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#! /usr/bin/env python |
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# |
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# Copyright (C) 2016 Rich Lewis <[email protected]> |
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# License: 3-clause BSD |
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""" |
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# skchem.filters.stereo |
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Stereo filters for scikit-chem. |
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""" |
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from rdkit.Chem.MolKey.InchiInfo import InchiInfo |
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import pandas as pd |
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from .base import Filter |
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from ..utils import Suppressor |
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class ChiralFilter(Filter): |
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""" Filter chiral compounds. |
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Examples: |
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>>> import skchem |
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>>> cf = skchem.filters.ChiralFilter() |
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>>> ms = [ |
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... skchem.Mol.from_smiles('F[C@@H](F)[C@H](F)F', name='achiral'), |
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... skchem.Mol.from_smiles('F[C@@H](Br)[C@H](Br)F', name='chiral'), |
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... skchem.Mol.from_smiles('F[C@H](Br)[C@H](Br)F', name='meso'), |
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... skchem.Mol.from_smiles('FC(Br)C(Br)F', name='racemic') |
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... ] |
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>>> cf.transform(ms) |
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achiral False |
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chiral True |
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meso False |
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racemic False |
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Name: is_chiral, dtype: bool |
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""" |
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def __init__(self, check_meso=True, n_jobs=1, verbose=True): |
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""" Initialize a `ChiralFilter` object. |
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Args: |
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check_meso (bool): |
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Whether to include a check for meso compounds. |
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n_jobs (int): |
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The number of procesess to run the filter in. |
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verbose (bool): |
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Whether to output a progress bar. |
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""" |
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self.check_meso = check_meso |
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super(ChiralFilter, self).__init__(agg='any', n_jobs=n_jobs, |
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verbose=verbose) |
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@property |
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def columns(self): |
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return pd.Index(['is_chiral']) |
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@staticmethod |
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def is_meso(mol): |
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""" Determines whether the molecule is meso. |
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Meso compounds have chiral centres, but has a mirror plane allowing |
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superposition. |
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Examples: |
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>>> import skchem |
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>>> cf = skchem.filters.ChiralFilter() |
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>>> meso = skchem.Mol.from_smiles('F[C@H](Br)[C@H](Br)F') |
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>>> cf.is_meso(meso) |
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True |
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>>> non_meso = skchem.Mol.from_smiles('F[C@H](Br)[C@@H](Br)F') |
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>>> cf.is_meso(non_meso) |
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False |
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""" |
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with Suppressor(): |
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info = InchiInfo(mol.to_inchi()) |
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return info.get_sp3_stereo()['main']['non-isotopic'][2] |
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def _transform_mol(self, mol): |
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is_meso = self.is_meso(mol) if self.check_meso else False |
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return any(atom.GetChiralTag() for atom in mol.atoms) and not is_meso |
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richlewis42 /
scikit-chem
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