Merge pull request #41 from pnnl/develop

Separate `finish` and `parse` functionality

.github/workflows/actions.yml

@@ -35,10 +35,10 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
-          miniforge-version: 4.9.2-4
+          miniforge-version: latest
           use-mamba: true
           environment-file: envs/linux.yml
-          use-only-tar-bz2: true
+          use-only-tar-bz2: false
           auto-activate-base: false
           activate-environment: isicle
 
@@ -65,10 +65,10 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
-          miniforge-version: 4.9.2-4
+          miniforge-version: latest
           use-mamba: true
           environment-file: envs/osx.yml
-          use-only-tar-bz2: true
+          use-only-tar-bz2: false
           auto-activate-base: false
           activate-environment: isicle
 
@@ -97,11 +97,11 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
-          miniforge-version: 4.9.2-4
+          miniforge-version: latest
           use-mamba: true
-          python-version: 3.9
+          python-version: 3.12
           channels: conda-forge,bioconda
-          use-only-tar-bz2: true
+          use-only-tar-bz2: false
           auto-activate-base: true
 
       - name: Install dependencies

conda-recipe/meta.yaml

@@ -32,7 +32,7 @@ requirements:
     - openbabel >=3.0.0
     - openmpi
     - pandas >=1.1.4
-    - python =3.9
+    - python >=3.9
     - rdkit >=2023.09.1
     - snakemake >=6.3.0
     - statsmodels >=0.11.1

envs/linux.yml

@@ -13,7 +13,7 @@ dependencies:
   - openbabel >=3.0.0
   - openmpi
   - pandas >=1.1.4
-  - python =3.9
+  - python >=3.9
   - rdkit >=2023.09.1
   - snakemake >=6.3.0
   - statsmodels >=0.11.1

envs/osx.yml

@@ -11,7 +11,7 @@ dependencies:
   - openbabel >=3.0.0
   - openmpi
   - pandas >=1.1.4
-  - python =3.9
+  - python >=3.9
   - rdkit >=2023.09.1
   - snakemake >=6.3.0
   - statsmodels >=0.11.1

isicle/__init__.py

@@ -1,4 +1,4 @@
-from isicle import adducts, conformers, geometry, md, mobility, qm
+from isicle import adducts, conformers, geometry, md, mobility, parse, qm
 from isicle.io import load, save
 
 __version__ = "2.0.0"

isicle/adducts.py

@@ -4,11 +4,9 @@
 import pickle
 import re
 
-import rdkit.Chem.rdchem as rdc
 from rdkit import Chem
 
 import isicle
-from isicle.conformers import ConformationalEnsemble
 from isicle.interfaces import WrapperInterface
 from isicle.md import md
 from isicle.utils import safelist
@@ -296,13 +294,6 @@ def set_geometry(self, geom):
         else:
             raise ValueError('Could not find self.mol or self.geom')
 
-    def set_charge(self):
-        '''
-        '''
-
-        if self.geom.__dict__.get('charge') is None:
-            self.geom.__dict__.update(charge=self.geom.get_charge())
-
     def _set_ions(self, ion_path=None, ion_list=None):
         '''
         '''
@@ -468,6 +459,7 @@ def _forcefield_selector(self, forcefield, mw):
             raise ValueError(
                 'RDKit only supports UFF, MMFF, MMFF94, MMFF94s as forcefields.')
 
+    # TODO: update this
     def _update_geometry_charge(self, geom):
         '''
         '''
@@ -873,9 +865,6 @@ def run(self, geom, ion_path=None, ion_list=None, **kwargs):
         # Sets geom to self.geom
         self.set_geometry(geom)
 
-        # Infers charge of geom.mol
-        self.set_charge()
-
         # Load specified ions by type
         # Validity check if negative ionization can be done
         self.configure(ion_path=ion_path, ion_list=ion_list)
@@ -975,18 +964,6 @@ def set_geometry(self, geom):
         else:
             raise ValueError('Could not find self.xyz, self.mol, or self.geom')
 
-    def set_charge(self):
-        '''
-        '''
-
-        if self.geom.__dict__.get('charge') is None:
-            if self.geom.load.get('filetype') == '.xyz':
-                # self.geom.__dict__.update(charge=charge)
-                raise ValueError(
-                    'Must first run geom.set_charge for an xyz structure')
-            else:
-                self.geom.__dict__.update(charge=self.geom.get_charge())
-
     def _set_ions(self, ion_path=None, ion_list=None):
         cations, anions, complex = _parse_ions(
             ion_path=ion_path, ion_list=ion_list)
@@ -1032,11 +1009,11 @@ def _check_valid(self):
         self.adducts['complex'] = self._filter_supported_by_xtb(
             self.adducts['complex'])
 
-        if self.geom.load['filetype'] != '.xyz':
-            self.adducts['anions'] = _filter_by_substructure_match(
-                self.geom.mol, self.adducts['anions'])
-            self.adducts['complex'] = _filter_by_substructure_match(
-                self.geom.mol, self.adducts['complex'])
+
+        self.adducts['anions'] = _filter_by_substructure_match(
+            self.geom.mol, self.adducts['anions'])
+        self.adducts['complex'] = _filter_by_substructure_match(
+            self.geom.mol, self.adducts['complex'])
 
     def configure(self, ion_path=None, ion_list=None):
         self._set_ions(ion_path=ion_path, ion_list=ion_list)
@@ -1054,14 +1031,15 @@ def _parse_ion_charge(self, ion):
             charge = int(charge[0])
         return charge
 
+    # TODO: update this
     def _update_geometry_charge(self, geom, adduct, ion_charge, mode):
         '''
         '''
 
         if mode == 'negative':
-            charge = geom.__dict__.get('charge') - ion_charge
+            charge = geom.get_charge() - ion_charge
         elif mode == 'positive':
-            charge = geom.__dict__.get('charge') + ion_charge
+            charge = geom.get_charge() + ion_charge
         adduct.__dict__.update(charge=charge)
 
     def _positive_mode(self, geom, forcefield, ewin, cation, optlevel, dryrun, processes, solvation, ignore_topology):
@@ -1070,7 +1048,7 @@ def _positive_mode(self, geom, forcefield, ewin, cation, optlevel, dryrun, proce
         '''
 
         output = md(geom, program='xtb', task='protonate', forcefield=forcefield,
-                    ewin=ewin, ion=cation, optlevel=optlevel, dryrun=dryrun, charge=geom.charge, processes=processes, solvation=solvation, ignore_topology=ignore_topology)
+                    ewin=ewin, ion=cation, optlevel=optlevel, dryrun=dryrun, processes=processes, solvation=solvation, ignore_topology=ignore_topology)
         ion_charge = self._parse_ion_charge(cation)
         for adduct in output.geom:
             self._update_geometry_charge(geom, adduct, ion_charge, 'positive')
@@ -1082,7 +1060,7 @@ def _negative_mode(self, geom, forcefield, ewin, anion, optlevel, dryrun, proces
         '''
 
         output = md(geom, program='xtb', task='deprotonate', forcefield=forcefield,
-                    ewin=ewin, ion=anion, optlevel=optlevel, dryrun=dryrun, charge=geom.charge, processes=processes, solvation=solvation, ignore_topology=ignore_topology)
+                    ewin=ewin, ion=anion, optlevel=optlevel, dryrun=dryrun, processes=processes, solvation=solvation, ignore_topology=ignore_topology)
         ion_charge = self._parse_ion_charge(anion)
         for adduct in output.geom:
             self._update_geometry_charge(geom, adduct, ion_charge, 'negative')
@@ -1181,9 +1159,6 @@ def run(self, geom, ion_path=None, ion_list=None, **kwargs):
 
         self.set_geometry(geom)
 
-        # Infers charge for non xyz files, infers default neutral for xyz files
-        self.set_charge()
-
         # Load specified ions by type
         # Validity check if negative ionization can be done
         # Validity check if CREST supports the ions specified

isicle/conformers.py

@@ -2,8 +2,7 @@
 import pandas as pd
 from statsmodels.stats.weightstats import DescrStatsW
 
-from isicle import io
-from isicle.geometry import Geometry, XYZGeometry
+from isicle.geometry import Geometry
 from isicle.utils import TypedList, safelist
 
 
@@ -382,7 +381,7 @@ def __init__(self, *args):
 
         '''
 
-        super().__init__((Geometry, XYZGeometry), *args)
+        super().__init__(Geometry, *args)
 
     def _check_attributes(self, attr):
         '''