Commit 00d80849 authored by marta-sd's avatar marta-sd
Browse files

added sanitize flag

parent 22798d00

deepchem/feat/rdkit_grid_featurizer.py

+36 −16
Original line number Diff line number Diff line
@@ -910,6 +910,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer): 
               voxel_width=1.0,

               flatten=False,

               verbose=True,

               sanitize=False,

               **kwargs):

    """Parameters:

    -----------
@@ -967,6 +968,10 @@ class RdkitGridFeaturizer(ComplexFeaturizer): 
        'box_x', 'box_y', 'box_z', 'save_intermediates', 'voxelize_features',

        'parallel', 'voxel_feature_types'

    ]



    # list of features that require sanitized molecules

    require_sanitized = ['pi_stack', 'cation_pi']



    for arg in deprecated_args:

      if arg in kwargs and verbose:

        warn('%s argument was removed and it is ignored,'
@@ -974,6 +979,7 @@ class RdkitGridFeaturizer(ComplexFeaturizer): 
             DeprecationWarning)



    self.verbose = verbose

    self.sanitize = sanitize

    self.flatten = flatten



    self.ecfp_degree = ecfp_degree
@@ -1222,8 +1228,20 @@ class RdkitGridFeaturizer(ComplexFeaturizer): 
    # each entry is a tuple (is_flat, feature_name)

    self.feature_types = []



    # list of features that cannot be calculated with specified parameters

    # this list is used to define <flat/voxel/all>_combined subset

    ignored_features = []

    if self.sanitize is False:

      ignored_features += require_sanitized



    # parse provided feature types

    for feature_type in feature_types:

      if self.sanitize is False and feature_type in require_sanitized:

        if self.verbose:

          warn('sanitize is set to False, %s feature will be ignored' %

               feature_type)

        continue



      if feature_type in self.FLAT_FEATURES:

        self.feature_types.append((True, feature_type))

        if self.flatten is False:
@@ -1235,28 +1253,28 @@ class RdkitGridFeaturizer(ComplexFeaturizer): 
        self.feature_types.append((False, feature_type))



      elif feature_type == 'flat_combined':

        self.feature_types += list(

            zip([True] * len(self.FLAT_FEATURES),

                sorted(self.FLAT_FEATURES.keys())))

        self.feature_types += [(True, ftype)

                               for ftype in sorted(self.FLAT_FEATURES.keys())

                               if ftype not in ignored_features]

        if self.flatten is False:

          if self.verbose:

            warn('flat features are used, output will be flattened')

            warn('Flat features are used, output will be flattened')

          self.flatten = True



      elif feature_type == 'voxel_combined':

        self.feature_types += list(

            zip([False] * len(self.VOXEL_FEATURES),

                sorted(self.VOXEL_FEATURES.keys())))

        self.feature_types += [(False, ftype)

                               for ftype in sorted(self.VOXEL_FEATURES.keys())

                               if ftype not in ignored_features]

      elif feature_type == 'all_combined':

        self.feature_types += list(

            zip([True] * len(self.FLAT_FEATURES),

                sorted(self.FLAT_FEATURES.keys())))

        self.feature_types += list(

            zip([False] * len(self.VOXEL_FEATURES),

                sorted(self.VOXEL_FEATURES.keys())))

        self.feature_types += [(True, ftype)

                               for ftype in sorted(self.FLAT_FEATURES.keys())

                               if ftype not in ignored_features]

        self.feature_types += [(False, ftype)

                               for ftype in sorted(self.VOXEL_FEATURES.keys())

                               if ftype not in ignored_features]

        if self.flatten is False:

          if self.verbose:

            warn('flat feature are used, output will be flattened')

            warn('Flat feature are used, output will be flattened')

          self.flatten = True

      elif self.verbose:

        warn('Ignoring unknown feature %s' % feature_type)
@@ -1333,7 +1351,8 @@ class RdkitGridFeaturizer(ComplexFeaturizer): 
    ############################################################## TIMING



    if not self.ligand_only:

      protein_xyz, protein_rdk = load_molecule(protein_pdb, calc_charges=True)

      protein_xyz, protein_rdk = load_molecule(

          protein_pdb, calc_charges=True, sanitize=self.sanitize)

    ############################################################## TIMING

    time2 = time.time()

    log("TIMING: Loading protein coordinates took %0.3f s" % (time2 - time1),
@@ -1342,7 +1361,8 @@ class RdkitGridFeaturizer(ComplexFeaturizer): 
    ############################################################## TIMING

    time1 = time.time()

    ############################################################## TIMING

    ligand_xyz, ligand_rdk = load_molecule(ligand_file, calc_charges=True)

    ligand_xyz, ligand_rdk = load_molecule(

        ligand_file, calc_charges=True, sanitize=self.sanitize)

    ############################################################## TIMING

    time2 = time.time()

    log("TIMING: Loading ligand coordinates took %0.3f s" % (time2 - time1),

deepchem/feat/tests/test_rdkit_grid_features.py

+10 −10
Original line number Diff line number Diff line
@@ -8,7 +8,7 @@ import unittest 
import numpy as np

np.random.seed(123)



from rdkit.Chem import MolFromMolFile, MolFromSmiles, MolFromPDBFile, SDMolSupplier

from rdkit.Chem import MolFromSmiles

from rdkit.Chem.AllChem import Mol, ComputeGasteigerCharges



from deepchem.feat import rdkit_grid_featurizer as rgf
@@ -205,15 +205,13 @@ class TestPiInteractions(unittest.TestCase): 
    self.cycle4.Compute2DCoords()



    # load and sanitize two real molecules

    self.prot = MolFromPDBFile(

    _, self.prot = rgf.load_molecule(

        os.path.join(current_dir, '3ws9_protein_fixer_rdkit.pdb'),

        sanitize=True,

        removeHs=False)

        add_hydrogens=False, calc_charges=False, sanitize=True)



    self.lig = SDMolSupplier(

    _, self.lig = rgf.load_molecule(

        os.path.join(current_dir, '3ws9_ligand.sdf'),

        sanitize=True,

        removeHs=False)[0]

        add_hydrogens=False, calc_charges=False, sanitize=True)



  def test_compute_ring_center(self):

    # FIXME might break with different version of rdkit
@@ -334,7 +332,7 @@ class TestFeaturizationFunctions(unittest.TestCase): 
    self.ligand_file = os.path.join(current_dir, '3ws9_ligand.sdf')



  def test_compute_all_ecfp(self):

    mol = MolFromMolFile(self.ligand_file)

    _, mol = rgf.load_molecule(self.ligand_file)

    num_atoms = mol.GetNumAtoms()

    for degree in range(1, 4):

      # TODO test if dict contains smiles
@@ -482,7 +480,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase): 
        ],

        ecfp_power=ecfp_power,

        splif_power=splif_power,

        flatten=True)

        flatten=True,

        sanitize=True)

    self.assertIsInstance(featurizer, rgf.RdkitGridFeaturizer)

    feature_tensor = featurizer.featurize_complexes([self.ligand_file],

                                                    [self.protein_file])
@@ -510,7 +509,8 @@ class TestRdkitGridFeaturizer(unittest.TestCase): 
        box_width=box_w,

        ecfp_power=f_power,

        feature_types=['all_combined'],

        flatten=True)

        flatten=True,

        sanitize=True)



    prot_tensor = rgf_featurizer._voxelize(

        rgf.convert_atom_to_voxel,

deepchem/utils/rdkit_util.py

+7 −2
Original line number Diff line number Diff line
@@ -87,7 +87,8 @@ def compute_charges(mol): 
  return mol





def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True):

def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True,

                  sanitize=False):

  """

  Converts molecule file to (xyz-coords, obmol object)
@@ -99,7 +100,7 @@ def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True): 
  :return: (xyz, mol)

  """

  if ".mol2" in molecule_file:

    my_mol = Chem.MolFromMol2File(molecule_file)

    my_mol = Chem.MolFromMol2File(molecule_file, sanitize=False, removeHs=False)

  elif ".sdf" in molecule_file:

    suppl = Chem.SDMolSupplier(str(molecule_file), sanitize=False)

    my_mol = suppl[0]
@@ -118,6 +119,10 @@ def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True): 


  if add_hydrogens or calc_charges:

    my_mol = add_hydrogens_to_mol(my_mol)

  # TODO: mol should be always sanitized when charges are calculated

  # can't change it now because it would break a lot of examples

  if sanitize:

    Chem.SanitizeMol(my_mol)

  if calc_charges:

    compute_charges(my_mol)

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