ChiralFilter

Complexity

Total Complexity

7

Size/Duplication

Total Lines	74
Duplicated Lines	0 %

Test Coverage

Coverage

100%

Importance

Changes

0

4 Methods

Rating	Name	Duplication	Size	Complexity
A	columns()	0	3	1
A	_transform_mol()	0	5	3
B	is_meso()	0	24	2
A	__init__()	0	18	1

#! /usr/bin/env python
#
# Copyright (C) 2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD

"""
# skchem.filters.stereo

Stereo filters for scikit-chem.
"""

from rdkit.Chem.MolKey.InchiInfo import InchiInfo

The import rdkit.Chem.MolKey.InchiInfo could not be resolved.

import pandas as pd

The import pandas could not be resolved.

from .base import Filter
from ..utils import Suppressor


class ChiralFilter(Filter):

    """ Filter chiral compounds.

    Examples:
        >>> import skchem
        >>> cf = skchem.filters.ChiralFilter()
        >>> ms = [
        ...    skchem.Mol.from_smiles('F[C@@H](F)[C@H](F)F', name='achiral'),
        ...    skchem.Mol.from_smiles('F[C@@H](Br)[C@H](Br)F', name='chiral'),
        ...    skchem.Mol.from_smiles('F[C@H](Br)[C@H](Br)F', name='meso'),
        ...    skchem.Mol.from_smiles('FC(Br)C(Br)F', name='racemic')
        ... ]
        >>> cf.transform(ms)
        achiral    False
        chiral      True
        meso       False
        racemic    False
        Name: is_chiral, dtype: bool

    """
    def __init__(self, check_meso=True, n_jobs=1, verbose=True):

        """ Initialize a `ChiralFilter` object.

        Args:
            check_meso (bool):
                Whether to include a check for meso compounds.

            n_jobs (int):
                The number of procesess to run the filter in.

            verbose (bool):
                Whether to output a progress bar.
        """

        self.check_meso = check_meso
        super(ChiralFilter, self).__init__(agg='any', n_jobs=n_jobs,
                                           verbose=verbose)

    @property
    def columns(self):
        return pd.Index(['is_chiral'])

    @staticmethod
    def is_meso(mol):
        """ Determines whether the molecule is meso.

        Meso compounds have chiral centres, but has a mirror plane allowing
        superposition.

        Examples:
            >>> import skchem

            >>> cf = skchem.filters.ChiralFilter()

            >>> meso = skchem.Mol.from_smiles('F[C@H](Br)[C@H](Br)F')

            >>> cf.is_meso(meso)
            True

            >>> non_meso = skchem.Mol.from_smiles('F[C@H](Br)[C@@H](Br)F')
            >>> cf.is_meso(non_meso)
            False
        """
        with Suppressor():
            info = InchiInfo(mol.to_inchi())
            return info.get_sp3_stereo()['main']['non-isotopic'][2]

    def _transform_mol(self, mol):

This method seems to be hidden by an attribute defined in skchem.filters.base on line 174.

        is_meso = self.is_meso(mol) if self.check_meso else False

        return any(atom.GetChiralTag() for atom in mol.atoms) and not is_meso