Source Code for Package rdkit.Chem.Draw

  1  # $Id: __init__.py 1763 2011-06-18 04:48:57Z glandrum $ 
  2  # 
  3  # Copyright (C) 2006-2011 Greg Landrum 
  4  #  All Rights Reserved 
  5  # 
  6  import os 
  7   
  8 -def _getCanvas(): 
  9    useAGG=False 
 10    useCairo=False 
 11    Canvas=None 
 12    if not os.environ.get('RDKIT_CANVAS',''): 
 13      try: 
 14        from cairoCanvas import Canvas 
 15        useCairo=True 
 16      except ImportError: 
 17        try: 
 18          from aggCanvas import Canvas 
 19          useAGG=True 
 20        except ImportError: 
 21          from spingCanvas import Canvas 
 22    else: 
 23      canv=os.environ['RDKIT_CANVAS'].lower() 
 24      if canv =='cairo': 
 25        from cairoCanvas import Canvas 
 26        useCairo=True 
 27      elif canv =='agg': 
 28        from aggCanvas import Canvas 
 29        useAGG=True 
 30      else: 
 31        from spingCanvas import Canvas       
 32    return useAGG,useCairo,Canvas 
 33   
 34 -def MolToImage(mol, size=(300,300), kekulize=True, wedgeBonds=True, 
 35                 canvas=None, **kwargs): 
 36    """ returns a PIL image containing a drawing of the molecule 
 37   
 38      Keyword arguments: 
 39      kekulize -- run kekulization routine on input `mol` (default True) 
 40      size -- final image size, in pixel (default (300,300)) 
 41      wedgeBonds -- draw wedge (stereo) bonds (default True) 
 42      highlightAtoms -- list of atoms to highlight (default []) 
 43      highlightMap -- dictionary of (atom, color) pairs (default None) 
 44    """ 
 45    from MolDrawing import MolDrawing 
 46    if not mol: 
 47      raise ValueError,'Null molecule provided' 
 48    if canvas is None: 
 49      useAGG,useCairo,Canvas=_getCanvas() 
 50      if useAGG or useCairo: 
 51        import Image 
 52        img = Image.new("RGBA",size,"white") 
 53        canvas = Canvas(img) 
 54      else: 
 55        from spingCanvas import Canvas 
 56        canvas = Canvas(size=size,name='MolToImageFile') 
 57        img = canvas._image 
 58    drawer = MolDrawing(canvas) 
 59   
 60    if kekulize: 
 61      from rdkit import Chem 
 62      mol = Chem.Mol(mol.ToBinary()) 
 63      Chem.Kekulize(mol) 
 64       
 65    if not mol.GetNumConformers(): 
 66      from rdkit.Chem import AllChem 
 67      AllChem.Compute2DCoords(mol) 
 68     
 69    drawer.wedgeDashedBonds=wedgeBonds 
 70    drawer.AddMol(mol,**kwargs) 
 71    canvas.flush() 
 72   
 73    return img 
 74   
 75 -def MolToFile(mol,fileName,size=(300,300),kekulize=True, wedgeBonds=True, 
 76                imageType=None,**kwargs): 
 77    """ Generates a drawing of a molecule and writes it to a file 
 78    """ 
 79    from MolDrawing import MolDrawing 
 80    # original contribution from Uwe Hoffmann 
 81    if not fileName: 
 82      raise ValueError,'no fileName provided' 
 83    if not mol: 
 84      raise ValueError,'Null molecule provided' 
 85   
 86     
 87    if imageType is None: 
 88      imageType=os.path.splitext(fileName)[1][1:] 
 89   
 90    useAGG,useCairo,Canvas = _getCanvas() 
 91    if useCairo or useAGG: 
 92      canvas = Canvas(size=size,imageType=imageType, 
 93                                fileName=fileName) 
 94    else: 
 95      canvas = Canvas(size=size,name=fileName,imageType=imageType) 
 96    drawer = MolDrawing(canvas) 
 97    if kekulize: 
 98      from rdkit import Chem 
 99      mol = Chem.Mol(mol.ToBinary()) 
100      Chem.Kekulize(mol) 
101       
102    if not mol.GetNumConformers(): 
103      from rdkit.Chem import AllChem 
104      AllChem.Compute2DCoords(mol) 
105     
106    drawer.wedgeDashedBonds=wedgeBonds 
107    drawer.AddMol(mol,**kwargs) 
108    if useCairo or useAGG: 
109      canvas.flush() 
110    else: 
111      canvas.save() 
112   
113 -def MolToImageFile(mol,filename,size=(300,300),kekulize=True, wedgeBonds=True, 
114                     **kwargs): 
115    """  DEPRECATED:  please use MolToFile instead 
116   
117    """ 
118    img = MolToImage(mol,size=size,kekulize=kekulize,wedgeBonds=wedgeBonds,**kwargs) 
119    img.save(filename) 
120       
121  tkRoot=None 
122  tkLabel=None 
123  tkPI=None 
124 -def ShowMol(mol,size=(300,300),kekulize=True,wedgeBonds=True, 
125              title='RDKit Molecule',**kwargs): 
126    """ Generates a picture of a molecule and displays it in a Tkinter window 
127    """ 
128    global tkRoot,tkLabel,tkPI 
129    import Tkinter 
130    import ImageTk 
131   
132    img = MolToImage(mol,size,kekulize,wedgeBonds,**kwargs) 
133   
134    if not tkRoot: 
135      tkRoot = Tkinter.Tk() 
136      tkRoot.title(title) 
137      tkPI = ImageTk.PhotoImage(img) 
138      tkLabel = Tkinter.Label(tkRoot,image=tkPI) 
139      tkLabel.place(x=0,y=0,width=img.size[0],height=img.size[1]) 
140    else: 
141      tkPI.paste(img) 
142    tkRoot.geometry('%dx%d'%(img.size)) 
143