Merge pull request #147 from martimunicoy/devel

1.3.3 Release

docs/releasehistory.rst

@@ -7,6 +7,19 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``minor`` increments add features but do not break API compatibility
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
+1.3.3 - Explicit hydrogens support
+---------------------------------------------------------
+
+This is a micro release of peleffy that includes support for the new OpenFF flag to manage explicit and implicit hydrogen atoms.
+
+New features
+""""""""""""
+- `PR #146 <https://github.com/martimunicoy/peleffy/pull/146>`_: Adds support for the new explicit hydrogens flag
+
+Tests added
+"""""""""""
+- `PR #146 <https://github.com/martimunicoy/peleffy/pull/146>`_: New test to check new explicit hydrogens flag
+
 
 1.3.2 - Migration and support for openff.toolkit
 ---------------------------------------------------------

peleffy/data/tests/ethane_noH.pdb

@@ -0,0 +1,5 @@
+HETATM    1  C1  UNK     1       0.755   0.000   0.000  1.00  0.00           C  
+HETATM    2  C2  UNK     1      -0.755   0.000   0.000  1.00  0.00           C  
+CONECT    1    2
+END
+

peleffy/forcefield/forcefield.py

@@ -404,9 +404,7 @@ 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']

peleffy/tests/test_molecule.py

@@ -32,7 +32,7 @@ def test_smiles_initialization(self):
         """
         It checks the initialization from a SMILES tag.
         """
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # Save it
         with tempfile.TemporaryDirectory() as tmpdir:
@@ -59,12 +59,13 @@ def test_molecule_name_assignment(self):
         assert molecule.name == 'benzene', 'Unexpected atom name'
 
         # Look for the SMILES name when a Molecule is loaded from a SMILES tag
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
         assert molecule.name == 'c1ccccc1', 'Unexpected atom name'
 
         # Look for benzene name when a Molecule is loaded from a SMILES tag
         # with a custom name
-        molecule = Molecule(smiles='c1ccccc1', name='benzene')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene',
+                            hydrogens_are_explicit=False)
         assert molecule.name == 'benzene', 'Unexpected atom name'
 
     def test_molecule_tag_assignment(self):
@@ -88,12 +89,13 @@ def test_molecule_tag_assignment(self):
         assert molecule.tag == 'BEN', 'Unexpected atom tag'
 
         # Look for UNK tag when a Molecule is loaded from a SMILES tag
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
         assert molecule.tag == 'UNK', 'Unexpected atom tag'
 
         # Look for BNZ tag when a Molecule is loaded from a SMILES tag with
         # a custom tag
-        molecule = Molecule(smiles='c1ccccc1', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', tag='BNZ',
+                            hydrogens_are_explicit=False)
         assert molecule.tag == 'BNZ', 'Unexpected atom tag'
 
     def test_PDB_connectivity_template(self):
@@ -198,23 +200,24 @@ def check_residue_name(name):
                 check_residue_name('TAG')
 
         # Checking default tag assignment from SMILES
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
         with tempfile.TemporaryDirectory() as tmpdir:
             with temporary_cd(tmpdir):
                 assert molecule.tag == 'UNK', 'Unexpected molecule tag'
                 molecule.to_pdb_file('molecule.pdb')
                 check_residue_name('UNK')
 
         # Checking custom tag assignment from SMILES
-        molecule = Molecule(smiles='c1ccccc1', tag='BEN')
+        molecule = Molecule(smiles='c1ccccc1', tag='BEN',
+                            hydrogens_are_explicit=False)
         with tempfile.TemporaryDirectory() as tmpdir:
             with temporary_cd(tmpdir):
                 assert molecule.tag == 'BEN', 'Unexpected molecule tag'
                 molecule.to_pdb_file('molecule.pdb')
                 check_residue_name('BEN')
 
         # Checking second custom tag assignment from SMILES
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
         with tempfile.TemporaryDirectory() as tmpdir:
             with temporary_cd(tmpdir):
                 molecule.set_tag('BNZ')
@@ -281,11 +284,13 @@ def test_undefined_stereo(self):
 
         # This should crash due to an undefined stereochemistry error
         with pytest.raises(UndefinedStereochemistryError):
-            mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3')
+            mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3',
+                           hydrogens_are_explicit=False)
 
         # This now should work
         mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3',
-                       allow_undefined_stereo=True)
+                       allow_undefined_stereo=True,
+                       hydrogens_are_explicit=False)
 
         # And we can parameterize it
         ff = OpenForceField('openff_unconstrained-1.2.1.offxml')
@@ -330,7 +335,9 @@ def test_from_openff(self):
         """
         from openff.toolkit.topology import Molecule as OpenFFMolecule
 
-        openff_molecule = OpenFFMolecule.from_smiles('C(C(=O)[O-])C(=O)[OH]')
+        openff_molecule = \
+            OpenFFMolecule.from_smiles('C(C(=O)[O-])C(=O)[OH]',
+                                       hydrogens_are_explicit=False)
 
         molecule = Molecule.from_openff(openff_molecule)
 
@@ -350,6 +357,75 @@ def test_from_openff(self):
         assert molecule.graph is not None, \
             'Molecule\' graph should be initialized'
 
+    def test_explicit_hydrogens(self):
+        """
+        It checks initialization of a Molecule with the explicit hydrogens
+        flag.
+        """
+
+        # Load ethane from SMILES with implicit hydrogen atoms
+        molecule = Molecule(smiles='CC')
+        atom_names = molecule.get_pdb_atom_names()
+
+        for atom_name in atom_names:
+            assert 'H' not in atom_name, 'Unexpected H in molecule without ' \
+                + 'explicit hydrogen atoms and hydrogens_are_explicit ' \
+                + 'set to True'
+
+        # Load ethane from SMILES without explicit hydrogen atoms
+        molecule = Molecule(smiles='CC', hydrogens_are_explicit=False)
+        atom_names = molecule.get_pdb_atom_names()
+
+        found_hydrogen = False
+        for atom_name in atom_names:
+            if 'H' in atom_name:
+                found_hydrogen = True
+                break
+
+        assert found_hydrogen, 'Hydrogen not found regardless of setting ' \
+            + 'hydrogens_are_explicit to False'
+
+        # Load ethane from SMILES with explicit hydrogen atoms
+        molecule = Molecule(smiles='[H]C([H])([H])C([H])([H])([H])',
+                            hydrogens_are_explicit=True)
+        atom_names = molecule.get_pdb_atom_names()
+
+        found_hydrogen = False
+        for atom_name in atom_names:
+            if 'H' in atom_name:
+                found_hydrogen = True
+                break
+
+        assert found_hydrogen, 'Hydrogen not found regardless of being ' \
+                               + 'explicitly defined in the SMILES tag'
+
+        # Load ethane from PDB with implicit hydrogen atoms
+        pdb_path = get_data_file_path('tests/ethane_noH.pdb')
+        molecule = Molecule(pdb_path,
+                            hydrogens_are_explicit=True)
+        atom_names = molecule.get_pdb_atom_names()
+
+        for atom_name in atom_names:
+            assert 'H' not in atom_name, 'Unexpected H in molecule without ' \
+                + 'explicit hydrogen atoms and hydrogens_are_explicit ' \
+                + 'set to True'
+
+        # Load ethane from PDB without explicit hydrogen atoms
+        pdb_path = get_data_file_path('tests/ethane_noH.pdb')
+        molecule = Molecule(pdb_path,
+                            hydrogens_are_explicit=False)
+        atom_names = molecule.get_pdb_atom_names()
+
+        found_hydrogen = False
+        for atom_name in atom_names:
+            if 'H' in atom_name:
+                found_hydrogen = True
+                break
+
+        assert found_hydrogen, 'Hydrogen not found regardless of setting ' \
+            + 'hydrogens_are_explicit to False'
+
+
     def test_pdb_fixer(self):
         """
         It checks the PDB fixer prior parsing a PDB input file for
@@ -443,7 +519,7 @@ def test_molecule_display(self):
 
         from IPython.display import display
 
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # This should not raise any Exception
         display(molecule)

peleffy/tests/test_parameters.py

@@ -314,7 +314,7 @@ def test_OFF_parameters(self):
         MAX_THRESHOLD = 1e-3
 
         # Load benzene ring
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -369,7 +369,7 @@ def test_Impact_writable_parameters(self):
         """
 
         # Load benzene ring
-        molecule = Molecule(smiles='CC=O')
+        molecule = Molecule(smiles='CC=O', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -407,7 +407,7 @@ def test_OFF_parameters(self):
         MAX_THRESHOLD = 1e-3
 
         # Load benzene ring
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -475,7 +475,7 @@ def test_Impact_writable_parameters(self):
         """
 
         # Load benzene ring
-        molecule = Molecule(smiles='CC=O')
+        molecule = Molecule(smiles='CC=O', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -515,7 +515,7 @@ def test_OFF_parameters(self):
         """
 
         # Load molecule
-        molecule = Molecule(smiles='C=CC(=O)O')
+        molecule = Molecule(smiles='C=CC(=O)O', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -635,7 +635,7 @@ def test_Impact_writable_parameters(self):
         """
 
         # Load benzene ring
-        molecule = Molecule(smiles='CC=O')
+        molecule = Molecule(smiles='CC=O', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -793,7 +793,8 @@ def test_nonstandard_dihedrals_writable_parameters(self):
         It checks the writable representation of non standard dihedrals.
         """
         # Load molecule
-        molecule = Molecule(smiles='c1c(c(n(n1)S(=O)(=O)C))O')
+        molecule = Molecule(smiles='c1c(c(n(n1)S(=O)(=O)C))O',
+                            hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)

peleffy/tests/test_toolkits.py

@@ -110,7 +110,7 @@ def test_get_Schrodinger_parameters(self):
         from peleffy.utils.toolkits import ToolkitUnavailableException
 
         # Load benzene ring
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # Load OPLS2005 force field
         opls2005 = OPLS2005ForceField()

peleffy/tests/test_utils.py

@@ -172,7 +172,8 @@ def test_non_datalocal_paths(self):
         from peleffy.forcefield import OpenForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
 
         # Load force field
         openff = OpenForceField('openff_unconstrained-1.2.1.offxml')
@@ -225,7 +226,8 @@ def test_datalocal_paths_for_openff(self):
         from peleffy.forcefield import OpenForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
 
         # Load force field
         openff = OpenForceField('openff_unconstrained-1.2.1.offxml')
@@ -289,7 +291,8 @@ def test_datalocal_paths_for_opls(self):
         from peleffy.forcefield import OPLS2005ForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
 
         # Load force field
         opls2005 = OPLS2005ForceField()
@@ -358,7 +361,8 @@ def test_datalocal_paths_for_offopls(self):
         from peleffy.forcefield import OpenFFOPLS2005ForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
         molecule._forcefield = OpenFFOPLS2005ForceField('OPLS2005')
 
         # Load force field
@@ -484,7 +488,8 @@ def test_folder_creation(self):
         from peleffy.forcefield import OpenForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
 
         # Load force field
         openff = OpenForceField('openff_unconstrained-1.2.1.offxml')