Source Code for Module Chem.CDXMLWriter

  1  # $Id: CDXMLWriter.py 455 2007-12-18 06:37:48Z glandrum $ 
  2  # 
  3  # Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  """  
  8   
  9  Dumping CDXML from python 
 10   
 11  """ 
 12  from elementtree.SimpleXMLWriter import XMLWriter 
 13  import Chem 
 14   
 15  header = """<?xml version="1.0" encoding="UTF-8" ?> 
 16  <!DOCTYPE CDXML SYSTEM "http://www.camsoft.com/xml/cdxml.dtd" > 
 17  """ 
 18  _fontsStartId=0 
 19   
 20 -def DumpAtom(atom,w,highlightAtoms=[], 
 21               highlightParms={'color':'4','size':'18'}): 
 22    global _fontsStartId 
 23    attrs = {'id':str(atom.GetIdx())} 
 24    if atom.GetAtomicNum()!=6: 
 25      attrs['Element'] = str(atom.GetAtomicNum()) 
 26    if atom.GetFormalCharge()!=0: 
 27      attrs['Charge'] = str(atom.GetFormalCharge()) 
 28    #if atom.ExplicitHydrogenCount()!=0: 
 29    #  attrs['NumHydrogens'] = str(atom.ExplicitHydrogenCount()) 
 30    #  attrs['ImplicitHydrogens'] = "0" 
 31    w.start('n',attrs) 
 32    if highlightAtoms and atom.GetIdx() in highlightAtoms: 
 33      attrs = {} 
 34      attrs.update(highlightParms) 
 35      attrs['font']=attrs.get('font',str(_fontsStartId)) 
 36      w.start('t') 
 37      w.start('s',attrs) 
 38      w.data(atom.GetSymbol()) 
 39      w.end() 
 40      w.end() 
 41    w.end() 
 42   
 43 -def DumpBond(bond,w,baseIdx,highlightBonds=[], 
 44               highlightParms={'color':'4','LineWidth':'2'}): 
 45    attrs = {'id':str(bond.GetIdx()+baseIdx)} 
 46    if bond.GetBondType()!=Chem.BondType.AROMATIC: 
 47      attrs['Order'] = str(int(bond.GetBondType())); 
 48    else: 
 49      attrs['Order'] = str(1.5) 
 50      attrs['Display'] = "Dash" 
 51    attrs['B'] = str(bond.GetBeginAtomIdx()) 
 52    attrs['E'] = str(bond.GetEndAtomIdx()) 
 53    bondDir = bond.GetBondDir() 
 54    if bondDir==Chem.BondDir.BEGINWEDGE: 
 55      attrs['Display'] = "WedgeBegin" 
 56    elif bondDir==Chem.BondDir.ENDWEDGE: 
 57      attrs['Display'] = "WedgeEnd" 
 58    if bond.GetIdx() in highlightBonds: 
 59      attrs.update(highlightParms) 
 60    w.start('b',attrs) 
 61    w.end() 
 62     
 63 -def DumpFrag(frag,w,extrasId,highlightBonds=[],highlightAtoms=[]): 
 64    w.start('fragment',id=str(extrasId)) 
 65    extrasId+=1 
 66    for at in frag.GetAtoms(): 
 67      DumpAtom(at,w,highlightAtoms=highlightAtoms) 
 68    for bond in frag.GetBonds(): 
 69      DumpBond(bond,w,frag.GetNumAtoms()+1,highlightBonds=highlightBonds) 
 70    w.end() 
 71   
 72   
 73 -def MolToCDXML(mol,outF,highlightBonds=[],highlightAtoms=[]): 
 74    global header,_fontsStartId 
 75    outF.write(header) 
 76    w = XMLWriter(outF) 
 77    extrasId = mol.GetNumAtoms()+mol.GetNumBonds()+2 
 78    cdxml = w.start('CDXML') 
 79    w.start('colortable') 
 80    w.element('color',r="1",g="1",b="1") 
 81    w.element('color',r="0",g="0",b="0") 
 82    w.element('color',r="1",g="0",b="0") 
 83    w.element('color',r="0",g="0",b="1") 
 84    w.element('color',r="1",g="1",b="0") 
 85    w.element('color',r="1",g="0",b="1") 
 86    w.end() 
 87    w.start('fonttable') 
 88    _fontsStartId=extrasId 
 89    w.element('font',id=str(extrasId),charset="iso-8859-1",name="Arial") 
 90    extrasId+=1 
 91    w.element('font',id=str(extrasId),charset="iso-8859-1",name="Times New Roman") 
 92    extrasId+=1 
 93    w.end() 
 94    w.start('page',id=str(extrasId)) 
 95    extrasId+=1 
 96    DumpFrag(mol,w,extrasId,highlightBonds=highlightBonds, 
 97             highlightAtoms=highlightAtoms) 
 98    w.end() 
 99    w.close(cdxml) 
100   
101  if __name__ == '__main__': 
102    import sys,cStringIO 
103    try: 
104      from utils import chemdraw 
105    except: 
106      chemdraw = None 
107    import Chem 
108    for smi in ['c1cnccc1','C1=CN=CC=C1']: 
109      print '---------------------------------' 
110      m = Chem.MolFromSmiles(smi) 
111      io = cStringIO.StringIO() 
112      MolToCDXML(m,io,highlightBonds=[1,2,3],highlightAtoms=[3]) 
113      txt = io.getvalue() 
114      txt = txt.replace('><','>\n<') 
115      cdxml = txt 
116      if chemdraw: 
117        chemdraw.CDXDisplay(cdxml) 
118      print cdxml 
119