From f15592ab8357e25792b0a24166dd3062a286e625 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Iv=C3=A1n=20Pulido?=
 <2949729+ijpulidos@users.noreply.github.com>
Date: Mon, 28 Oct 2024 11:25:12 -0400
Subject: [PATCH] Convergence tests for protein mutation protocol (#95)

* Neutral protein mutation convergence test

* Charge changing protein mutation convergence test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Using GUFE's JSON decoder

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Using forward-reverse utility function in all tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 feflow/tests/data/capped_AAs/ARG_capped.pdb   |  53 +++
 feflow/tests/data/capped_AAs/LYS_capped.pdb   |  51 +++
 .../data/capped_AAs/ala_to_arg_mapping.json   |   1 +
 .../data/capped_AAs/ala_to_lys_mapping.json   |   1 +
 feflow/tests/test_protein_mutation.py         | 306 +++++++++++++++++-
 5 files changed, 401 insertions(+), 11 deletions(-)
 create mode 100644 feflow/tests/data/capped_AAs/ARG_capped.pdb
 create mode 100644 feflow/tests/data/capped_AAs/LYS_capped.pdb
 create mode 100644 feflow/tests/data/capped_AAs/ala_to_arg_mapping.json
 create mode 100644 feflow/tests/data/capped_AAs/ala_to_lys_mapping.json

diff --git a/feflow/tests/data/capped_AAs/ARG_capped.pdb b/feflow/tests/data/capped_AAs/ARG_capped.pdb
new file mode 100644
index 0000000..d41e7d3
--- /dev/null
+++ b/feflow/tests/data/capped_AAs/ARG_capped.pdb
@@ -0,0 +1,53 @@
+REMARK   1 CREATED WITH OPENMM 8.1.1, 2024-10-22
+HETATM    1  H1  ACE A   1       1.328   2.173   0.000  1.00  0.00           H
+HETATM    2  CH3 ACE A   1       2.006   1.318   0.000  1.00  0.00           C
+HETATM    3  H2  ACE A   1       2.634   1.352   0.890  1.00  0.00           H
+HETATM    4  H3  ACE A   1       2.634   1.352  -0.890  1.00  0.00           H
+HETATM    5  C   ACE A   1       1.229   0.000   0.000  1.00  0.00           C
+HETATM    6  O   ACE A   1       0.000   0.000   0.000  1.00  0.00           O
+ATOM      7  N   ARG A   2       1.954  -1.121   0.000  1.00  0.00           N
+ATOM      8  H   ARG A   2       3.113  -0.999  -0.240  1.00  0.00           H
+ATOM      9  CA  ARG A   2       1.337  -2.432  -0.001  1.00  0.00           C
+ATOM     10  HA  ARG A   2       0.663  -2.344  -0.981  1.00  0.00           H
+ATOM     11  CB  ARG A   2       2.391  -3.535  -0.001  1.00  0.00           C
+ATOM     12  HB2 ARG A   2       3.180  -3.267  -0.861  1.00  0.00           H
+ATOM     13  HB3 ARG A   2       3.041  -3.594   1.003  1.00  0.00           H
+ATOM     14  C   ARG A   2       0.461  -2.626   1.229  1.00  0.00           C
+ATOM     15  O   ARG A   2      -0.621  -3.201   1.139  1.00  0.00           O
+ATOM     16  CG  ARG A   2       2.084  -5.004  -0.344  1.00  0.00           C
+ATOM     17  HG2 ARG A   2       1.598  -5.507   0.625  1.00  0.00           H
+ATOM     18  HG3 ARG A   2       3.136  -5.550  -0.506  1.00  0.00           H
+ATOM     19  CD  ARG A   2       1.099  -5.210  -1.499  1.00  0.00           C
+ATOM     20  HD2 ARG A   2       1.752  -5.185  -2.502  1.00  0.00           H
+ATOM     21  HD3 ARG A   2       0.191  -4.493  -1.801  1.00  0.00           H
+ATOM     22  NE  ARG A   2       0.404  -6.514  -1.519  1.00  0.00           N
+ATOM     23  HE  ARG A   2      -0.766  -6.478  -1.303  1.00  0.00           H
+ATOM     24  CZ  ARG A   2       0.893  -7.771  -1.573  1.00  0.00           C
+ATOM     25  NH1 ARG A   2       2.182  -8.043  -1.320  1.00  0.00           N
+ATOM     26 HH11 ARG A   2       2.609  -8.561  -0.336  1.00  0.00           H
+ATOM     27 HH12 ARG A   2       2.902  -8.196  -2.257  1.00  0.00           H
+ATOM     28  NH2 ARG A   2       0.038  -8.772  -1.831  1.00  0.00           N
+ATOM     29 HH21 ARG A   2      -0.588  -8.881  -2.837  1.00  0.00           H
+ATOM     30 HH22 ARG A   2      -0.095  -9.737  -1.148  1.00  0.00           H
+HETATM   31  N   NME A   3       0.933  -2.143   2.381  1.00  0.00           N
+HETATM   32  H   NME A   3       1.829  -1.678   2.404  1.00  0.00           H
+HETATM   33  C   NME A   3       0.194  -2.264   3.621  1.00  0.00           C
+HETATM   34  H1  NME A   3      -0.745  -2.786   3.436  1.00  0.00           H
+HETATM   35  H2  NME A   3       0.786  -2.827   4.344  1.00  0.00           H
+HETATM   36  H3  NME A   3      -0.014  -1.271   4.019  1.00  0.00           H
+TER      37      NME A   3
+CONECT    1    2
+CONECT    2    5    1    3    4
+CONECT    3    2
+CONECT    4    2
+CONECT    5    2    6    7
+CONECT    6    5
+CONECT    7    5
+CONECT   14   31
+CONECT   31   14   33   32
+CONECT   32   31
+CONECT   33   34   35   36   31
+CONECT   34   33
+CONECT   35   33
+CONECT   36   33
+END
diff --git a/feflow/tests/data/capped_AAs/LYS_capped.pdb b/feflow/tests/data/capped_AAs/LYS_capped.pdb
new file mode 100644
index 0000000..1dab32d
--- /dev/null
+++ b/feflow/tests/data/capped_AAs/LYS_capped.pdb
@@ -0,0 +1,51 @@
+REMARK   1 CREATED WITH OPENMM 8.1.1, 2024-10-22
+HETATM    1  H1  ACE A   1       1.328   2.173   0.000  1.00  0.00           H
+HETATM    2  CH3 ACE A   1       2.006   1.318   0.000  1.00  0.00           C
+HETATM    3  H2  ACE A   1       2.634   1.352   0.890  1.00  0.00           H
+HETATM    4  H3  ACE A   1       2.634   1.352  -0.890  1.00  0.00           H
+HETATM    5  C   ACE A   1       1.229   0.000   0.000  1.00  0.00           C
+HETATM    6  O   ACE A   1       0.000   0.000   0.000  1.00  0.00           O
+ATOM      7  N   LYS A   2       1.954  -1.121   0.000  1.00  0.00           N
+ATOM      8  H   LYS A   2       3.122  -1.025  -0.195  1.00  0.00           H
+ATOM      9  CA  LYS A   2       1.337  -2.432  -0.001  1.00  0.00           C
+ATOM     10  HA  LYS A   2       0.565  -2.458  -0.915  1.00  0.00           H
+ATOM     11  CB  LYS A   2       2.391  -3.535  -0.001  1.00  0.00           C
+ATOM     12  HB2 LYS A   2       1.702  -4.515   0.088  1.00  0.00           H
+ATOM     13  HB3 LYS A   2       3.047  -3.497   0.998  1.00  0.00           H
+ATOM     14  C   LYS A   2       0.461  -2.626   1.229  1.00  0.00           C
+ATOM     15  O   LYS A   2      -0.621  -3.201   1.139  1.00  0.00           O
+ATOM     16  CG  LYS A   2       3.224  -3.837  -1.235  1.00  0.00           C
+ATOM     17  HG2 LYS A   2       2.315  -3.880  -2.010  1.00  0.00           H
+ATOM     18  HG3 LYS A   2       4.035  -3.108  -1.721  1.00  0.00           H
+ATOM     19  CD  LYS A   2       4.148  -4.963  -0.767  1.00  0.00           C
+ATOM     20  HD2 LYS A   2       4.973  -4.351  -0.150  1.00  0.00           H
+ATOM     21  HD3 LYS A   2       3.850  -5.847  -0.026  1.00  0.00           H
+ATOM     22  CE  LYS A   2       4.914  -5.474  -1.977  1.00  0.00           C
+ATOM     23  HE2 LYS A   2       5.858  -5.939  -1.402  1.00  0.00           H
+ATOM     24  HE3 LYS A   2       5.434  -4.831  -2.835  1.00  0.00           H
+ATOM     25  NZ  LYS A   2       4.338  -6.749  -2.436  1.00  0.00           N
+ATOM     26  HZ1 LYS A   2       4.059  -6.551  -3.589  1.00  0.00           H
+ATOM     27  HZ2 LYS A   2       5.104  -7.672  -2.508  1.00  0.00           H
+ATOM     28  HZ3 LYS A   2       3.279  -7.099  -1.995  1.00  0.00           H
+HETATM   29  N   NME A   3       0.933  -2.143   2.381  1.00  0.00           N
+HETATM   30  H   NME A   3       1.829  -1.678   2.404  1.00  0.00           H
+HETATM   31  C   NME A   3       0.194  -2.264   3.621  1.00  0.00           C
+HETATM   32  H1  NME A   3      -0.745  -2.786   3.436  1.00  0.00           H
+HETATM   33  H2  NME A   3       0.786  -2.827   4.344  1.00  0.00           H
+HETATM   34  H3  NME A   3      -0.014  -1.271   4.019  1.00  0.00           H
+TER      35      NME A   3
+CONECT    1    2
+CONECT    2    5    1    3    4
+CONECT    3    2
+CONECT    4    2
+CONECT    5    2    6    7
+CONECT    6    5
+CONECT    7    5
+CONECT   14   29
+CONECT   29   14   31   30
+CONECT   30   29
+CONECT   31   32   33   34   29
+CONECT   32   31
+CONECT   33   31
+CONECT   34   31
+END
diff --git a/feflow/tests/data/capped_AAs/ala_to_arg_mapping.json b/feflow/tests/data/capped_AAs/ala_to_arg_mapping.json
new file mode 100644
index 0000000..8528731
--- /dev/null
+++ b/feflow/tests/data/capped_AAs/ala_to_arg_mapping.json
@@ -0,0 +1 @@
+{"componentA": {"atoms": [[1, "1", 1, 0, " ", "H1", "ACE", 1, "N", 0], [6, "1", 2, 0, " ", "CH3", "ACE", 1, "N", 0], [1, "1", 3, 0, " ", "H2", "ACE", 1, "N", 0], [1, "1", 4, 0, " ", "H3", "ACE", 1, "N", 0], [6, "1", 5, 0, " ", "C", "ACE", 1, "N", 0], [8, "1", 6, 0, " ", "O", "ACE", 1, "N", 0], [7, "1", 7, 0, " ", "N", "ALA", 2, "N", 0], [1, "1", 8, 0, " ", "H", "ALA", 2, "N", 0], [6, "1", 9, 0, " ", "CA", "ALA", 2, "N", 0], [1, "1", 10, 0, " ", "HA", "ALA", 2, "N", 0], [6, "1", 11, 0, " ", "CB", "ALA", 2, "N", 0], [1, "1", 12, 0, " ", "HB1", "ALA", 2, "N", 0], [1, "1", 13, 0, " ", "HB2", "ALA", 2, "N", 0], [1, "1", 14, 0, " ", "HB3", "ALA", 2, "N", 0], [6, "1", 15, 0, " ", "C", "ALA", 2, "N", 0], [8, "1", 16, 0, " ", "O", "ALA", 2, "N", 0], [7, "1", 17, 0, " ", "N", "NME", 3, "N", 0], [1, "1", 18, 0, " ", "H", "NME", 3, "N", 0], [6, "1", 19, 0, " ", "C", "NME", 3, "N", 0], [1, "1", 20, 0, " ", "H1", "NME", 3, "N", 0], [1, "1", 21, 0, " ", "H2", "NME", 3, "N", 0], [1, "1", 22, 0, " ", 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\ No newline at end of file
diff --git a/feflow/tests/data/capped_AAs/ala_to_lys_mapping.json b/feflow/tests/data/capped_AAs/ala_to_lys_mapping.json
new file mode 100644
index 0000000..3147aec
--- /dev/null
+++ b/feflow/tests/data/capped_AAs/ala_to_lys_mapping.json
@@ -0,0 +1 @@
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"14": 13, "15": 14, "16": 28, "18": 30}, "annotations": "{}", "__qualname__": "LigandAtomMapping", "__module__": "gufe.mapping.ligandatommapping", ":version:": 1}
\ No newline at end of file
diff --git a/feflow/tests/test_protein_mutation.py b/feflow/tests/test_protein_mutation.py
index b0b3237..75fff13 100644
--- a/feflow/tests/test_protein_mutation.py
+++ b/feflow/tests/test_protein_mutation.py
@@ -4,9 +4,11 @@
 from importlib.resources import files
 from pathlib import Path
 
+import numpy as np
 import pytest
-from gufe import ProteinComponent, ChemicalSystem, ProtocolDAGResult
+from gufe import ProteinComponent, ChemicalSystem, ProtocolDAGResult, LigandAtomMapping
 from gufe.protocols.protocoldag import execute_DAG
+from gufe.tokenization import JSON_HANDLER
 from feflow.protocols import ProteinMutationProtocol
 
 
@@ -45,6 +47,24 @@ def leu_capped():
     return protein_comp
 
 
+@pytest.fixture(scope="session")
+def arg_capped():
+    """ProteinComponent for Arginine residue capped by ACE and NME.
+    This is meant to be used for testing charge transformations."""
+    input_pdb = str(files("feflow.tests.data.capped_AAs").joinpath("ARG_capped.pdb"))
+    protein_comp = ProteinComponent.from_pdb_file(input_pdb)
+    return protein_comp
+
+
+@pytest.fixture(scope="session")
+def lys_capped():
+    """ProteinComponent for Lysine residue capped by ACE and NME.
+    This is meant to be used for testing charge transformations."""
+    input_pdb = str(files("feflow.tests.data.capped_AAs").joinpath("LYS_capped.pdb"))
+    protein_comp = ProteinComponent.from_pdb_file(input_pdb)
+    return protein_comp
+
+
 @pytest.fixture(scope="session")
 def ala_capped_system(ala_capped, solvent_comp):
     """Solvated capped Alanine ChemicalSystem"""
@@ -70,15 +90,89 @@ def leu_capped_system(leu_capped, solvent_comp):
 
 
 @pytest.fixture(scope="session")
-def ala_to_gly_mapping(ala_capped, gly_capped):
-    """Mapping from ALA to GLY (capped)"""
-    from gufe import LigandAtomMapping
+def arg_capped_system(arg_capped, solvent_comp):
+    """Solvated capped Arginine ChemicalSystem"""
+    return ChemicalSystem({"protein": arg_capped, "solvent": solvent_comp})
+
+
+@pytest.fixture(scope="session")
+def lys_capped_system(lys_capped, solvent_comp):
+    """Solvated capped Lysine ChemicalSystem"""
+    return ChemicalSystem({"protein": lys_capped, "solvent": solvent_comp})
 
+
+@pytest.fixture(scope="session")
+def ala_to_gly_mapping():
+    """Mapping from ALA to GLY (capped)"""
     input_file = str(
         files("feflow.tests.data.capped_AAs").joinpath("ala_to_gly_mapping.json")
     )
     with open(input_file) as in_file:
-        mapping = LigandAtomMapping.from_dict(json.load(in_file))
+        mapping = LigandAtomMapping.from_dict(
+            json.load(in_file, cls=JSON_HANDLER.decoder)
+        )
+    return mapping
+
+
+@pytest.fixture(scope="session")
+def gly_to_ala_mapping(ala_capped, gly_capped, ala_to_gly_mapping):
+    """GLY to ALA mapping. Inverts the ala_to_gly_mapping fixture."""
+    gly_to_ala_map = ala_to_gly_mapping.componentB_to_componentA
+    mapping = LigandAtomMapping(
+        componentA=gly_capped,
+        componentB=ala_capped,
+        componentA_to_componentB=gly_to_ala_map,
+    )
+    return mapping
+
+
+@pytest.fixture(scope="session")
+def ala_to_arg_mapping():
+    """Mapping from ALA to ARG (capped). Positive charge transformation."""
+    input_file = str(
+        files("feflow.tests.data.capped_AAs").joinpath("ala_to_arg_mapping.json")
+    )
+    with open(input_file) as in_file:
+        mapping = LigandAtomMapping.from_dict(
+            json.load(in_file, cls=JSON_HANDLER.decoder)
+        )
+    return mapping
+
+
+@pytest.fixture(scope="session")
+def arg_to_ala_mapping(ala_capped, arg_capped, ala_to_arg_mapping):
+    """ARG to ALA mapping. Inverts the ala_to_arg_mapping fixture."""
+    arg_to_ala_map = ala_to_arg_mapping.componentB_to_componentA
+    mapping = LigandAtomMapping(
+        componentA=arg_capped,
+        componentB=ala_capped,
+        componentA_to_componentB=arg_to_ala_map,
+    )
+    return mapping
+
+
+@pytest.fixture(scope="session")
+def ala_to_lys_mapping():
+    """Mapping from ALA to LYS (capped)."""
+    input_file = str(
+        files("feflow.tests.data.capped_AAs").joinpath("ala_to_lys_mapping.json")
+    )
+    with open(input_file) as in_file:
+        mapping = LigandAtomMapping.from_dict(
+            json.load(in_file, cls=JSON_HANDLER.decoder)
+        )
+    return mapping
+
+
+@pytest.fixture(scope="session")
+def lys_to_ala_mapping(ala_capped, lys_capped, ala_to_lys_mapping):
+    """GLY to ALA mapping. Inverts the ala_to_gly_mapping fixture."""
+    lys_to_ala_map = ala_to_lys_mapping.componentB_to_componentA
+    mapping = LigandAtomMapping(
+        componentA=lys_capped,
+        componentB=ala_capped,
+        componentA_to_componentB=lys_to_ala_map,
+    )
     return mapping
 
 
@@ -91,7 +185,9 @@ def asp_to_leu_mapping(asp_capped, leu_capped):
         files("feflow.tests.data.capped_AAs").joinpath("asp_to_leu_mapping.json")
     )
     with open(input_file) as in_file:
-        mapping = LigandAtomMapping.from_dict(json.load(in_file))
+        mapping = LigandAtomMapping.from_dict(
+            json.load(in_file, cls=JSON_HANDLER.decoder)
+        )
     return mapping
 
 
@@ -100,8 +196,8 @@ class TestProtocolMutation:
     def short_settings_protein_mutation(self):
         settings = ProteinMutationProtocol.default_settings()
 
-        settings.integrator_settings.equlibrium_steps = 1000
-        settings.integrator_settings.nonequlibrium_steps = 1000
+        settings.integrator_settings.equilibrium_steps = 1000
+        settings.integrator_settings.nonequilibrium_steps = 1000
         settings.work_save_frequency = 50
         settings.traj_save_frequency = 250
         settings.num_cycles = 5
@@ -122,6 +218,7 @@ def protocol_ala_to_gly_result(
         ala_to_gly_mapping,
         tmpdir,
     ):
+        """Short protocol execution for capped ALA to GLY mutation"""
         dag = protocol_short.create(
             stateA=ala_capped_system,
             stateB=gly_capped_system,
@@ -151,11 +248,12 @@ def protocol_asp_to_leu_result(
         asp_to_leu_mapping,
         tmpdir,
     ):
+        """Short protocol execution for charge-changing mutation of capped ASP to LEU."""
         dag = protocol_short.create(
-            stateA=ala_capped_system,
-            stateB=gly_capped_system,
+            stateA=asp_capped_system,
+            stateB=leu_capped_system,
             name="Short vacuum transformation",
-            mapping=ala_to_gly_mapping,
+            mapping=asp_to_leu_mapping,
         )
 
         with tmpdir.as_cwd():
@@ -171,6 +269,89 @@ def protocol_asp_to_leu_result(
 
         return protocol_short, dag, dagresult
 
+    def execute_forward_reverse_dag(
+        self, component_a, component_b, system_a, system_b, mapping_obj, tmpdir
+    ):
+        """
+        Perform a forward and reverse free energy (FE) estimation between two protein mutation systems.
+
+        This function creates and executes forward and reverse directed acyclic graphs (DAGs) for
+        computing the free energy difference between two protein systems, typically involving
+        a mutation (e.g., Arginine to Alanine). It calculates the forward and reverse free energy
+        estimates, and checks that their sum is close to zero (indicating a consistent reversible
+        transformation).
+
+        Parameters
+        ----------
+        component_a: ProteinComponent
+        component_b: ProteinComponent
+        system_a: ChemicalSystem
+        system_b: ChemicalSystem
+        mapping_obj: LigandAtomMapping
+        tmpdir
+
+        Returns
+        -------
+        dict
+            A dictionary containing FE estimates and uncertainties for both forward and reverse
+            transformations:
+            `{"forward": (forward_fe, forward_error), "reverse": (reverse_fe, reverse_error)}`.
+        """
+        settings = ProteinMutationProtocol.default_settings()
+        protocol = ProteinMutationProtocol(settings=settings)
+
+        forward_dag = protocol.create(
+            stateA=system_a,
+            stateB=system_b,
+            name="Short vacuum transformation",
+            mapping=mapping_obj,
+        )
+        # Reverse mapping
+        arg_to_ala_dict = mapping_obj.componentB_to_componentA
+        arg_to_ala_mapping = LigandAtomMapping(
+            componentA=component_b,
+            componentB=component_a,
+            componentA_to_componentB=arg_to_ala_dict,
+        )
+        reverse_dag = protocol.create(
+            stateA=system_b,
+            stateB=system_a,
+            name="Short vacuum transformation",
+            mapping=arg_to_ala_mapping,
+        )
+
+        # Execute DAGs
+        with tmpdir.as_cwd():
+            shared = Path("shared")
+            shared.mkdir()
+
+            scratch = Path("scratch")
+            scratch.mkdir()
+
+            forward_dagresult: ProtocolDAGResult = execute_DAG(
+                forward_dag, shared_basedir=shared, scratch_basedir=scratch
+            )
+            reverse_dagresult: ProtocolDAGResult = execute_DAG(
+                reverse_dag, shared_basedir=shared, scratch_basedir=scratch
+            )
+
+        # Verify DAGs were executed correctly
+        assert forward_dagresult.ok()
+        assert reverse_dagresult.ok()
+
+        # Get FE estimate
+        forward_fe = forward_dagresult.get_estimate()
+        forward_error = forward_dagresult.get_uncertainty()
+        reverse_fe = reverse_dagresult.get_estimate()
+        reverse_error = reverse_dagresult.get_uncertainty()
+
+        data_obj = {
+            "forward": (forward_fe, forward_error),
+            "reverse": (reverse_fe, reverse_error),
+        }
+
+        return data_obj
+
     def test_ala_to_gly_execute(self, protocol_ala_to_gly_result):
         """Takes a protocol result from an executed DAG and checks the OK status
         as well as the name of the resulting unit."""
@@ -192,3 +373,106 @@ def test_asp_to_leu_execute(self, protocol_asp_to_leu_result):
         # the FinishUnit will always be the last to execute
         finishresult = dagresult.protocol_unit_results[-1]
         assert finishresult.name == "result"
+
+    @pytest.mark.slow
+    def test_ala_gly_convergence(
+        self,
+        ala_capped,
+        gly_capped,
+        ala_capped_system,
+        gly_capped_system,
+        ala_to_gly_mapping,
+        gly_to_ala_mapping,
+        tmpdir,
+    ):
+        """Convergence test for ALA to GLY forward and reverse neutral protein mutation protocol
+        execution with default (production-ready) settings. Runs ALA to GLY and compares the
+        FE estimate with running GLY to ALA."""
+
+        results = self.execute_forward_reverse_dag(
+            ala_capped,
+            gly_capped,
+            ala_capped_system,
+            gly_capped_system,
+            ala_to_gly_mapping,
+            tmpdir,
+        )
+
+        # they should add up to close to zero
+        forward_reverse_sum = abs(results["forward"][0] + results["reverse"][0])
+        forward_reverse_sum_err = np.sqrt(
+            results["forward"][1] ** 2 + results["reverse"][1] ** 2
+        )
+        print(
+            f"DDG: {forward_reverse_sum}, 6*dDDG: {6 * forward_reverse_sum_err}"
+        )  # DEBUG
+        assert forward_reverse_sum < 6 * forward_reverse_sum_err, (
+            f"DDG ({forward_reverse_sum}) is greater than "
+            f"6 * dDDG ({6 * forward_reverse_sum_err})"
+        )
+
+    @pytest.mark.slow
+    def test_charge_changing_convergence(
+        self,
+        arg_capped,
+        ala_capped,
+        lys_capped,
+        ala_capped_system,
+        arg_capped_system,
+        lys_capped_system,
+        arg_to_ala_mapping,
+        lys_to_ala_mapping,
+        tmpdir,
+    ):
+        """
+        Test for charge changing transformation for the protein mutation protocol.
+
+        We perform two forward and reverse and check the mutual convergence.
+            Positive: ARG -> ALA -> ARG
+            Negative: LYS -> ALA -> LYS
+
+        The need to do it this way is because since we are introducing counterions the energies for
+        each will not match, therefore to cancel this contribution we compare between both positive
+        and negative full cycles.
+        """
+        # Create and execute DAGs
+        arg_results = self.execute_forward_reverse_dag(
+            arg_capped,
+            ala_capped,
+            arg_capped_system,
+            ala_capped_system,
+            arg_to_ala_mapping,
+            tmpdir,
+        )
+        lys_results = self.execute_forward_reverse_dag(
+            lys_capped,
+            ala_capped,
+            lys_capped_system,
+            ala_capped_system,
+            lys_to_ala_mapping,
+            tmpdir,
+        )
+
+        # they should add up to close to zero
+        arg_forward_reverse_sum = arg_results["forward"][0] + arg_results["reverse"][0]
+        arg_forward_reverse_sum_error = (
+            arg_results["forward"][1] ** 2 + arg_results["reverse"][1] ** 2
+        )
+        lys_forward_reverse_sum = lys_results["forward"][0] + lys_results["reverse"][0]
+        lys_forward_reverse_sum_error = (
+            lys_results["forward"][1] ** 2 + lys_results["reverse"][1] ** 2
+        )
+
+        # FE estimates are the first element, errors are the second element in the tuple
+        arg_lys_diff = abs(arg_forward_reverse_sum - lys_forward_reverse_sum)
+        arg_lys_diff_error = np.sqrt(
+            arg_forward_reverse_sum_error + lys_forward_reverse_sum_error
+        )
+
+        print(
+            f"DDG: {arg_lys_diff}, 6*dDDG: {6 * arg_lys_diff_error}"
+        )  # debug control print
+        assert arg_lys_diff < 6 * arg_lys_diff_error, (
+            f"DDG ({arg_lys_diff}) is greater than "
+            f"6 * dDDG ({6 * arg_lys_diff_error})"
+        )