schrodinger.application.matsci.mlearn.descriptor module

Create polymer descriptor and molecule features using rdkit.

Copyright Schrodinger, LLC. All rights reserved.

exception schrodinger.application.matsci.mlearn.descriptor.FeaturizeError

Bases: RuntimeError

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.mlearn.descriptor.Featurize(dataframe, smile_col='smiles', feature_types=('rdkit_descriptor', 'Morgan'), return_float64=False, logger=None)

Bases: object

Create features from the structures

__init__(dataframe, smile_col='smiles', feature_types=('rdkit_descriptor', 'Morgan'), return_float64=False, logger=None)

Initialize FeaturizeStructure class

Parameters

  • dataframe (pandas.DataFrame) – pandas dataframe containing structures

  • smile_col (str) – Name of smiles column.

  • feature_types (list) – list of features to be calculated for given structures

  • return_float64 (bool) –

  • logger (logging.Logger) – The logger to log with

getFeatures()

Create features from SMILES pattern of dataset

Return type

pandas.DataFrame

Returns

Dataframe containing structure, SMILES and full feature vector

clearDataFrame()

Clear data

createMols()

Create rdkit molecules from SMILES

createRdkitDescriptors()

Create RDKit descriptors for the molecules

findBondGroups(mol)

Find largest size of contiguous rotatable bonds present in the system

Parameters

mol (rdkit.Chem.mol) – rdkit molecule

Return type

int

Returns

length of largest contiguous rotatable bonds present

createMatMinerDescriptors()

Create Mat-Miner descriptor from the rdkit molecule

createMorganDescriptors()

Create Morgan descriptor from the rdkit molecule

getMorganCount(mol, morgan_fp_generator)

Generate morgan fingerprint for one molecule

Parameters

  • mol (rdkit.Chem.mol) – rdkit molecule

  • morgan_fp_generator (class object) – Morgan fingerprint generator object

Returns

Dictionary with key as fingerprint name and value as fingerprint

Return type

Dict

createPolymerDescriptors()

Create polymer descriptors in the pandas dataframe.

exception schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptorError

Bases: RuntimeError

__init__(*args, **kwargs)
args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.mlearn.descriptor.PolymerDescriptor(smiles)

Bases: object

Class to create the polymer descriptor

FLOAT_BASE = 'r_matsci'
DESCRIPTORS = {'r_matsci_Backbone_Atoms_Fraction': 'backboneAtomsFraction', 'r_matsci_Double_Ring_Atoms_Fraction': 'doubleRingAtomsFraction', 'r_matsci_Ring_Atoms_Fraction': 'ringAtomsFraction', 'r_matsci_Rotatable_Bonds_Fraction': 'rotatableBondsFraction', 'r_matsci_Sp3_Atoms_Fraction': 'sp3AtomsFraction', 'r_matsci_Triple_Ring_Atoms_Fraction': 'tripleRingAtomsFraction'}
__init__(smiles)

Initialize polymer descriptor class

Parameters

mol (rdkit.Chem.rdchem.Mol) – rdkit mol object of polymer

getFeatures()

Get descriptor for given polymer

Return dict

Dictionary with key as name of the descriptor and value as descriptor

run()

Generate polymer descriptors for the structure

getDoubleAndTripleRingAtoms()

Calculate the number of atoms in double and triple fused rings

ringAtomsFraction()

Get the fraction of atoms in rings in the polymer

Return type

float

Returns

The fraction of atoms in rings

doubleRingAtomsFraction()

Get the fraction of atoms in double fused ring systems in the polymer

Return type

float

Returns

The fraction of atoms in double fused ring systems

tripleRingAtomsFraction()

Get the fraction of atoms in triple fused ring systems in the polymer

Return type

float

Returns

The fraction of atoms in triple fused ring systems

backboneAtomsFraction()

Get the fraction of backbone atoms in the polymer

Return type

float

Returns

The fraction of backbone atoms

rotatableBondsFraction()

Get the fraction of rotatable bonds in the polymer

Return type

float

Returns

The fraction of rotatable bonds

sp3AtomsFraction()

Get the fraction of sp3 atoms in the polymer

Return type

float

Returns

The fraction of sp3 atoms bonds

schrodinger.application.matsci.mlearn.descriptor.create_oligomer(smiles, monomers)

Create an oligomer given the monomer SMILES and the number of monomer repetitions. The head and tail of the monomer should be denoted by the atom [At].

Parameters

  • smiles (str) – The SMILES string of the monomer

  • monomers (int) – The number of monomers to repeat

Return type

Chem.rdchem.Mol

Returns

The oligomer as Chem.rdchem.Mol