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#! /usr/bin/env python |
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# |
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# Copyright (C) 2015-2016 Rich Lewis <[email protected]> |
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# License: 3-clause BSD |
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""" |
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## skchem.core.bond |
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Defining chemical bonds in scikit-chem. |
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""" |
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from itertools import chain, combinations |
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import pandas as pd |
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import rdkit.Chem |
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import numpy as np |
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from .atom import Atom |
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from .base import ChemicalObject, PropertyView, ChemicalObjectView |
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class Bond(rdkit.Chem.rdchem.Bond, ChemicalObject): |
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""" |
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Class representing a chemical bond in scikit-chem. |
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""" |
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@property |
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def index(self): |
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""" int: the index of the bond in the atom. """ |
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return self.GetIdx() |
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@property |
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def atoms(self): |
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""" tuple[Atom]: list of atoms involved in the bond. """ |
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return (Atom.from_super(self.GetBeginAtom()), |
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Atom.from_super(self.GetEndAtom())) |
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@property |
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def atom_idxs(self): |
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""" tuple[int]: list of atom indexes involved in the bond. """ |
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return (self.GetBeginAtomIdx(), self.GetEndAtomIdx()) |
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@property |
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def props(self): |
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""" PropertyView: rdkit properties of the atom. """ |
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if not hasattr(self, '_props'): |
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self._props = PropertyView(self) |
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return PropertyView(self) |
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@property |
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def order(self): |
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""" int: the order of the bond. """ |
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return self.GetBondTypeAsDouble() |
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@property |
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def is_aromatic(self): |
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""" bool: whether the bond is aromatic. """ |
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return self.GetIsAromatic() |
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@property |
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def is_conjugated(self): |
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""" bool: whether the bond is conjugated. """ |
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return self.GetIsConjugated() |
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@property |
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def owner(self): |
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""" skchem.Mol: the molecule this bond is a part of. """ |
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from .mol import Mol |
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return Mol.from_super(self.GetOwningMol()) |
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@property |
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def stereo_symbol(self): |
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""" str: the stereo label of the bond ('Z', 'E', 'ANY', 'NONE') """ |
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return self.GetStereo().name.lstrip('STEREO') |
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@property |
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def is_in_ring(self): |
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""" bool: whether the bond is in a ring. """ |
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return self.IsInRing() |
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def draw(self): |
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""" str: Draw the bond in ascii. """ |
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return '{}{}{}'.format(self.atoms[0].symbol, |
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'-' if self.order == 1 else self.GetSmarts(), |
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self.atoms[1].symbol) |
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def to_dict(self): |
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""" dict: Convert to a dictionary representation. """ |
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return {"b": self.GetBeginAtomIdx(), |
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"e": self.GetEndAtomIdx(), |
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"o": self.order} |
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def __repr__(self): |
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return '<{klass} type="{bond}" at {address}>'.format( |
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klass=self.__class__.__name__, |
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bond=self.draw(), |
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address=hex(id(self))) |
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def __str__(self): |
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return self.draw() |
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class BondView(ChemicalObjectView): |
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""" Bond interface wrapper """ |
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def __getitem__(self, index): |
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res = super(BondView, self).__getitem__(index) |
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if res is None: |
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if abs(index) >= len(self): |
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raise IndexError('Index {} out of range for molecule with ' |
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'{} bonds.'.format(index, len(self))) |
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# index is negative, so adding gives desired indexing from back |
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if index < 0: |
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index += len(self) |
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return Bond.from_super(self.owner.GetBondWithIdx(index)) |
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else: |
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return res |
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def __len__(self): |
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return self.owner.GetNumBonds() |
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@property |
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def atom_idxs(self): |
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""" The atom indices for the bonds in the view. """ |
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return np.array([atom.atom_idxs for atom in self]) |
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@property |
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def order(self): |
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""" np.array<int> the bond orders of the bonds in the view. """ |
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return np.array([bond.order for bond in self]) |
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@property |
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def is_aromatic(self): |
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""" np.array<bool> whether each of the bonds in the view are |
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aromatic. """ |
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return np.array([bond.is_aromatic for bond in self]) |
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@property |
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def is_conjugated(self): |
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""" np.array<bool> whether each of the bonds in the view are c |
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onjugated. """ |
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return np.array([bond.is_conjugated for bond in self]) |
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@property |
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def is_in_ring(self): |
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""" np.array<bool> whether each of the bonds in the view are in a |
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ring. """ |
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return np.array([bond.is_in_ring for bond in self]) |
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@property |
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def stereo_symbol(self): |
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""" np.array<str> the stereo symbol of the bonds in the view. """ |
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return np.array([bond.stereo_symbol for bond in self]) |
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@property |
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def index(self): |
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""" pd.Index: an index of the bonds in the `BondView`. """ |
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return pd.RangeIndex(len(self), name='bond_idx') |
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def adjacency_matrix(self): |
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""" np.array[int]: the bond adjacency matrix. """ |
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res = np.zeros((len(self), len(self))) |
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ixs = zip(*chain(*(combinations((bond.index for bond in atom.bonds), 2) |
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for atom in self.owner.atoms))) |
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res[tuple(ixs)] = 1 |
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res += res.T |
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return res.astype(int) |
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__all__ = ['Atom', 'AtomView'] |
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richlewis42 /
scikit-chem
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