Merge pull request #52 from martimunicoy/pdb_connectivity

Pdb connectivity

docs/releasehistory.rst

@@ -16,11 +16,12 @@ This is a micro release that includes general bug fixes and stability improvemen
 Bugfixes
 """"""""
 - `PR #48 <https://github.com/martimunicoy/offpele/pull/48>`_: Fixes CLI's default output paths.
+- `PR #52 <https://github.com/martimunicoy/offpele/pull/52>`_: Molecule connectivity can be assigned from an RDKit molecular template when loading it from a PDB file without connectivity.
 
 Tests added
 """""""""""
 - `PR #48 <https://github.com/martimunicoy/offpele/pull/48>`_: Adds tests to validate the assignment of the default output paths.
-
+- `PR #52 <https://github.com/martimunicoy/offpele/pull/52>`_: Adds tests to validate the initialization using a connectivity template.
 
 0.3.0 - Rotamers, OPLS2005, SMILES and stability improvements
 -------------------------------------------------------------

offpele/tests/test_molecule.py

@@ -111,3 +111,72 @@ def test_molecule_tag_assignment(self):
         # a custom tag
         molecule = Molecule(smiles='c1ccccc1', tag='BNZ')
         assert molecule.tag == 'BNZ', 'Unexpected atom tag'
+
+    def test_PDB_connectivity_template(self):
+        """
+        It tests the initialization of an offpele's Molecule representation
+        from a PDB file without connectivity and a connectivity template.
+        """
+        # Initialize an empty Molecule object
+        molecule = Molecule()
+        assert molecule.connectivity_template is None, \
+            'Unexpected connectivity template'
+
+        # Initialize a Molecule from a PDB without connectivity and
+        # without a connectivity template
+        ligand_path = get_data_file_path(
+            'ligands/BNZ_without_connectivity.pdb')
+        molecule = Molecule(ligand_path)
+
+        expected_bond_ids = [(1, 0, False), (2, 1, False), (3, 2, False),
+                             (4, 3, False), (5, 4, False), (5, 0, False),
+                             (6, 0, False), (7, 1, False), (8, 2, False),
+                             (9, 3, False), (10, 4, False), (11, 5, False)]
+
+        for bond in molecule.rdkit_molecule.GetBonds():
+            bond_id = (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(),
+                       bond.GetIsAromatic())
+            assert bond_id in expected_bond_ids, 'Unexpected bond id ' \
+                + '{}'.format(bond_id)
+
+        # Initialize a Molecule from a PDB without connectivity but with
+        # a connectivity template
+        template_path = get_data_file_path(
+            'ligands/BNZ.pdb')
+        template = Molecule(template_path)
+        ligand_path = get_data_file_path(
+            'ligands/BNZ_without_connectivity.pdb')
+        molecule = Molecule(ligand_path,
+                            connectivity_template=template.rdkit_molecule)
+
+        expected_bond_ids = [(1, 0, True), (2, 1, True), (3, 2, True),
+                             (4, 3, True), (5, 4, True), (5, 0, True),
+                             (6, 0, False), (7, 1, False), (8, 2, False),
+                             (9, 3, False), (10, 4, False), (11, 5, False)]
+
+        for bond in molecule.rdkit_molecule.GetBonds():
+            bond_id = (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(),
+                       bond.GetIsAromatic())
+            assert bond_id in expected_bond_ids, 'Unexpected bond id ' \
+                + '{}'.format(bond_id)
+
+        # Initialize a Molecule from a PDB with connectivity and with
+        # a connectivity template
+        template_path = get_data_file_path(
+            'ligands/BNZ.pdb')
+        template = Molecule(template_path)
+        ligand_path = get_data_file_path(
+            'ligands/BNZ.pdb')
+        molecule = Molecule(ligand_path,
+                            connectivity_template=template.rdkit_molecule)
+
+        expected_bond_ids = [(0, 1, True), (1, 2, True), (2, 3, True),
+                             (3, 4, True), (4, 5, True), (0, 5, True),
+                             (0, 6, False), (1, 7, False), (2, 8, False),
+                             (3, 9, False), (4, 10, False), (5, 11, False)]
+
+        for bond in molecule.rdkit_molecule.GetBonds():
+            bond_id = (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(),
+                       bond.GetIsAromatic())
+            assert bond_id in expected_bond_ids, 'Unexpected bond id ' \
+                + '{}'.format(bond_id)

offpele/topology/molecule.py

@@ -447,7 +447,8 @@ class Molecule(object):
     """
 
     def __init__(self, path=None, smiles=None, rotamer_resolution=30,
-                 exclude_terminal_rotamers=True, name='', tag='UNK'):
+                 exclude_terminal_rotamers=True, name='', tag='UNK',
+                 connectivity_template=None):
         """
         It initializes a Molecule object through a PDB file or a SMILES
         tag.
@@ -468,6 +469,9 @@ def __init__(self, path=None, smiles=None, rotamer_resolution=30,
             The molecule name
         tag : str
             The molecule tag. It must be a 3-character string
+        connectivity_template : an rdkit.Chem.rdchem.Mol object
+            A molecule represented with RDKit to use when assigning the
+            connectivity of this Molecule object
 
         Examples
         --------
@@ -478,7 +482,7 @@ def __init__(self, path=None, smiles=None, rotamer_resolution=30,
         >>> from offpele.topology import Molecule
 
         >>> molecule = Molecule('molecule.pdb')
-        >>> molecule.parameterize('openff_unconstrained-1.1.1.offxml')
+        >>> molecule.parameterize('openff_unconstrained-1.2.0.offxml')
 
         Load a molecule using a SMILES tag and parameterize it with Open
         Force Field
@@ -488,11 +492,30 @@ def __init__(self, path=None, smiles=None, rotamer_resolution=30,
         >>> molecule = Molecule(smiles='Cc1ccccc1')
         >>> molecule.parameterize('openff_unconstrained-1.2.0.offxml')
 
+        Load a molecule usign a PDB file (without connectivity) and assign
+        the missing connectivity from an RDKit template (e.g. obtained
+        from qcportal and the Open Force Field Toolkit)
+
+        >>> import qcportal as ptl
+        >>> from openforcefield.topology import Molecule as OFFMolecule
+
+        >>> ds = client.get_collection('OptimizationDataset',
+                                       'Kinase Inhibitors: WBO Distributions')
+        >>> entry = ds.get_entry(ds.df.index[0])
+        >>> mol_record = OFFMolecule.from_qcschema(entry)
+        >>> template = mol_record.to_rdkit()
+
+        >>> from offpele.topology import Molecule
+
+        >>> molecule = Molecule('PDB_without_connectivity.pdb',
+                                template=template)
+
         """
         self._name = name
         self._tag = tag
         self._rotamer_resolution = rotamer_resolution
         self._exclude_terminal_rotamers = exclude_terminal_rotamers
+        self._connectivity_template = connectivity_template
 
         if isinstance(path, str):
             from pathlib import Path
@@ -539,28 +562,38 @@ def _initialize_from_pdb(self, path):
         path : str
             The path to a PDB with the molecule structure
         """
+        print(' - Initializing molecule from PDB')
         self._initialize()
-        print(' - Loading molecule from RDKit')
 
+        print('   - Loading molecule from RDKit')
         rdkit_toolkit = RDKitToolkitWrapper()
         self._rdkit_molecule = rdkit_toolkit.from_pdb(path)
 
+        # Use RDKit template, if any, to assign the connectivity to
+        # the current Molecule object
+        if self.connectivity_template is not None:
+            print('   - Assigning connectivity from template')
+            rdkit_toolkit.assign_connectivity_from_template(self)
+
         # RDKit must generate stereochemistry specifically from 3D coords
+        print('   - Assigning stereochemistry from 3D coordinates')
         rdkit_toolkit.assign_stereochemistry_from_3D(self)
 
         # Set molecule name according to PDB name
         if self.name == '':
             from pathlib import Path
             name = Path(path).stem
+            print('   - Setting molecule name to \'{}\''.format(name))
             self.set_name(name)
 
         # Set molecule tag according to PDB's residue name
         if self.tag == 'UNK':
             tag = rdkit_toolkit.get_residue_name(self)
+            print('   - Setting molecule tag to \'{}\''.format(tag))
             self.set_tag(tag)
 
+        print('   - Representing molecule with the Open Force Field Toolkit')
         openforcefield_toolkit = OpenForceFieldToolkitWrapper()
-
         self._off_molecule = openforcefield_toolkit.from_rdkit(self)
 
     def _initialize_from_smiles(self, smiles):
@@ -572,9 +605,10 @@ def _initialize_from_smiles(self, smiles):
         smiles : str
             The SMILES tag to construct the molecule structure with
         """
+        print(' - Initializing molecule from a SMILES tag')
         self._initialize()
-        print(' - Constructing molecule from a SMILES tag with RDKit')
 
+        print('   - Loading molecule from RDKit')
         rdkit_toolkit = RDKitToolkitWrapper()
         self._rdkit_molecule = rdkit_toolkit.from_smiles(smiles)
 
@@ -584,10 +618,11 @@ def _initialize_from_smiles(self, smiles):
 
         # Set molecule name according to the SMILES tag
         if self.name == '':
+            print('   - Setting molecule name to \'{}\''.format(smiles))
             self.set_name(smiles)
 
+        print('   - Representing molecule with the Open Force Field Toolkit')
         openforcefield_toolkit = OpenForceFieldToolkitWrapper()
-
         self._off_molecule = openforcefield_toolkit.from_rdkit(self)
 
     def _build_rotamers(self):
@@ -1254,6 +1289,20 @@ def exclude_terminal_rotamers(self):
         """
         return self._exclude_terminal_rotamers
 
+    @property
+    def connectivity_template(self):
+        """
+        The template containing the correct connectivity for this Molecule
+        object.
+
+        Returns
+        -------
+        connectivity_template : an rdkit.Chem.rdchem.Mol object
+            A molecule represented with RDKit to use when assigning the
+            connectivity of this Molecule object
+        """
+        return self._connectivity_template
+
     @property
     def off_molecule(self):
         """
@@ -1452,5 +1501,8 @@ def _ipython_display_(self):
         """
         from IPython.display import display
 
+        # Get 2D molecular representation
         rdkit_toolkit = RDKitToolkitWrapper()
-        return display(rdkit_toolkit.get_2D_representation(self))
+        representation = rdkit_toolkit.get_2D_representation(self)
+
+        return display(representation)

offpele/utils/toolkits.py

@@ -10,7 +10,7 @@
 import subprocess
 from collections import defaultdict
 from pathlib import Path
-from copy import copy
+from copy import deepcopy
 
 import numpy as np
 from simtk import unit
@@ -143,6 +143,29 @@ def from_smiles(self, smiles):
 
         return molecule
 
+    def assign_connectivity_from_template(self, molecule):
+        """
+        It assigns the connectivity to an RDKit molecule according to the
+        connectivity from an RDKit connectivity template.
+
+        Parameters
+        ----------
+        molecule : an offpele.topology.Molecule
+            The offpele's Molecule object
+        """
+        from rdkit.Chem import AllChem
+
+        if molecule.connectivity_template is None:
+            raise ValueError('A connectivity template must be previously '
+                             + 'assigned to the molecule')
+
+        rdkit_molecule = molecule.rdkit_molecule
+
+        rdkit_molecule = AllChem.AssignBondOrdersFromTemplate(
+            molecule.connectivity_template, rdkit_molecule)
+
+        molecule._rdkit_molecule = rdkit_molecule
+
     def assign_stereochemistry_from_3D(self, molecule):
         """
         It assigns the stereochemistry to an RDKit molecule according to the
@@ -308,7 +331,7 @@ def get_atom_ids_with_rotatable_bonds(self, molecule):
         """
         from rdkit import Chem
 
-        rdkit_molecule = molecule.rdkit_molecule
+        rdkit_molecule = deepcopy(molecule.rdkit_molecule)
 
         rot_bonds_atom_ids = set([
             frozenset(atom_pair) for atom_pair in
@@ -369,7 +392,8 @@ def get_2D_representation(self, molecule):
         from rdkit.Chem import AllChem
 
         rdkit_molecule = molecule.rdkit_molecule
-        representation_2D = copy(rdkit_molecule)
+        representation_2D = deepcopy(rdkit_molecule)
+
         AllChem.Compute2DCoords(representation_2D)
         return representation_2D