# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
You can freely use and distribute it. If you hava
any problem, you could contact with us timely!
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.06.04
Email: gadsby@163.com
contains SMARTS definitions and calculators for EState atom types
defined in: Hall and Kier JCICS _35_ 1039-1045 (1995) Table 1
"""
from rdkit import Chem
import numpy
import sys
_rawD = [
('sLi','[LiD1]-*'),
('ssBe','[BeD2](-*)-*'),
('ssssBe','[BeD4](-*)(-*)(-*)-*'),
('ssBH', '[BD2H](-*)-*'),
('sssB', '[BD3](-*)(-*)-*'),
('ssssB','[BD4](-*)(-*)(-*)-*'),
('sCH3', '[CD1H3]-*'),
('dCH2', '[CD1H2]=*'),
('ssCH2','[CD2H2](-*)-*'),
('tCH', '[CD1H]#*'),
('dsCH', '[CD2H](=*)-*'),
('aaCH', '[C,c;D2H](:*):*'),
('sssCH','[CD3H](-*)(-*)-*'),
('ddC', '[CD2H0](=*)=*'),
('tsC', '[CD2H0](#*)-*'),
('dssC', '[CD3H0](=*)(-*)-*'),
('aasC', '[C,c;D3H0](:*)(:*)-*'),
('aaaC', '[C,c;D3H0](:*)(:*):*'),
('ssssC','[CD4H0](-*)(-*)(-*)-*'),
('sNH3', '[ND1H3]-*'),
('sNH2', '[ND1H2]-*'),
('ssNH2','[ND2H2](-*)-*'),
('dNH', '[ND1H]=*'),
('ssNH', '[ND2H](-*)-*'),
('aaNH', '[N,nD2H](:*):*'),
('tN', '[ND1H0]#*'),
('sssNH','[ND3H](-*)(-*)-*'),
('dsN', '[ND2H0](=*)-*'),
('aaN', '[N,nD2H0](:*):*'),
('sssN', '[ND3H0](-*)(-*)-*'),
('ddsN', '[ND3H0](~[OD1H0])(~[OD1H0])-,:*'), # mod
('aasN', '[N,nD3H0](:*)(:*)-,:*'), # mod
('ssssN','[ND4H0](-*)(-*)(-*)-*'),
('sOH','[OD1H]-*'),
('dO', '[OD1H0]=*'),
('ssO','[OD2H0](-*)-*'),
('aaO','[O,oD2H0](:*):*'),
('sF','[FD1]-*'),
('sSiH3', '[SiD1H3]-*'),
('ssSiH2','[SiD2H2](-*)-*'),
('sssSiH','[SiD3H1](-*)(-*)-*'),
('ssssSi','[SiD4H0](-*)(-*)(-*)-*'),
('sPH2', '[PD1H2]-*'),
('ssPH', '[PD2H1](-*)-*'),
('sssP', '[PD3H0](-*)(-*)-*'),
('dsssP', '[PD4H0](=*)(-*)(-*)-*'),
('sssssP','[PD5H0](-*)(-*)(-*)(-*)-*'),
('sSH', '[SD1H1]-*'),
('dS', '[SD1H0]=*'),
('ssS', '[SD2H0](-*)-*'),
('aaS', '[S,sD2H0](:*):*'),
('dssS', '[SD3H0](=*)(-*)-*'),
('ddssS','[SD4H0](~[OD1H0])(~[OD1H0])(-*)-*'), # mod
('sCl', '[ClD1]-*'),
('sGeH3', '[GeD1H3](-*)'),
('ssGeH2','[GeD2H2](-*)-*'),
('sssGeH','[GeD3H1](-*)(-*)-*'),
('ssssGe','[GeD4H0](-*)(-*)(-*)-*'),
('sAsH2', '[AsD1H2]-*'),
('ssAsH', '[AsD2H1](-*)-*'),
('sssAs', '[AsD3H0](-*)(-*)-*'),
('sssdAs', '[AsD4H0](=*)(-*)(-*)-*'),
('sssssAs','[AsD5H0](-*)(-*)(-*)(-*)-*'),
('sSeH', '[SeD1H1]-*'),
('dSe', '[SeD1H0]=*'),
('ssSe', '[SeD2H0](-*)-*'),
('aaSe', '[SeD2H0](:*):*'),
('dssSe', '[SeD3H0](=*)(-*)-*'),
('ddssSe','[SeD4H0](=*)(=*)(-*)-*'),
('sBr','[BrD1]-*'),
('sSnH3', '[SnD1H3]-*'),
('ssSnH2','[SnD2H2](-*)-*'),
('sssSnH','[SnD3H1](-*)(-*)-*'),
('ssssSn','[SnD4H0](-*)(-*)(-*)-*'),
('sI','[ID1]-*'),
('sPbH3', '[PbD1H3]-*'),
('ssPbH2','[PbD2H2](-*)-*'),
('sssPbH','[PbD3H1](-*)(-*)-*'),
('ssssPb','[PbD4H0](-*)(-*)(-*)-*'),
]
esPatterns=None
[docs]def BuildPatts(rawV=None):
""" Internal Use Only
"""
global esPatterns,_rawD
if rawV is None:
rawV = _rawD
esPatterns = [None]*len(rawV)
for i,(name,sma) in enumerate(rawV):
try:
patt = Chem.MolFromSmarts(sma)
except:
sys.stderr.write('WARNING: problems with pattern %s (name: %s), skipped.\n'%(sma,name))
else:
esPatterns[i] = name,patt
[docs]def TypeAtoms(mol):
""" assigns each atom in a molecule to an EState type
**Returns:**
list of tuples (atoms can possibly match multiple patterns) with atom types
"""
if esPatterns is None:
BuildPatts()
nAtoms = mol.GetNumAtoms()
res = [None]*nAtoms
for name,patt in esPatterns:
matches = mol.GetSubstructMatches(patt,uniquify=0)
for match in matches:
idx = match[0]
if res[idx] is None:
res[idx] = [name]
elif name not in res[idx]:
res[idx].append(name)
for i,v in enumerate(res):
if v is not None:
res[i] = tuple(v)
else:
res[i] = ()
return res
[docs]def GetAtomLabel(mol):
"""
Obtain the atom index in a molecule for the above given atom types
"""
if esPatterns is None:
BuildPatts()
res=[]
for name, patt in esPatterns:
matches = mol.GetSubstructMatches(patt,uniquify=0)
cc=[]
for match in matches:
# remain=match[1:]
cc.append(match[0])
bb=list(numpy.unique(numpy.array(cc)))
res.append(bb)
return res
