Re: [Rdkit-discuss] multiline legend in MolsToGridImage
Open-Source Cheminformatics and Machine Learning
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From: David H. <li...@co...> - 2016-12-20 10:59:55
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The replace and split methods were removed from the string module in python3. You can replace the code as follows: s = s.replace('\r\n', '\n') s = s.replace('\n\r', '\n') s = s.replace('\r', '\n') lines = s.split('\n') On Tue, Dec 20, 2016 at 2:45 AM, Pavel Polishchuk <pav...@uk...> wrote: > Hi, > > I try to print multiline legends for molecules in a grid and use the > following code from notebook > > from rdkit import Chem > from rdkit.Chem import Draw > # from rdkit.Chem.Draw import IPythonConsole > > mols = [Chem.MolFromSmiles(s) for s in ["CCC", "CCCCC"]] > legends = ["1\nCCC", "2\nCCCCC"] > Draw.MolsToGridImage(mols, molsPerRow=5, subImgSize=(200,200), > legends=legends) > > it returns error: AttributeError: module 'string' has no attribute > 'replace' (full stack is below) > > If I uncomment IPythonConsole import then it returns the picture with > labels, but with spaces instead of new line symbols. > > What can I do in this situation? RDKit 2016.03.2 > > Kind regards, > Pavel. > > > ---------------------------------------------------------------------------AttributeError Traceback (most recent call last)<ipython-input-2-684f4abceace> in <module>() 1 mols = [Chem.MolFromSmiles(s) for s in ["CCC", "CCCCC"]] 2 legends = ["1\nCCC", "2\nCCCCC"]----> 3 p = Draw.MolsToGridImage(mols, molsPerRow=5, subImgSize=(200,200), legends=legends) > /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py in MolsToGridImage(mols, molsPerRow, subImgSize, legends, highlightAtomLists, useSVG, **kwargs) 387 else: 388 return _MolsToGridImage(mols,molsPerRow=molsPerRow,subImgSize=subImgSize,--> 389 legends=legends, highlightAtomLists=highlightAtomLists, **kwargs) 390 391 def ReactionToImage(rxn, subImgSize=(200,200),**kwargs): > /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py in _MolsToGridImage(mols, molsPerRow, subImgSize, legends, highlightAtomLists, **kwargs) 334 highlights=highlightAtomLists[i] 335 if mol is not None:--> 336 img = _moltoimg(mol,subImgSize,highlights,legends[i],**kwargs) 337 res.paste(img,(col*subImgSize[0],row*subImgSize[1])) 338 return res > /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py in _moltoimg(mol, sz, highlights, legend, **kwargs) 302 if not hasattr(rdMolDraw2D,'MolDraw2DCairo'): 303 img = MolToImage(mol,sz,legend=legend,highlightAtoms=highlights,--> 304 **kwargs) 305 else: 306 nmol = rdMolDraw2D.PrepareMolForDrawing(mol,kekulize=kwargs.get('kekulize',True)) > /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py in MolToImage(mol, size, kekulize, wedgeBonds, fitImage, options, canvas, **kwargs) 132 # color=(0,0,1),fill=False,stroke=True) 133 font=Font(face='sans',size=12)--> 134 canvas.addCanvasText(legend,pos,font) 135 136 if kwargs.get('returnCanvas',False): > /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/spingCanvas.py in addCanvasText(self, text, pos, font, color, **kwargs) 72 labelP = pos[0]-txtWidth/2+offset,pos[1]+txtHeight/2 73 color = convertColor(color)---> 74 self.canvas.drawString(text,labelP[0],labelP[1],font,color=color) 75 return (bw,bh,offset) 76 > /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/PIL/pidPIL.py in drawString(self, s, x, y, font, color, angle, **kwargs) 313 if '\n' in s or '\r' in s: 314 self.drawMultiLineString(s, x,y, font, color, angle,--> 315 **kwargs) 316 return 317 if not font: font = self.defaultFont > /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/pid.py in drawMultiLineString(self, s, x, y, font, color, angle, **kwargs) 393 dy = h * math.cos(angle*math.pi/180.0) 394 dx = h * math.sin(angle*math.pi/180.0)--> 395 s = string.replace(s, '\r\n', '\n') 396 s = string.replace(s, '\n\r', '\n') 397 s = string.replace(s, '\r', '\n') > AttributeError: module 'string' has no attribute 'replace' > > > > ------------------------------------------------------------ > ------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today.http://sdm.link/intel > _______________________________________________ > Rdkit-discuss mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > |