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#! /usr/bin/env python |
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# Copyright (C) 2015 Rich Lewis <[email protected]> |
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# License: 3-clause BSD |
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import pandas as pd |
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from rdkit import Chem |
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from rdkit.Chem import Crippen |
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from rdkit.Chem import Lipinski |
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from rdkit.Chem import rdMolDescriptors |
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from rdkit.Chem.rdchem import HybridizationType |
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import skchem |
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import functools |
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from skchem.data import periodic_table |
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from .filters import organic |
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def is_element(a, element=0): |
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""" Is the atom of a given element """ |
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return a.GetSymbol() == element |
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element_features = {'is_{}'.format(e): functools.partial(is_element, element=e) for e in organic} |
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def is_h_acceptor(a): |
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""" Is an H acceptor? """ |
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m = a.GetOwningMol() |
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idx = a.GetIdx() |
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return idx in [i[0] for i in Lipinski._HAcceptors(m)] |
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def is_h_donor(a): |
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""" Is an H donor? """ |
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m = a.GetOwningMol() |
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idx = a.GetIdx() |
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return idx in [i[0] for i in Lipinski._HDonors(m)] |
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def is_hetero(a): |
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""" Is a heteroatom? """ |
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m = a.GetOwningMol() |
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idx = a.GetIdx() |
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return idx in [i[0] for i in Lipinski._Heteroatoms(m)] |
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def atomic_number(a): |
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""" Atomic number of atom """ |
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return a.GetAtomicNum() |
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def atomic_mass(a): |
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""" Atomic mass of atom """ |
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return a.GetMass() |
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def explicit_valence(a): |
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""" Explicit valence of atom """ |
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return a.GetExplicitValence() |
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def implicit_valence(a): |
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""" Implicit valence of atom """ |
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return a.GetImplicitValence() |
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def valence(a): |
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""" returns the valence of the atom """ |
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return explicit_valence(a) + implicit_valence(a) |
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def formal_charge(a): |
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""" Formal charge of atom """ |
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return a.GetFormalCharge() |
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def is_aromatic(a): |
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""" Boolean if atom is aromatic""" |
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return a.GetIsAromatic() |
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def num_implicit_hydrogens(a): |
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""" Number of implicit hydrogens """ |
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return a.GetNumImplicitHs() |
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def num_explicit_hydrogens(a): |
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""" Number of explicit hydrodgens """ |
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return a.GetNumExplicitHs() |
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def num_hydrogens(a): |
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""" Number of hydrogens """ |
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return num_implicit_hydrogens(a) + num_explicit_hydrogens(a) |
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def is_in_ring(a): |
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""" Whether the atom is in a ring """ |
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return a.IsInRing() |
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def crippen_log_p_contrib(a): |
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""" Hacky way of getting logP contribution. """ |
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idx = a.GetIdx() |
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m = a.GetOwningMol() |
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return Crippen._GetAtomContribs(m)[idx][0] |
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def crippen_molar_refractivity_contrib(a): |
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""" Hacky way of getting molar refractivity contribution. """ |
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idx = a.GetIdx() |
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m = a.GetOwningMol() |
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return Crippen._GetAtomContribs(m)[idx][1] |
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def tpsa_contrib(a): |
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""" Hacky way of getting total polar surface area contribution. """ |
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idx = a.GetIdx() |
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m = a.GetOwningMol() |
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return rdMolDescriptors._CalcTPSAContribs(m)[idx] |
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def labute_asa_contrib(a): |
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""" Hacky way of getting accessible surface area contribution. """ |
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idx = a.GetIdx() |
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m = a.GetOwningMol() |
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return rdMolDescriptors._CalcLabuteASAContribs(m)[0][idx] |
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def is_hybridized(a, hybrid_type=HybridizationType.SP3): |
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""" Hybridized as type hybrid_type, default SP3 """ |
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return a.GetHybridization() is hybrid_type |
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pt = periodic_table() |
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def electronegativity(a): |
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return a.GetSymbol() |
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hybridization_features = {'is_' + n + '_hybridized': functools.partial(is_hybridized, hybrid_type=n) for n in HybridizationType.names} |
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atom_features = { |
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'atomic_number': atomic_number, |
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'atomic_mass': atomic_mass, |
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'formal_charge': formal_charge, |
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'valence': valence, |
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'is_aromatic': is_aromatic, |
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'num_hydrogens': num_hydrogens, |
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'is_in_ring': is_in_ring, |
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'log_p_contrib': crippen_log_p_contrib, |
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'molar_refractivity_contrib': crippen_molar_refractivity_contrib, |
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'is_h_acceptor': is_h_acceptor, |
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'is_h_donor': is_h_donor, |
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'is_heteroatom': is_hetero, |
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'total_polar_surface_area_contrib': tpsa_contrib, |
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'total_labute_accessible_surface_area': labute_asa_contrib, |
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} |
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atom_features.update(element_features) |
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atom_features.update(hybridization_features) |
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class AtomFeatureCalculator(object): |
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def __init__(self, features=atom_features): |
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self.features = pd.Series(features) |
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@property |
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def feature_names(self): |
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return self.features.index |
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def calculate(self, obj): |
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if isinstance(obj, skchem.core.Atom): |
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return self._calculate_atom(obj) |
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elif isinstance(obj, skchem.core.Mol): |
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return self._calculate_mol(obj) |
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def _calculate_atom(self, atom): |
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return self.features.apply(lambda f: f(atom)) |
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def _calculate_mol(self, mol): |
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return pd.DataFrame(self(a) for a in mol.atoms) |
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def __call__(self, *args, **kwargs): |
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return self.calculate(*args, **kwargs) |
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The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods:
If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions.