e.g., `-p`), you can use the wildcard character (`*`) to collectively input multiple files instead of listing each file individually. ::: -:::important TOML File formats +:::important TOML File Formats -The input and output files of ChemEx use the -[TOML](https://en.wikipedia.org/wiki/TOML) file format. You can find a detailed -description of this file format on the [TOML website](https://toml.io/). +ChemEx uses the [TOML](https://toml.io/) file format for its input and output files. You can find detailed information about this format on the [TOML website](https://en.wikipedia.org/wiki/TOML). ::: -## Combining multiple experiments - -ChemEx offers a very simple way to jointly analyse multiple experiments. For -each experiment, simply add the corresponding -[experiment file](experiment_files.md) right after the `--experiments` (or `-e`) -option in the command-line. +## Combining Multiple Experiments -This is useful, for example, when you want to fit CEST experiments with -different B1 field together, or CPMG relaxation dispersion -experiments recorded at different B0 field together, or even a -combination of the two. +ChemEx facilitates the combined analysis of multiple experiments. To include various experiments in a fit, add their corresponding [experiment files](experiment_files.md) after the `--experiments` (or `-e`) option in the command line. This is particularly useful for fitting different types of CEST or CPMG experiments, or a combination thereof. -An example illustrating -[the study of protein-ligand binding with CPMG and CEST experiments](examples/binding.md) -is available -[here](https://github.com/gbouvignies/chemex/tree/master/examples/Combinations/2stBinding/). +See an [example of protein-ligand binding analysis](https://github.com/gbouvignies/chemex/tree/master/examples/Combinations/2stBinding/) using both CPMG and CEST experiments [here](examples/binding.md). ## Example -A typical command line invocation would be: +A typical command for invoking ChemEx is as follows: ```shell chemex fit -e Experiments/*.toml \ @@ -82,14 +62,11 @@ chemex fit -e Experiments/*.toml \ -o Output ``` -Output files are located in the directory specified with the option `-o`. Plots -showing the line of best fit are also produced and saved to the disk by default -– you can modulate this behaviour with the option `--plot`. +The output files are saved in the directory specified by `-o`. The default setting includes the generation of plots to illustrate the best fit lines, which can be adjusted using the `--plot` option. :::tip -You can save the command in a shell script (typically called `run.sh` in most -examples) to save some typing efforts. +For convenience, consider saving this command in a shell script, commonly named `run.sh` in examples: ```shell title=run.sh #!/bin/sh @@ -100,7 +77,7 @@ chemex fit -e Experiments/*.toml \ -o Output ``` -Make it executable with the following command: +To make the script executable, use: ```shell chmod +x run.sh diff --git a/website/docs/user_guide/fitting/data_files.md b/website/docs/user_guide/fitting/data_files.mdx similarity index 100% rename from website/docs/user_guide/fitting/data_files.md rename to website/docs/user_guide/fitting/data_files.mdx diff --git a/website/docs/user_guide/fitting/experiment_files.md b/website/docs/user_guide/fitting/experiment_files.md index bf23141b..73e83e53 100644 --- a/website/docs/user_guide/fitting/experiment_files.md +++ b/website/docs/user_guide/fitting/experiment_files.md @@ -16,10 +16,10 @@ chemex fit -e [...] Experiment files are divided in 3 different sections: -- `[experiment]` includes the information about the experiment. -- `[conditions]` provides the sample conditions. -- `[data]` contains the details about the data location, spin system assignment - as well as methods to estimate uncertainties or filter out some measurements. +- `[experiment]` includes the information about the experiment. +- `[conditions]` provides the sample conditions. +- `[data]` contains the details about the data location, spin system assignment + as well as methods to estimate uncertainties or filter out some measurements. ## Example @@ -100,10 +100,10 @@ sample. The labeling information is used in some experiments to take into account some isotopic effects that may affect relaxation rates or the presence of scalar couplings. -- Use `"2H"` for deuterated samples to obtain accurate initial estimates of - relaxation rates based on model-free parameters. -- Use `"13C"` for uniformly 13C-labeled samples to account for scalar - couplings in CEST experiments properly. +- Use `"2H"` for deuterated samples to obtain accurate initial estimates of + relaxation rates based on model-free parameters. +- Use `"13C"` for uniformly 13C-labeled samples to account for scalar + couplings in CEST experiments properly. For example, for a uniformly 13C-labeled, perdeuterated sample, use the following configuration: @@ -192,3 +192,96 @@ user-supplied spin system names automatically, we recommend that you be as accurate as possible when choosing them. ::: + +--- +sidebar_position: 3 +--- + +# Experiment Files + +## Overview + +Experiment files in ChemEx are used to provide detailed information about datasets and file locations for analysis. These files are accessible through the `-e` or `--experiments` command line option as shown below: + +```shell +chemex fit -e [...] +``` + +## Structure of Experiment Files + +Experiment files consist of three primary sections: + +1. **`[experiment]`**: Contains experiment-related information. +2. **`[conditions]`**: Details sample conditions. +3. **`[data]`**: Includes data location, spin system assignments, and methods for uncertainty estimation or filtering measurements. + +### Example of an Experiment File + +```toml title="experiment.toml" +[experiment] +name = "cest_15n" +time_t1 = 0.5 +carrier = 118.987 +b1_frq = 26.3 + +[conditions] +h_larmor_frq = 499.243 +# p_total = 2.0e-3 +# sample = "A39G FF domain" +# temperature = 1.0 + +[data] +path = "../Data/26Hz/" +error = "scatter" +filter_offsets = [[0.0, 26.0]] + + [data.profiles] + 13N = "13N-HN.out" + 26N = "26N-HN.out" + 28N = "28N-HN.out" + 29N = "29N-HN.out" +``` + +:::note +Each experiment in ChemEx comes with a sample configuration file. These files, accessible in the [Experiments](/docs/experiments) section, include detailed key-value pair descriptions. +::: + +## Detailed Sections + +### `[experiment]` + +This section includes pulse sequence type and settings. Common keys found here are: + +- `name`: Name of the pulse sequence. +- `carrier`: Carrier position in ppm. +- `time_t1`, `time_t2`: Relaxation delays in seconds. +- `pw90`: 90 degree pulse width in seconds. +- `b1_frq`: B1 field strength in Hz. +- `observed_state`: Observed state ID (a, b, c, d). + +### `[conditions]` + +Provides experimental and sample conditions like Larmor frequency, sample temperature, protein concentration, and labeling. While `h_larmor_frq` (Larmor frequency) is always required, `temperature`, `p_total`, and `l_total` depend on the kinetic model used. + +#### `label` +The `label` key, specifying the sample's labeling scheme, is crucial for certain experiments. Examples include `"2H"` for deuterated samples and `"13C"` for 13C-labeled samples. + +### `[data]` + +Details data location, spin system assignments, and methods for error estimation and data filtering. + +#### `error` +Methods for error estimation include: +- `"file"`: Direct from file. +- `"duplicates"`: Pooled standard deviation or average error values. +- `"scatter"`: Gaussian noise estimation on CEST profiles. + +#### `filter_offsets` +Used to exclude specific offsets from CEST profiles, typically provided as pairs of values indicating offset and bandwidth. + +#### `[data.profiles]` +Lists filenames of experimental profiles and their spin-system assignments. Names should follow Sparky-NMR peak label conventions. + +:::note +Ensure accuracy in naming spin-systems, as it impacts experiment specificity. +::: \ No newline at end of file diff --git a/website/docs/user_guide/fitting/index.md b/website/docs/user_guide/fitting/index.mdx similarity index 93% rename from website/docs/user_guide/fitting/index.md rename to website/docs/user_guide/fitting/index.mdx index b7534db7..1e0006e7 100644 --- a/website/docs/user_guide/fitting/index.md +++ b/website/docs/user_guide/fitting/index.mdx @@ -1,5 +1,5 @@ --- -sidebar_position: 3 +sidebar_position: 2 --- import DocCardList from '@theme/DocCardList'; diff --git a/website/docs/user_guide/fitting/method_files.md b/website/docs/user_guide/fitting/method_files.md index 687f99c9..fa5aeb07 100644 --- a/website/docs/user_guide/fitting/method_files.md +++ b/website/docs/user_guide/fitting/method_files.md @@ -9,10 +9,10 @@ sidebar_position: 6 The method file contains the fitting methods to be used during the fitting process. This is where you can: -- define which parameters are fit, fixed, or constrained, -- select the profiles to include in the calculation, -- activate additional calculations, such as grid search, Monte Carlo or - bootstrap analyses. +- define which parameters are fit, fixed, or constrained, +- select the profiles to include in the calculation, +- activate additional calculations, such as grid search, Monte Carlo or + bootstrap analyses. This file is provided to ChemEx using the `-m` or `--method` option. @@ -105,13 +105,13 @@ FIT = [ In this example: -- `"R2_A, NUC->G23N, B0->800.13MHz, T->23C"` corresponds to the amide nitrogen - R2 of state A of Gly23 measured at 23 ºC, 800.13 MHz. -- `"R1_A, B0->800.13MHz"` selects all the state A R1 values measured - at 800.13 MHz, independently of the residue number and temperature. -- `"DW_AB, NUC->N"` corresponds to all the amide nitrogen chemical shift - differences between states A and B . -- `"R2_B"` selects all R2 values os state B. +- `"R2_A, NUC->G23N, B0->800.13MHz, T->23C"` corresponds to the amide nitrogen + R2 of state A of Gly23 measured at 23 ºC, 800.13 MHz. +- `"R1_A, B0->800.13MHz"` selects all the state A R1 values measured + at 800.13 MHz, independently of the residue number and temperature. +- `"DW_AB, NUC->N"` corresponds to all the amide nitrogen chemical shift + differences between states A and B . +- `"R2_B"` selects all R2 values os state B. ### `FIX` @@ -189,23 +189,23 @@ are fixed to the value of the grid that is evaluated, while the other parameters are set as defined by the `FIX`, `FIT` and `CONSTRAINTS` options. Points of the grid can be defined using a linear scale, a log scale or point by point: -- Linear scale: +- Linear scale: - ```toml - "[PB] = lin(, , )" - ``` + ```toml + "[PB] = lin(, , )" + ``` -- Log scale: +- Log scale: - ```toml - "[PB] = log(, , )" - ``` + ```toml + "[PB] = log(, , )" + ``` -- Point by point: +- Point by point: - ```toml - "[PB] = (, , ..., )" - ``` + ```toml + "[PB] = (, , ..., )" + ``` Example: @@ -277,9 +277,9 @@ profile to generate new ones with the same number of points as the original. For the nucleus-specific bootstrap analysis, full profiles are randomly selected based on their associated nucleus to generate the synthetic datasets. In other -words, if we have a dataset that depends on the nuclei {G2N, H8N, R9N, R9H}, +words, if we have a dataset that depends on the nuclei \{G2N, H8N, R9N, R9H\}, potential new datasets could include the profiles of the following sets of -nuclei {H8N, H8N, R9N, R9H} or {G2N, G2N, G2N, R9H}. +nuclei \{H8N, H8N, R9N, R9H\} or \{G2N, G2N, G2N, R9H\}. :::note @@ -309,9 +309,9 @@ where MC is the type of simulation and 100 is the number of simulations. Types can be: -- "MC" for Monte Carlo -- "BS" for bootstrap -- "BSN" for nucleus-specific bootstrap +- "MC" for Monte Carlo +- "BS" for bootstrap +- "BSN" for nucleus-specific bootstrap To run two or more types of simulation just add additional pairs of values: diff --git a/website/docs/user_guide/fitting/outputs.md b/website/docs/user_guide/fitting/outputs.mdx similarity index 100% rename from website/docs/user_guide/fitting/outputs.md rename to website/docs/user_guide/fitting/outputs.mdx diff --git a/website/docs/user_guide/fitting/parameter_files.md b/website/docs/user_guide/fitting/parameter_files.md index 5f6a85ca..08c72d99 100644 --- a/website/docs/user_guide/fitting/parameter_files.md +++ b/website/docs/user_guide/fitting/parameter_files.md @@ -21,7 +21,7 @@ Parameter files are divided in multiple sections: parameter name, such as `[CS_A]`. Multiple parameter files can be provided if necessary. -:::caution +:::warning Due to the multidimensional searching feature of $χ^2$ minimization process, it is essential to set a suitable initial value for each parameter to avoid getting diff --git a/website/docs/user_guide/index.md b/website/docs/user_guide/index.mdx similarity index 100% rename from website/docs/user_guide/index.md rename to website/docs/user_guide/index.mdx diff --git a/website/docs/user_guide/introduction.md b/website/docs/user_guide/introduction.md deleted file mode 100644 index 2883bd9c..00000000 --- a/website/docs/user_guide/introduction.md +++ /dev/null @@ -1,51 +0,0 @@ ---- -sidebar_position: 1 ---- - -# Introduction - -## Context - -Biological macromolecules such as proteins and nucleic acids are inherently -flexible molecules, whose function (or malfunction) critically depends on -interconversions between different conformational states. Understanding how -biomolecules work therefore requires a quantitative characterization of their -thermally accessible conformational landscape. The task is challenging, however, -because many of the populated conformers are only transiently formed and -marginally populated, so that they remain invisible to most standard biophysical -techniques. Over the past two decades, nuclear magnetic resonance (NMR) has -emerged as an extremely powerful tool to study these elusive states at atomic -resolution. Central to this success has been the development of chemical -exchange-based approaches, such as (CPMG, R$_{1ρ}$) relaxation dispersion and -chemical exchange saturation transfer (CEST) experiments, with the numerical -tools needed to extract the kinetic (rates) and thermodynamic (populations) -parameters associated with the exchange process and the structural information -(chemical shifts) of the sparsely populated, "invisible" excited states. - - -![exchange_cest_cpmg_figure](/img/exchange_cest_cpmg_figure.png) - -## About ChemEx - -ChemEx is an open-source [Python](https://www.python.org) application for the -analysis of NMR chemical exchange data, whose general idea is to integrate the -evolution matrix of the spin-system of interest over the pulse sequence and -extract the best-fit parameters by least-squares optimization. As ChemEx does -not rely on analytical equations to fit the data sets, any type of experiments -(e.g., D-CEST/COS-CEST) or kinetic models (e.g., 3-state exchange model) can be -simulated, and most experimental details (e.g., finite pulse width, -off-resonance effects, etc.) can be taken into account. ChemEx offers a wide -range of pulse sequences and kinetic models to choose from. Some of its main -features include multi-step fits, joint analysis of datasets from different -experiments, error analysis, grid search, etc. This documentation provides an -overview of these different features, along with a description of different -examples illustrating their use. - -ChemEx is a pure [Python](https://www.python.org) package that builds upon well -established open-source packages, including [NumPy](https://numpy.org), -[SciPy](https://scipy.org), [Matplotlib](https://matplotlib.org), -[Rich](https://rich.readthedocs.io/en/stable/), and -[pydantic](https://pydantic-docs.helpmanual.io). The minimization procedure is -carried out using the [LMFIT](https://lmfit.github.io/lmfit-py/) module, which -supports many of the optimization algorithms available in -[SciPy](https://scipy.org/). diff --git a/website/docs/user_guide/running_chemex.md b/website/docs/user_guide/running_chemex.md index 5a84527c..e9a458df 100644 --- a/website/docs/user_guide/running_chemex.md +++ b/website/docs/user_guide/running_chemex.md @@ -1,43 +1,34 @@ --- -sidebar_position: 2 -lastmod: 2022-04-19T20:14:49.735Z +sidebar_position: 1 --- # Running ChemEx -ChemEx is a command-line application. After the installation, you can run the -program directly from the shell prompt using the command `chemex`: +ChemEx operates as a command-line tool. Once installed, execute it from the shell prompt with the `chemex` command: ```shell chemex ``` -Four **sub-commands** are available, each corresponding to a specific task: +It offers four **sub-commands**, each dedicated to a distinct functionality: -- [`fit`](fitting/chemex_fit.md) starts the fits of experimental datasets: if - you are interested in ChemEx, this is likely the sub-command you are looking - for. -- `simulate` executes the module, which allows to calculate synthetic profiles - from a given experiment and a given model. -- `pick_cest` is a small GUI application, which plots CEST, cos-CEST and D-CEST - profiles for interactive dip picking and obtaining starting minor state - position values. -- `plot_param` produces plots of selected parameters based on fitting output - results. +- [`fit`](fitting/chemex_fit.md): Initiates the fitting of experimental data. This is the primary sub-command for most ChemEx users. +- `simulate`: Runs the module to generate synthetic profiles using specified experiments and models. +- `pick_cest`: Provides a small GUI for plotting CEST, cos-CEST, and D-CEST profiles. It facilitates interactive dip picking and initial estimation of minor state positions. +- `plot_param`: Generates plots for selected parameters derived from fitting results. :::tip -You can obtain the list of available sub-commands using the `--help` option. +Retrieve a list of all sub-commands by using the `--help` option: ```bash chemex --help ``` -You can display the list of options associated with each sub-command using the -sub-command name followed by the `--help` option. +For details on each sub-command's options, append `--help` after the sub-command: ```bash chemex --help ``` -::: +::: \ No newline at end of file diff --git a/website/docs/welcome_to_chemex.md b/website/docs/welcome_to_chemex.md new file mode 100644 index 00000000..79d85f05 --- /dev/null +++ b/website/docs/welcome_to_chemex.md @@ -0,0 +1,61 @@ +--- +sidebar_position: 1 +--- + +# Welcome to ChemEx + +## Quick Overview + +ChemEx is a comprehensive tool for analyzing NMR experimental data to characterize chemical exchange processes. This guide will help you get started with ChemEx, covering everything from installation to initial usage. Primarily, ChemEx facilitates analysis of experiments like Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion and Chemical Exchange Saturation Transfer (CEST). + +## Prerequisites + +Before installing ChemEx, ensure you have Python installed. For a hassle-free setup, especially for beginners, we recommend the [Anaconda Distribution](https://www.anaconda.com/distribution/). It comes bundled with Python, Numpy, and a suite of scientific computing tools. + +## Installation Methods{#installation} + +ChemEx offers flexible installation options: through **conda**, **pip**, or directly [from the source](https://github.com/gbouvignies/ChemEx/). Choose the method that best suits your setup. + +### Using conda + +For an optimal experience, install ChemEx using **conda**. This method is ideal as it handles dependencies efficiently and is available in all versions of [Anaconda](https://www.anaconda.com/distribution/) and [Miniconda](https://docs.conda.io/en/latest/miniconda.html). + +```shell +# Create and activate a new environment for ChemEx +conda create -n chemex +conda activate chemex + +# Ensure Python 3.11 is installed +conda install python=3.11 + +# Add conda-forge channel and install ChemEx +conda config --env --add channels conda-forge +conda install chemex +``` + +### Using pip + +Alternatively, you can install ChemEx using pip, available via the [Python Package Index](https://pypi.org/project/chemex/). + +```shell +pip install chemex +``` + +:::tip + +Utilize a virtual environment when installing with pip. [Here's a helpful guide](https://dev.to/bowmanjd/python-tools-for-managing-virtual-environments-3bko#howto). + +::: + +### From source + +For those interested in the latest features and updates, install the development version of ChemEx directly from [GitHub](https://github.com/gbouvignies/ChemEx/). + +```shell +pip install git+https://github.com/gbouvignies/ChemEx.git +``` + + +## Performance Optimization + +ChemEx performance is significantly enhanced by using numerically optimized modules. We recommend installing [NumPy](https://numpy.org) and [SciPy](https://scipy.org) with Intel® Math Kernel Library (Intel® MKL) for the best performance. These optimized modules are available via [Anaconda](https://www.anaconda.com/distribution/) or the [Intel® Distribution for Python](https://software.intel.com/en-us/distribution-for-python). Note that the standard pip installations of these modules might not offer the same level of optimization. diff --git a/website/docusaurus.config.js b/website/docusaurus.config.js index e4500d4b..25eee277 100644 --- a/website/docusaurus.config.js +++ b/website/docusaurus.config.js @@ -1,8 +1,7 @@ // @ts-check // Note: type annotations allow type checking and IDEs autocompletion -const lightCodeTheme = require('prism-react-renderer/themes/github'); -const darkCodeTheme = require('prism-react-renderer/themes/dracula'); +import { themes as prismThemes } from 'prism-react-renderer'; const math = require('remark-math'); const katex = require('rehype-katex'); @@ -26,13 +25,13 @@ const config = { /** @type {import('@docusaurus/preset-classic').Options} */ ({ docs: { - sidebarPath: require.resolve('./sidebars.js'), + sidebarPath: './sidebars.js', editUrl: 'https://github.com/gbouvignies/chemex/tree/main/website/', remarkPlugins: [math], rehypePlugins: [katex], }, theme: { - customCss: require.resolve('./src/css/custom.css'), + customCss: './src/css/custom.css', }, }), ], @@ -61,7 +60,7 @@ const config = { items: [ { type: 'doc', - docId: 'getting_started', + docId: 'welcome_to_chemex', position: 'left', label: 'Docs', }, @@ -86,7 +85,7 @@ const config = { items: [ { label: 'Installation', - to: '/docs/getting_started#Installation', + to: '/docs/welcome_to_chemex#installation', }, { label: 'User Guide', @@ -132,8 +131,8 @@ const config = { copyright: `Copyright © ${new Date().getFullYear()} Guillaume Bouvignies, Inc. Built with Docusaurus.`, }, prism: { - theme: lightCodeTheme, - darkTheme: darkCodeTheme, + theme: prismThemes.github, + darkTheme: prismThemes.dracula, additionalLanguages: ['toml', "markdown"], }, algolia: { @@ -162,4 +161,4 @@ const config = { }), }; -module.exports = config; +export default config; diff --git a/website/package-lock.json b/website/package-lock.json index 2645aa4c..0f0e57fb 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -1,29 +1,32 @@ { "name": "website", - "version": "2022.3.5", - "lockfileVersion": 2, + "version": "2023.11.0", + "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "website", - "version": "2022.3.5", - "dependencies": { - "@docusaurus/core": "^2.4.1", - "@docusaurus/preset-classic": "^2.4.0", - "@mdx-js/react": "^1.6.22", - "clsx": "^1.1.1", - "hast-util-is-element": "^2.1.3", - "prism-react-renderer": "^1.3.1", - "raw-loader": "^4.0.2", - "react": "^17.0.2", - "react-dom": "^17.0.2", - "rehype-katex": "^5.0.0", - "remark-math": "^3.0.1" + "version": "2023.11.0", + "dependencies": { + "@docusaurus/core": "^3.0.1", + "@docusaurus/preset-classic": "^3.0.1", + "@mdx-js/react": "^3.0.0", + "clsx": "^1.2.1", + "prism-react-renderer": "^2.1.0", + "react": "^18.0.0", + "react-dom": "^18.0.0", + "rehype-katex": "^7.0.0", + "remark-math": "^6.0.0" }, "devDependencies": { - "@docusaurus/eslint-plugin": "^2.4.1", + "@docusaurus/module-type-aliases": "^3.0.1", + "@docusaurus/types": "^3.0.1", "eslint": "^8.44.0", - "eslint-plugin-react": "^7.32.2" + "eslint-plugin-react": "^7.32.2", + "prettier": "^3.1.0" + }, + "engines": { + "node": ">=18.0" } }, "node_modules/@aashutoshrathi/word-wrap": { @@ -36,19 +39,31 @@ } }, "node_modules/@algolia/autocomplete-core": { - "version": "1.7.4", - "resolved": "https://registry.npmjs.org/@algolia/autocomplete-core/-/autocomplete-core-1.7.4.tgz", - "integrity": "sha512-daoLpQ3ps/VTMRZDEBfU8ixXd+amZcNJ4QSP3IERGyzqnL5Ch8uSRFt/4G8pUvW9c3o6GA4vtVv4I4lmnkdXyg==", + 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"version": "2022.3.5", + "version": "2023.11.0", "private": true, "scripts": { "docusaurus": "docusaurus", @@ -14,17 +14,22 @@ "write-heading-ids": "docusaurus write-heading-ids" }, "dependencies": { - "@docusaurus/core": "^2.4.1", - "@docusaurus/preset-classic": "^2.4.0", - "@mdx-js/react": "^1.6.22", - "clsx": "^1.1.1", - "hast-util-is-element": "^2.1.3", - "prism-react-renderer": "^1.3.1", - "raw-loader": "^4.0.2", - "react": "^17.0.2", - "react-dom": "^17.0.2", - "rehype-katex": "^5.0.0", - "remark-math": "^3.0.1" + "@docusaurus/core": "^3.0.1", + "@docusaurus/preset-classic": "^3.0.1", + "@mdx-js/react": "^3.0.0", + "clsx": "^1.2.1", + "prism-react-renderer": "^2.1.0", + "react": "^18.0.0", + "react-dom": "^18.0.0", + "rehype-katex": "^7.0.0", + "remark-math": "^6.0.0" + }, + "devDependencies": { + "@docusaurus/module-type-aliases": "^3.0.1", + "@docusaurus/types": "^3.0.1", + "eslint": "^8.44.0", + "eslint-plugin-react": "^7.32.2", + "prettier": "^3.1.0" }, "browserslist": { "production": [ @@ -33,14 +38,12 @@ "not op_mini all" ], "development": [ - "last 1 chrome version", - "last 1 firefox version", - "last 1 safari version" + "last 3 chrome version", + "last 3 firefox version", + "last 3 safari version" ] }, - "devDependencies": { - "@docusaurus/eslint-plugin": "^2.4.1", - "eslint": "^8.44.0", - "eslint-plugin-react": "^7.32.2" + "engines": { + "node": ">=18.0" } } diff --git a/website/src/pages/index.js b/website/src/pages/index.js index 5ba08583..ccabe7e8 100644 --- a/website/src/pages/index.js +++ b/website/src/pages/index.js @@ -25,7 +25,7 @@ function HomepageHeader() {
+ to="/docs/welcome_to_chemex"> Get started