First removal

"""

Basic molecular features.

"""

__author__ = "Steven Kearnes"

__copyright__ = "Copyright 2014, Stanford University"

__license__ = "MIT"

from deepchem.feat import Featurizer

class MolecularWeight(Featurizer):

  """

  Molecular weight.

  """

  name = ['mw', 'molecular_weight']

  def _featurize(self, mol):

    """

    Calculate molecular weight.

    Parameters

    ----------

    mol : RDKit Mol

        Molecule.

    """

    from rdkit.Chem import Descriptors

    wt = Descriptors.ExactMolWt(mol)

    wt = [wt]

    return wt

class RDKitDescriptors(Featurizer):

  """

  RDKit descriptors.

  See http://rdkit.org/docs/GettingStartedInPython.html

  #list-of-available-descriptors.

  """

  name = 'descriptors'

  # (ytz): This is done to avoid future compatibility issues like inclusion of

  # the 3D descriptors or changing the feature size.

  allowedDescriptors = set([

      'MaxAbsPartialCharge', 'MinPartialCharge', 'MinAbsPartialCharge',

      'HeavyAtomMolWt', 'MaxAbsEStateIndex', 'NumRadicalElectrons',

      'NumValenceElectrons', 'MinAbsEStateIndex', 'MaxEStateIndex',

      'MaxPartialCharge', 'MinEStateIndex', 'ExactMolWt', 'MolWt', 'BalabanJ',

      'BertzCT', 'Chi0', 'Chi0n', 'Chi0v', 'Chi1', 'Chi1n', 'Chi1v', 'Chi2n',

      'Chi2v', 'Chi3n', 'Chi3v', 'Chi4n', 'Chi4v', 'HallKierAlpha', 'Ipc',

      'Kappa1', 'Kappa2', 'Kappa3', 'LabuteASA', 'PEOE_VSA1', 'PEOE_VSA10',

      'PEOE_VSA11', 'PEOE_VSA12', 'PEOE_VSA13', 'PEOE_VSA14', 'PEOE_VSA2',

      'PEOE_VSA3', 'PEOE_VSA4', 'PEOE_VSA5', 'PEOE_VSA6', 'PEOE_VSA7',

      'PEOE_VSA8', 'PEOE_VSA9', 'SMR_VSA1', 'SMR_VSA10', 'SMR_VSA2', 'SMR_VSA3',

      'SMR_VSA4', 'SMR_VSA5', 'SMR_VSA6', 'SMR_VSA7', 'SMR_VSA8', 'SMR_VSA9',

      'SlogP_VSA1', 'SlogP_VSA10', 'SlogP_VSA11', 'SlogP_VSA12', 'SlogP_VSA2',

      'SlogP_VSA3', 'SlogP_VSA4', 'SlogP_VSA5', 'SlogP_VSA6', 'SlogP_VSA7',

      'SlogP_VSA8', 'SlogP_VSA9', 'TPSA', 'EState_VSA1', 'EState_VSA10',

      'EState_VSA11', 'EState_VSA2', 'EState_VSA3', 'EState_VSA4',

      'EState_VSA5', 'EState_VSA6', 'EState_VSA7', 'EState_VSA8', 'EState_VSA9',

      'VSA_EState1', 'VSA_EState10', 'VSA_EState2', 'VSA_EState3',

      'VSA_EState4', 'VSA_EState5', 'VSA_EState6', 'VSA_EState7', 'VSA_EState8',

      'VSA_EState9', 'FractionCSP3', 'HeavyAtomCount', 'NHOHCount', 'NOCount',

      'NumAliphaticCarbocycles', 'NumAliphaticHeterocycles',

      'NumAliphaticRings', 'NumAromaticCarbocycles', 'NumAromaticHeterocycles',

      'NumAromaticRings', 'NumHAcceptors', 'NumHDonors', 'NumHeteroatoms',

      'NumRotatableBonds', 'NumSaturatedCarbocycles',

      'NumSaturatedHeterocycles', 'NumSaturatedRings', 'RingCount', 'MolLogP',

      'MolMR'

  ])

  def __init__(self):

    self.descriptors = []

    self.descList = []

    from rdkit.Chem import Descriptors

    for descriptor, function in Descriptors.descList:

      if descriptor in self.allowedDescriptors:

        self.descriptors.append(descriptor)

        self.descList.append((descriptor, function))

  def _featurize(self, mol):

    """

    Calculate RDKit descriptors.

    Parameters

    ----------

    mol : RDKit Mol

        Molecule.

    """

    rval = []

    for desc_name, function in self.descList:

      rval.append(function(mol))

    return rval