Change openff output for PELE

martimunicoy · Nov 23, 2020 · d17de67 · d17de67
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diff --git a/peleffy/data/tests/MET_parameters_to_string.txt b/peleffy/data/tests/MET_parameters_to_string.txt
@@ -1 +1,82 @@
-{'atom_names': ['_C1_', '_H1_', '_H2_', '_H3_', '_H4_'], 'atom_types': ['OFFT', 'OFFT', 'OFFT', 'OFFT', 'OFFT'], 'charges': '[-0.077576, 0.019394, 0.019394, 0.019394, 0.019394] * elementary_charge', 'sigmas': ['3.3996695084235347 * angstrom', '2.649532787749369 * angstrom', '2.649532787749369 * angstrom', '2.649532787749369 * angstrom', '2.649532787749369 * angstrom'], 'epsilons': ['0.1094 * mole**-1 * kilocalorie', '0.0157 * mole**-1 * kilocalorie', '0.0157 * mole**-1 * kilocalorie', '0.0157 * mole**-1 * kilocalorie', '0.0157 * mole**-1 * kilocalorie'], 'SGB_radii': [None, None, None, None, None], 'vdW_radii': ['1.6998347542117673 * angstrom', '1.3247663938746845 * angstrom', '1.3247663938746845 * angstrom', '1.3247663938746845 * angstrom', '1.3247663938746845 * angstrom'], 'gammas': [None, None, None, None, None], 'alphas': [None, None, None, None, None], 'GBSA_radii': [], 'GBSA_scales': [], 'bonds': [{'atom1_idx': 0, 'atom2_idx': 1, 'spring_constant': '376.8940758588 * angstrom**-2 * mole**-1 * kilocalorie', 'eq_dist': '1.094223427522 * angstrom'}, {'atom1_idx': 0, 'atom2_idx': 2, 'spring_constant': '376.8940758588 * angstrom**-2 * mole**-1 * kilocalorie', 'eq_dist': '1.094223427522 * angstrom'}, {'atom1_idx': 0, 'atom2_idx': 3, 'spring_constant': '376.8940758588 * angstrom**-2 * mole**-1 * kilocalorie', 'eq_dist': '1.094223427522 * angstrom'}, {'atom1_idx': 0, 'atom2_idx': 4, 'spring_constant': '376.8940758588 * angstrom**-2 * mole**-1 * kilocalorie', 'eq_dist': '1.094223427522 * angstrom'}], 'angles': [{'atom1_idx': 1, 'atom2_idx': 0, 'atom3_idx': 2, 'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * kilocalorie', 'eq_angle': '110.2468561538 * degree'}, {'atom1_idx': 1, 'atom2_idx': 0, 'atom3_idx': 3, 'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * kilocalorie', 'eq_angle': '110.2468561538 * degree'}, {'atom1_idx': 1, 'atom2_idx': 0, 'atom3_idx': 4, 'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * kilocalorie', 'eq_angle': '110.2468561538 * degree'}, {'atom1_idx': 2, 'atom2_idx': 0, 'atom3_idx': 3, 'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * kilocalorie', 'eq_angle': '110.2468561538 * degree'}, {'atom1_idx': 2, 'atom2_idx': 0, 'atom3_idx': 4, 'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * kilocalorie', 'eq_angle': '110.2468561538 * degree'}, {'atom1_idx': 3, 'atom2_idx': 0, 'atom3_idx': 4, 'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * kilocalorie', 'eq_angle': '110.2468561538 * degree'}], 'propers': [], 'impropers': []}
+{'GBSA_radii': [],
+ 'GBSA_scales': [],
+ 'SGB_radii': [None, None, None, None, None],
+ 'alphas': [None, None, None, None, None],
+ 'angles': [{'atom1_idx': 1,
+             'atom2_idx': 0,
+             'atom3_idx': 2,
+             'eq_angle': '110.2468561538 * degree',
+             'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * '
+                                'kilocalorie'},
+            {'atom1_idx': 1,
+             'atom2_idx': 0,
+             'atom3_idx': 3,
+             'eq_angle': '110.2468561538 * degree',
+             'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * '
+                                'kilocalorie'},
+            {'atom1_idx': 1,
+             'atom2_idx': 0,
+             'atom3_idx': 4,
+             'eq_angle': '110.2468561538 * degree',
+             'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * '
+                                'kilocalorie'},
+            {'atom1_idx': 2,
+             'atom2_idx': 0,
+             'atom3_idx': 3,
+             'eq_angle': '110.2468561538 * degree',
+             'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * '
+                                'kilocalorie'},
+            {'atom1_idx': 2,
+             'atom2_idx': 0,
+             'atom3_idx': 4,
+             'eq_angle': '110.2468561538 * degree',
+             'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * '
+                                'kilocalorie'},
+            {'atom1_idx': 3,
+             'atom2_idx': 0,
+             'atom3_idx': 4,
+             'eq_angle': '110.2468561538 * degree',
+             'spring_constant': '33.78875634641 * mole**-1 * radian**-2 * '
+                                'kilocalorie'}],
+ 'atom_names': ['_C1_', '_H1_', '_H2_', '_H3_', '_H4_'],
+ 'atom_types': ['OFFT', 'OFFT', 'OFFT', 'OFFT', 'OFFT'],
+ 'bonds': [{'atom1_idx': 0,
+            'atom2_idx': 1,
+            'eq_dist': '1.094223427522 * angstrom',
+            'spring_constant': '376.8940758588 * angstrom**-2 * mole**-1 * '
+                               'kilocalorie'},
+           {'atom1_idx': 0,
+            'atom2_idx': 2,
+            'eq_dist': '1.094223427522 * angstrom',
+            'spring_constant': '376.8940758588 * angstrom**-2 * mole**-1 * '
+                               'kilocalorie'},
+           {'atom1_idx': 0,
+            'atom2_idx': 3,
+            'eq_dist': '1.094223427522 * angstrom',
+            'spring_constant': '376.8940758588 * angstrom**-2 * mole**-1 * '
+                               'kilocalorie'},
+           {'atom1_idx': 0,
+            'atom2_idx': 4,
+            'eq_dist': '1.094223427522 * angstrom',
+            'spring_constant': '376.8940758588 * angstrom**-2 * mole**-1 * '
+                               'kilocalorie'}],
+ 'charges': '[-0.077576, 0.019394, 0.019394, 0.019394, 0.019394] * '
+            'elementary_charge',
+ 'epsilons': ['0.1094 * mole**-1 * kilocalorie',
+              '0.0157 * mole**-1 * kilocalorie',
+              '0.0157 * mole**-1 * kilocalorie',
+              '0.0157 * mole**-1 * kilocalorie',
+              '0.0157 * mole**-1 * kilocalorie'],
+ 'gammas': [None, None, None, None, None],
+ 'impropers': [],
+ 'propers': [],
+ 'sigmas': ['3.3996695084235347 * angstrom',
+            '2.649532787749369 * angstrom',
+            '2.649532787749369 * angstrom',
+            '2.649532787749369 * angstrom',
+            '2.649532787749369 * angstrom'],
+ 'vdW_radii': ['1.6998347542117673 * angstrom',
+               '1.3247663938746845 * angstrom',
+               '1.3247663938746845 * angstrom',
+               '1.3247663938746845 * angstrom',
+               '1.3247663938746845 * angstrom']}
diff --git a/peleffy/forcefield/forcefield.py b/peleffy/forcefield/forcefield.py
@@ -404,7 +404,9 @@ def _get_parameters(self, molecule):
 
         openff_parameters = self._openff.parameterize(molecule,
                                                       charge_method='dummy')
+        print(openff_parameters['sigmas'])
         oplsff_parameters = self._oplsff.parameterize(molecule)
+        print(oplsff_parameters['sigmas'])
 
         if self._nonbonding == 'openff':
             hybrid_parameters['atom_names'] = openff_parameters['atom_names']

diff --git a/peleffy/forcefield/parameters.py b/peleffy/forcefield/parameters.py
@@ -77,8 +77,6 @@ def __eq__(self, other):
         if not isinstance(other, BaseParameterWrapper):
             return False
 
-        print(self.forcefield_name, other.forcefield_name)
-
         return super().__eq__(other) and \
             self.forcefield_name == other.forcefield_name
 

diff --git a/peleffy/tests/test_parameters.py b/peleffy/tests/test_parameters.py
@@ -115,8 +115,18 @@ def test_to_string(self):
         with open(ref_string_file) as f:
             ref_string = f.read().strip('\n')
 
-        assert str(p_string) == str(ref_string), \
-            'Unexpected string representation of the parameter wrapper'
+        p_lines = p_string.split('\n')
+        ref_lines = ref_string.split('\n')
+
+        assert len(p_lines) == len(ref_lines), \
+            'Unexpected number of lines: ' \
+            + str(len(p_lines)) + ', expected ' + str(len(ref_lines))
+
+        for p_line, ref_line in zip(p_lines, ref_lines):
+            assert p_line == ref_line, \
+                'Unexpected string representation found in line: ' \
+                + '\'{}\' '.format(p_line) \
+                + 'which does not match with \'{}\''.format(ref_line)
 
     def test_to_json(self):
         """It tests the json representation of the parameter wrapper."""

diff --git a/peleffy/tests/test_utils.py b/peleffy/tests/test_utils.py
@@ -235,7 +235,7 @@ def test_datalocal_paths_for_openff(self):
             + '{}.rot.assign'.format(tag.upper()), \
             'Unexpected default rotamer library path'
         assert output_handler.get_impact_template_path() == \
-            './DataLocal/Templates/OFF/Parsley/HeteroAtoms/' \
+            './DataLocal/Templates/OpenFF/Parsley/' \
             + '{}z'.format(tag.lower()), \
             'Unexpected default Impact template path'
         assert output_handler.get_solvent_template_path() == \
@@ -253,8 +253,8 @@ def test_datalocal_paths_for_openff(self):
                              + '{}.rot.assign'.format(tag.upper())), \
                 'Unexpected default rotamer library path'
             assert output_handler.get_impact_template_path() == \
-                os.path.join(tmpdir, 'output', 'DataLocal/Templates/OFF/Pars'
-                             + 'ley/HeteroAtoms/{}z'.format(tag.lower())), \
+                os.path.join(tmpdir, 'output', 'DataLocal/Templates/'
+                             + 'OpenFF/Parsley/{}z'.format(tag.lower())), \
                 'Unexpected default Impact template path'
             assert output_handler.get_solvent_template_path() == \
                 os.path.join(tmpdir, 'output',
@@ -340,7 +340,7 @@ def test_datalocal_paths_for_offopls(self):
             + '{}.rot.assign'.format(tag.upper()), \
             'Unexpected default rotamer library path'
         assert output_handler.get_impact_template_path() == \
-            './DataLocal/Templates/OFF/Parsley/HeteroAtoms/' \
+            './DataLocal/Templates/OpenFF/Parsley/' \
             + '{}z'.format(tag.lower()), \
             'Unexpected default Impact template path'
         assert output_handler.get_solvent_template_path() == \
@@ -358,8 +358,8 @@ def test_datalocal_paths_for_offopls(self):
                              + '{}.rot.assign'.format(tag.upper())), \
                 'Unexpected default rotamer library path'
             assert output_handler.get_impact_template_path() == \
-                os.path.join(tmpdir, 'output', 'DataLocal/Templates/OFF/Pars'
-                             + 'ley/HeteroAtoms/{}z'.format(tag.lower())), \
+                os.path.join(tmpdir, 'output', 'DataLocal/Templates/'
+                             + 'OpenFF/Parsley/{}z'.format(tag.lower())), \
                 'Unexpected default Impact template path'
             assert output_handler.get_solvent_template_path() == \
                 os.path.join(tmpdir, 'output',

diff --git a/peleffy/tests/utils.py b/peleffy/tests/utils.py
@@ -309,6 +309,8 @@ def parameterize_openffopls2005(openffopls2005, molecule, ffld_file):
     # Set mock class to the OpenFFOPLS2005ForceField class
     openffopls2005._oplsff = oplsff
 
+    print(parameters['sigmas'])
+
     return openffopls2005.parameterize(molecule)
 
 

diff --git a/peleffy/utils/output.py b/peleffy/utils/output.py
@@ -14,7 +14,7 @@ class OutputPathHandler(object):
     It handles the output paths of peleffy parameter files.
     """
 
-    OFF_IMPACT_TEMPLATE_PATH = 'DataLocal/Templates/OFF/Parsley/HeteroAtoms/'
+    OFF_IMPACT_TEMPLATE_PATH = 'DataLocal/Templates/OpenFF/Parsley/'
     OPLS_IMPACT_TEMPLATE_PATH = 'DataLocal/Templates/OPLS2005/HeteroAtoms/'
     ROTAMER_LIBRARY_PATH = 'DataLocal/LigandRotamerLibs/'
     SOLVENT_TEMPLATE_PATH = 'DataLocal/OBC/'