Merge branch 'devel' into OBC_for_OPLS

docs/releasehistory.rst

@@ -17,12 +17,14 @@ New features
 - `PR #88 <https://github.com/martimunicoy/peleffy/pull/88>`_: New method to retrieve atom degrees with RDKit.
 - `PR #86 <https://github.com/martimunicoy/peleffy/pull/86>`_: New method to check the input PDB prior building the molecule.
 - `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: New method for the OPLS OBC parameters.
+- `PR #92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New parameter to skip the stereochemistry assignment (and the checking from the OpenFF toolkit).
 
 Tests added
 """""""""""
 - `PR #88 <https://github.com/martimunicoy/peleffy/pull/88>`_: Adds tests to validate the atom degrees getter.
 - `PR #86 <https://github.com/martimunicoy/peleffy/pull/86>`_: Adds tests to validate the PDB check up.
 - `PR #94 <https://github.com/martimunicoy/peleffy/pull/94>`_: Adds tests to validate the OPLS OBC parameters generator.
+- `PR #92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New test to check the behaviour of the allow_undefined_stereo parameter.
 
 
 1.0.0 - Full compatibility for OPLS2005 and OpenFF dihedrals and rotamer library improvements

peleffy/forcefield/parameters.py

@@ -184,6 +184,27 @@ def name(self):
         """
         return self._name
 
+    @staticmethod
+    def from_impact_template(molecule, impact_template_path):
+        """
+        It returns a parameter wrapper out of an impact template.
+
+        Parameters
+        ----------
+        molecule : a peleffy.topology.Molecule
+            The peleffy's Molecule object
+        impact_template_path : str
+            The path to the impact template from where the parameters
+            will be fetched
+
+        Returns
+        -------
+        parameters : a BaseParameterWrapper object
+            The resulting parameters wrapper
+        """
+
+        raise NotImplementedError()
+
 
 class OpenForceFieldParameterWrapper(BaseParameterWrapper):
     """

peleffy/tests/test_molecule.py

@@ -287,3 +287,27 @@ def test_PDB_checkup(self):
             assert output == "Input PDB has no information about the " \
                 + "connectivity and this could result in an unexpected " \
                 + "bond assignment\n"
+
+    def test_undefined_stereo(self):
+        """
+        It checks the behaviour when ignoring the stereochemistry
+        in the Molecule initialization.
+        """
+        from openforcefield.utils.toolkits import UndefinedStereochemistryError
+
+        # This should crash due to an undefined stereochemistry error
+        with pytest.raises(UndefinedStereochemistryError):
+            mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3')
+
+        # This now should work
+        mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3',
+                       allow_undefined_stereo=True)
+
+        # And we can parameterize it
+        mol.parameterize('openff_unconstrained-1.2.1.offxml',
+                         charge_method='gasteiger')
+
+        # Save it
+        with tempfile.TemporaryDirectory() as tmpdir:
+            with temporary_cd(tmpdir):
+                mol.to_pdb_file('molecule.pdb')

peleffy/topology/molecule.py

@@ -448,7 +448,8 @@ class Molecule(object):
 
     def __init__(self, path=None, smiles=None, rotamer_resolution=30,
                  exclude_terminal_rotamers=True, name='', tag='UNK',
-                 connectivity_template=None, core_constraints=[]):
+                 connectivity_template=None, core_constraints=[],
+                 allow_undefined_stereo=False):
         """
         It initializes a Molecule object through a PDB file or a SMILES
         tag.
@@ -477,6 +478,10 @@ def __init__(self, path=None, smiles=None, rotamer_resolution=30,
             the core will be forced to contain them. Atoms can be specified
             through integers that match the atom index or strings that
             match with the atom PDB name
+        allow_undefined_stereo : bool
+            Whether to allow a molecule with undefined stereochemistry
+            to be defined or try to assign the stereochemistry and
+            raise a complaint if not possible. Default is False
 
         Examples
         --------
@@ -535,6 +540,7 @@ def __init__(self, path=None, smiles=None, rotamer_resolution=30,
         self._exclude_terminal_rotamers = exclude_terminal_rotamers
         self._connectivity_template = connectivity_template
         self._core_constraints = core_constraints
+        self._allow_undefined_stereo = allow_undefined_stereo
 
         if isinstance(path, str):
             from pathlib import Path
@@ -636,9 +642,10 @@ def _initialize_from_pdb(self, path):
             logger.info('   - Assigning connectivity from template')
             rdkit_toolkit.assign_connectivity_from_template(self)
 
-        # RDKit must generate stereochemistry specifically from 3D coords
-        logger.info('   - Assigning stereochemistry from 3D coordinates')
-        rdkit_toolkit.assign_stereochemistry_from_3D(self)
+        if not self.allow_undefined_stereo:
+            # RDKit must generate stereochemistry specifically from 3D coords
+            logger.info('   - Assigning stereochemistry from 3D coordinates')
+            rdkit_toolkit.assign_stereochemistry_from_3D(self)
 
         # Set molecule name according to PDB name
         if self.name == '':
@@ -1202,6 +1209,21 @@ def connectivity_template(self):
         """
         return self._connectivity_template
 
+    @property
+    def allow_undefined_stereo(self):
+        """
+        Whether to allow a molecule with undefined stereochemistry
+        to be defined or try to assign the stereochemistry and
+        raise a complaint if not possible
+
+        Returns
+        -------
+        allow_undefined_stereo : bool
+            The current configuration towards the stereochemistry
+            behaviour of this molecule
+        """
+        return self._allow_undefined_stereo
+
     @property
     def core_constraints(self):
         """

peleffy/utils/output.py

@@ -116,6 +116,12 @@ def get_impact_template_path(self, create_missing_folders=True):
                 else:
                     path = os.path.join(self.output_path,
                                         self.OPLS_IMPACT_TEMPLATE_PATH)
+            else:
+                raise Exception('DataLocal output path for the impact '
+                                + 'template cannot be inferred because '
+                                + 'the forcefield for molecule '
+                                + '\'{}\' '.format(self.molecule)
+                                + 'has not been set yet')
         else:
             path = self.output_path
 

peleffy/utils/toolkits.py

@@ -649,7 +649,9 @@ def from_rdkit(self, molecule):
         from openforcefield.topology.molecule import Molecule
 
         rdkit_molecule = molecule.rdkit_molecule
-        return Molecule.from_rdkit(rdkit_molecule)
+        return Molecule.from_rdkit(
+            rdkit_molecule,
+            allow_undefined_stereo=molecule.allow_undefined_stereo)
 
     def get_forcefield(self, forcefield_name):
         """