Source Code for Package Chem

  1  # $Id: __init__.py 608 2008-04-10 08:12:17Z glandrum $ 
  2  # 
  3  #  Copyright (C) 2000-2008  greg Landrum and Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  """ A module for molecules and stuff 
  8   
  9   see Chem/index.html in the doc tree for documentation 
 10    
 11  """ 
 12  import rdBase 
 13  import RDConfig 
 14  import Numeric 
 15  import DataStructs 
 16  from Geometry import rdGeometry 
 17  import PeriodicTable as pyPeriodicTable 
 18  import rdchem 
 19  _HasSubstructMatchStr=rdchem._HasSubstructMatchStr 
 20  from rdchem import * 
 21  from rdmolfiles import * 
 22  from rdmolops import * 
 23   
 24 -def GetSmartsMatchCDXML(mol,patt,maps,which=0,showAllAtoms=0): 
 25    try: 
 26      from Chem import CDXMLWriter 
 27    except: 
 28      CDXMLWriter = None 
 29    if CDXMLWriter is None: 
 30      return '' 
 31    try: 
 32      from cStringIO import StringIO 
 33    except: 
 34      from StringIO import StringIO 
 35    if not showAllAtoms and (which < 0 or not len(maps) or len(maps)<which+1): 
 36      return '' 
 37    io = StringIO() 
 38    matchBonds = [] 
 39    matchAtoms = [] 
 40    if not showAllAtoms: 
 41      mapL = maps[which] 
 42      for bondIdx in range(patt.GetNumBonds()): 
 43        bnd = patt.GetBondWithIdx(bondIdx) 
 44        begIdx = bnd.GetBeginAtomIdx() 
 45        endIdx = bnd.GetEndAtomIdx() 
 46        molBegIdx = mapL[begIdx] 
 47        molEndIdx = mapL[endIdx] 
 48        matchBonds.append(mol.GetBondBetweenAtoms(molBegIdx,molEndIdx).GetIdx()) 
 49    else: 
 50      for mapL in maps: 
 51        for idx in mapL: 
 52          if idx not in matchAtoms: matchAtoms.append(idx) 
 53   
 54    CDXMLWriter.MolToCDXML(mol,io,highlightBonds=matchBonds, 
 55                           highlightAtoms=matchAtoms) 
 56    cdxml = io.getvalue() 
 57    cdxml = cdxml.replace('><','>\n<') 
 58    return cdxml 
 59   
 60 -def DisplaySmartsMatch(mol,patt,maps,which=0,showAllAtoms=0): 
 61    try: 
 62      from utils import chemdraw 
 63    except: 
 64      chemdraw = None 
 65    cdxml = GetSmartsMatchCDXML(mol,patt,maps,which=which,showAllAtoms=showAllAtoms) 
 66    if cdxml and chemdraw: 
 67      chemdraw.CDXDisplay(cdxml) 
 68    return cdxml 
 69     
 70 -def QuickSmartsMatch(smi,sma,unique=1,display=0): 
 71    m = MolFromSmiles(smi) 
 72    p = MolFromSmarts(sma) 
 73    res = m.GetSubstructMatches(p,unique) 
 74    if display: 
 75      DisplaySmartsMatch(m,p,res) 
 76    return res   
 77   
 78 -def CanonSmiles(smi,useChiral=1): 
 79    m = MolFromSmiles(smi) 
 80    return MolToSmiles(m,useChiral) 
 81   
 82 -def SmilesRoundtrip(smi,useChiral=1): 
 83    m = MolFromSmiles(smi) 
 84    refSmi = MolToSmiles(m,useChiral) 
 85    m2 = MolFromSmiles(refSmi) 
 86    smi = MolToSmiles(m2,useChiral) 
 87    if smi!=refSmi: 
 88      print refSmi 
 89      print smi 
 90    return refSmi==smi 
 91   
 92 -def SupplierFromFilename(fileN,delim='',**kwargs): 
 93    ext = fileN.split('.')[-1].lower() 
 94    if ext=='sdf': 
 95      suppl = SDMolSupplier(fileN,**kwargs) 
 96    elif ext=='csv': 
 97      if not delim: 
 98        delim = ',' 
 99      suppl = SmilesMolSupplier(fileN,delimiter=delim,**kwargs) 
100    elif ext=='txt': 
101      if not delim: 
102        delim='\t' 
103      suppl = SmilesMolSupplier(fileN,delimiter=delim,**kwargs) 
104    elif ext=='tdt': 
105      suppl = TDTMolSupplier(fileN,delimiter=delim,**kwargs) 
106    else: 
107      raise ValueError,"unrecognized extension: %s"%ext 
108       
109    return suppl 
110   
111 -def FindMolChiralCenters(mol): 
112    """ 
113      >>> mol = Chem.MolFromSmiles('[C@H](Cl)(F)Br') 
114      >>> FindMolChiralCenters(mol) 
115      [(0, 'R')] 
116      >>> mol = Chem.MolFromSmiles('[C@@H](Cl)(F)Br') 
117      >>> FindMolChiralCenters(mol) 
118      [(0, 'S')] 
119     
120      >>> FindMolChiralCenters(Chem.MolFromSmiles('CCC')) 
121      [] 
122     
123    """ 
124    AssignAtomChiralCodes(mol) 
125    centers = [] 
126    for atom in mol.GetAtoms(): 
127      if atom.HasProp('_CIPCode'): 
128        centers.append((atom.GetIdx(),atom.GetProp('_CIPCode'))) 
129    return centers 
130