Source Code for Module Chem.Draw.DrawUtils

  1  # $Id: DrawUtils.py 2 2006-05-06 22:54:39Z glandrum $ 
  2  # 
  3  #  Copyright (C) 2004-2006 Rational Discovery LLC 
  4  # 
  5  #   @@ All Rights Reserved  @@ 
  6  # 
  7  import os 
  8  from MolDrawing import MolDrawing 
  9  from sping.SVG.pidSVG import SVGCanvas as Canvas 
 10  from sping import pid 
 11  import tempfile 
 12   
 13  _batikLoc=os.environ.get('BATIK_HOME','/usr/local/src/batik-1.5.1/') 
 14  _batikJar='batik-rasterizer.jar' 
 15  _javaExe='/usr/java/j2sdk1.4.2_05/bin/java' 
 16   
 17 -def Init(batikLoc=None,batikJar=None,javaExe=None): 
 18    global _batikLoc,_batikJar,_javaExe 
 19    if batikLoc: _batikLoc = batikLoc 
 20    if batikJar: _batikJar = batikJar 
 21    if javaExe:  _javaExe  = javaExe 
 22   
 23    if os.path.exists(os.path.join(_batikLoc,_batikJar)): 
 24      return 1 
 25    else: 
 26      return 0 
 27       
 28 -def MolsToJpeg(mols,filenames,size=(200,200),dblSize=0,frame=0, 
 29                highlightAtoms=None, 
 30                verbose=0): 
 31    if isinstance(filenames,basestring): 
 32      mols = [mols] 
 33      filenames = [filenames] 
 34      if highlightAtoms: highlightAtoms = [highlightAtoms] 
 35   
 36    cmd = _javaExe 
 37    batik = os.path.join(_batikLoc,_batikJar) 
 38    javaArgs='-Djava.awt.headless=true -jar %s'%batik 
 39    canvas = Canvas(size=size) 
 40    drawing = MolDrawing(canvas) 
 41   
 42    if dblSize: 
 43      drawing.atomLabelFontSize=18 
 44      drawing.bondLineWidth *= 2 
 45      drawing.dblBondOffset *= 2 
 46       
 47    if verbose: sys.stderr.write('generating SVG\n') 
 48    svgNames = [] 
 49    for i,mol in enumerate(mols): 
 50      filename = filenames[i] 
 51      if highlightAtoms: 
 52        highlight=highlightAtoms[i] 
 53      else: 
 54        highlight=None 
 55      canvas.clear() 
 56      drawing.AddMol(mol,canvas=canvas,highlightAtoms=highlight) 
 57      svgName = '%s.svg'%(filename.split('.jpg')[0]) 
 58      if frame: 
 59        canvas.drawRect(0,0,size[0]-1,size[1]-1,edgeColor=pid.black) 
 60      canvas.save(svgName) 
 61      svgNames.append(svgName) 
 62   
 63    if verbose: sys.stderr.write('converting to jpg:\n') 
 64    fNames=' %s'%(' '.join(svgNames)) 
 65    fmtArgs='-m image/jpeg -dpi 100 -w %d -h %d -q .80'%(size[0],size[1]) 
 66   
 67    try: 
 68      #res = os.spawnlp(os.P_WAIT,cmd,javaArgs,'-m image/jpeg','-dpi 100', 
 69      #          '-q .80','-w',size[0],'-h',size[1],fNames) 
 70      arg = '%s %s %s %s &> /dev/null'%(cmd,javaArgs,fmtArgs,fNames) 
 71      os.system(arg) 
 72    except: 
 73      import traceback 
 74      if verbose: traceback.print_exc() 
 75      ok = 0 
 76    else: 
 77      ok = 1 
 78   
 79      for name in svgNames: 
 80        try: 
 81          #os.unlink(name) 
 82          pass 
 83        except: 
 84          import traceback 
 85          if verbose: traceback.print_exc() 
 86    return ok 
 87 -def SmilesToJpeg(smiles,filenames,**kwargs): 
 88    import Chem 
 89    if isinstance(filenames,basestring): 
 90      smiles = [smiles] 
 91      filenames = [filenames] 
 92    mols = [] 
 93    for smi in smiles: 
 94      mol = Chem.MolFromSmiles(smi) 
 95      Chem.Compute2DCoords(mol) 
 96      mols.append(mol) 
 97    return MolsToJpeg(mols,filenames,**kwargs) 
 98       
 99  if __name__=='__main__': 
100    import Chem 
101    import tempfile 
102    fN1 = tempfile.mktemp('.jpg') 
103    print fN1 
104    SmilesToJpeg(['c1ccccc1C(=O)O','c1ccccc1C(=O)N'], 
105                 [fN1,'foo2.jpg'],size=(300,300),verbose=1, 
106                 highlightAtoms=[range(3),range(4)],dblSize=1, 
107                 frame=1) 
108