Merge pull request #176 from martimunicoy/mulliken

Mulliken charge selector
martimunicoy · May 8, 2023 · 0de7dba · 0de7dba
2 parents 6ab135c + c1ebecf
commit 0de7dba
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Showing 5 changed files with 36 additions and 5 deletions.
diff --git a/peleffy/forcefield/calculators.py b/peleffy/forcefield/calculators.py
@@ -92,6 +92,14 @@ class GasteigerCalculator(_PartialChargeCalculator):
 
     _name = 'gasteiger'
 
+class MullikenCalculator(_PartialChargeCalculator):
+    """
+    Implementation of the Mulliken partial charge calculator (using
+    RDKit).
+    """
+
+    _name = 'mulliken'
+
 
 class OPLSChargeCalculator(_PartialChargeCalculator):
     """

diff --git a/peleffy/forcefield/selectors.py b/peleffy/forcefield/selectors.py
@@ -92,12 +92,14 @@ class ChargeCalculatorSelector(object):
     from peleffy.forcefield.calculators import (OPLSChargeCalculator,
                                                 Am1bccCalculator,
                                                 GasteigerCalculator,
-                                                DummyChargeCalculator)
+                                                DummyChargeCalculator,
+                                                MullikenCalculator)
 
     _AVAILABLE_TYPES = {'opls2005': OPLSChargeCalculator,
                         'am1bcc': Am1bccCalculator,
                         'gasteiger': GasteigerCalculator,
-                        'dummy': DummyChargeCalculator
+                        'dummy': DummyChargeCalculator,
+                        'mulliken': MullikenCalculator
                         }
 
     def get_by_name(self, charge_method, molecule):

diff --git a/peleffy/tests/test_forcefields.py b/peleffy/tests/test_forcefields.py
@@ -58,7 +58,7 @@ def test_charge_calculator_selector(self):
             peleffy.forcefield.calculators.GasteigerCalculator), \
             'Invalid custom selection 1 for the charge calculator'
 
-        # Check custom selection 1
+        # Check custom selection 2
         openff = OpenForceField(self.FORCE_FIELD_NAME)
         calculator = openff._get_charge_calculator('opls2005', dummy_mol)
 
@@ -67,6 +67,12 @@ def test_charge_calculator_selector(self):
             peleffy.forcefield.calculators.OPLSChargeCalculator), \
             'Invalid custom selection 2 for the charge calculator'
 
+        # Check custom selection 3
+        openff = OpenForceField(self.FORCE_FIELD_NAME)
+        calculator = openff._get_charge_calculator('mulliken', dummy_mol)
+        assert isinstance(calculator, peleffy.forcefield.calculators.MullikenCalculator), \
+            "Invalid custom selection 3 for the charge calculator"
+
     def test_parameterizer(self):
         """It checks the parameterized method."""
 

diff --git a/peleffy/tests/test_parameters.py b/peleffy/tests/test_parameters.py
@@ -922,6 +922,20 @@ def test_gasteiger_method(self):
         # Check charges
         check_CHO_charges(parameters)
 
+    def test_mulliken_method(self):
+        """It tests the mulliken method"""
+        ligand_path = get_data_file_path(self.LIGAND_PATH)
+
+        # Load molecule
+        molecule = Molecule(ligand_path)
+
+        # Parameterize
+        ff = OpenForceField(FORCEFIELD_NAME)
+        parameters = ff.parameterize(molecule, charge_method='mulliken')
+
+        # Check charges
+        check_CHO_charges(parameters)
+
     def test_OPLS_method(self):
         """It tests the OPLS method"""
 

diff --git a/peleffy/utils/toolkits.py b/peleffy/utils/toolkits.py
@@ -1010,7 +1010,7 @@ def compute_partial_charges(self, molecule, method='am1bcc'):
         molecule : an peleffy.topology.Molecule
             The peleffy's Molecule object
         method : str
-            The name of the method to use. One of ['gasteiger', 'am1bcc'].
+            The name of the method to use. One of ['gasteiger', 'am1bcc', 'mulliken'].
             If None, 'am1bcc' will be used
 
         Returns
@@ -1027,7 +1027,8 @@ def compute_partial_charges(self, molecule, method='am1bcc'):
         """
 
         SUPPORTED_CHARGE_METHODS = {'am1bcc': {'antechamber_keyword': 'bcc'},
-                                    'gasteiger': {'antechamber_keyword': 'gas'}
+                                    'gasteiger': {'antechamber_keyword': 'gas'},
+                                    'mulliken': {'antechamber_keyword': 'mul'}
                                     }
 
         if method not in SUPPORTED_CHARGE_METHODS: