Source Code for Package Chem

  1  ## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c 
  2   
  3  # $Id: __init__.py 742 2008-07-05 07:42:38Z glandrum $ 
  4  # 
  5  #  Copyright (C) 2000-2008  greg Landrum and Rational Discovery LLC 
  6  # 
  7  #   @@ All Rights Reserved  @@ 
  8  # 
  9  """ A module for molecules and stuff 
 10   
 11   see Chem/index.html in the doc tree for documentation 
 12    
 13  """ 
 14  import rdBase 
 15  import RDConfig 
 16   
 17  import DataStructs 
 18  from Geometry import rdGeometry 
 19  import PeriodicTable as pyPeriodicTable 
 20  import rdchem 
 21  _HasSubstructMatchStr=rdchem._HasSubstructMatchStr 
 22  from rdchem import * 
 23  from rdmolfiles import * 
 24  from rdmolops import * 
 25   
 26 -def GetSmartsMatchCDXML(mol,patt,maps,which=0,showAllAtoms=0): 
 27    try: 
 28      from Chem import CDXMLWriter 
 29    except: 
 30      CDXMLWriter = None 
 31    if CDXMLWriter is None: 
 32      return '' 
 33    try: 
 34      from cStringIO import StringIO 
 35    except: 
 36      from StringIO import StringIO 
 37    if not showAllAtoms and (which < 0 or not len(maps) or len(maps)<which+1): 
 38      return '' 
 39    io = StringIO() 
 40    matchBonds = [] 
 41    matchAtoms = [] 
 42    if not showAllAtoms: 
 43      mapL = maps[which] 
 44      for bondIdx in range(patt.GetNumBonds()): 
 45        bnd = patt.GetBondWithIdx(bondIdx) 
 46        begIdx = bnd.GetBeginAtomIdx() 
 47        endIdx = bnd.GetEndAtomIdx() 
 48        molBegIdx = mapL[begIdx] 
 49        molEndIdx = mapL[endIdx] 
 50        matchBonds.append(mol.GetBondBetweenAtoms(molBegIdx,molEndIdx).GetIdx()) 
 51    else: 
 52      for mapL in maps: 
 53        for idx in mapL: 
 54          if idx not in matchAtoms: matchAtoms.append(idx) 
 55   
 56    CDXMLWriter.MolToCDXML(mol,io,highlightBonds=matchBonds, 
 57                           highlightAtoms=matchAtoms) 
 58    cdxml = io.getvalue() 
 59    cdxml = cdxml.replace('><','>\n<') 
 60    return cdxml 
 61   
 62 -def DisplaySmartsMatch(mol,patt,maps,which=0,showAllAtoms=0): 
 63    try: 
 64      from utils import chemdraw 
 65    except: 
 66      chemdraw = None 
 67    cdxml = GetSmartsMatchCDXML(mol,patt,maps,which=which,showAllAtoms=showAllAtoms) 
 68    if cdxml and chemdraw: 
 69      chemdraw.CDXDisplay(cdxml) 
 70    return cdxml 
 71     
 72 -def QuickSmartsMatch(smi,sma,unique=1,display=0): 
 73    m = MolFromSmiles(smi) 
 74    p = MolFromSmarts(sma) 
 75    res = m.GetSubstructMatches(p,unique) 
 76    if display: 
 77      DisplaySmartsMatch(m,p,res) 
 78    return res   
 79   
 80 -def CanonSmiles(smi,useChiral=1): 
 81    m = MolFromSmiles(smi) 
 82    return MolToSmiles(m,useChiral) 
 83   
 84 -def SmilesRoundtrip(smi,useChiral=1): 
 85    m = MolFromSmiles(smi) 
 86    refSmi = MolToSmiles(m,useChiral) 
 87    m2 = MolFromSmiles(refSmi) 
 88    smi = MolToSmiles(m2,useChiral) 
 89    if smi!=refSmi: 
 90      print refSmi 
 91      print smi 
 92    return refSmi==smi 
 93   
 94 -def SupplierFromFilename(fileN,delim='',**kwargs): 
 95    ext = fileN.split('.')[-1].lower() 
 96    if ext=='sdf': 
 97      suppl = SDMolSupplier(fileN,**kwargs) 
 98    elif ext=='csv': 
 99      if not delim: 
100        delim = ',' 
101      suppl = SmilesMolSupplier(fileN,delimiter=delim,**kwargs) 
102    elif ext=='txt': 
103      if not delim: 
104        delim='\t' 
105      suppl = SmilesMolSupplier(fileN,delimiter=delim,**kwargs) 
106    elif ext=='tdt': 
107      suppl = TDTMolSupplier(fileN,delimiter=delim,**kwargs) 
108    else: 
109      raise ValueError,"unrecognized extension: %s"%ext 
110       
111    return suppl 
112   
113 -def FindMolChiralCenters(mol): 
114    """ 
115      >>> mol = Chem.MolFromSmiles('[C@H](Cl)(F)Br') 
116      >>> FindMolChiralCenters(mol) 
117      [(0, 'R')] 
118      >>> mol = Chem.MolFromSmiles('[C@@H](Cl)(F)Br') 
119      >>> FindMolChiralCenters(mol) 
120      [(0, 'S')] 
121     
122      >>> FindMolChiralCenters(Chem.MolFromSmiles('CCC')) 
123      [] 
124     
125    """ 
126    AssignAtomChiralCodes(mol) 
127    centers = [] 
128    for atom in mol.GetAtoms(): 
129      if atom.HasProp('_CIPCode'): 
130        centers.append((atom.GetIdx(),atom.GetProp('_CIPCode'))) 
131    return centers 
132