Hi Ed,
This is a weak spot; we haven't yet added decent reaction depiction.
The best that's currently available is to use the old drawing code
(Draw.ReactionToImage()) and to make sure that you have the cairo libraries
installed so that you at least have decent drawings. Which operating
system/version of Python are you using?
-greg
On Fri, May 19, 2017 at 5:47 PM, Ed Griffen <ed.grif...@medchemica.com>
wrote:
> Is there a reaction depiction option similar to the MolDraw2DCairo which
> produces much better depictions that the simple Chem.Draw PIL images?
>
> Or am I just doing this wrong?
>
>
> Attempting to push a reaction through MolDraw2DCairo fails with:
>
> Traceback (most recent call last):
> File "drawing_test.py", line 31, in <module>
> rc = rdMolDraw2D.PrepareMolForDrawing(rxn)
> Boost.Python.ArgumentError: Python argument types in
> rdkit.Chem.Draw.rdMolDraw2D.PrepareMolForDrawing(ChemicalReaction)
> did not match C++ signature:
> PrepareMolForDrawing(RDKit::ROMol const* mol, bool kekulize=True,
> bool addChiralHs=True, bool wedgeBonds=True, bool forceCoords=False)
>
> Cheers,
>
> Ed
>
>
> sample code below:
>
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> from rdkit.Chem import Draw
> from rdkit.Chem.Draw import rdMolDraw2D
> from rdkit.Chem import rdDepictor
> from rdkit.Chem.Draw import DrawingOptions
>
> m1 = AllChem.MolFromSmiles('c1ccccc1N(C)C')
> tmp = AllChem.Compute2DCoords(m1)
> Draw.MolToFile(m1,'test_mol_image.png')
> rdDepictor.Compute2DCoords(m1)
>
> rxn = AllChem.ReactionFromSmarts('[C:1](=[O:2])[N:3]>>[N:1][C:3]=[O:2]')
> rimage = Draw.ReactionToImage(rxn)
> rimage.save('test_reaction_image.png')
>
> mc = rdMolDraw2D.PrepareMolForDrawing(m1)
> drawer = Draw.MolDraw2DCairo(300, 300)
> drawer.DrawMolecule(mc)
> drawer.FinishDrawing()
> output = drawer.GetDrawingText()
> with open('test_mol_image_2.png', 'wb') as pngf:
> pngf.write(output)
>
>
> drawer2 = Draw.MolDraw2DCairo(600, 300)
> rc = rdMolDraw2D.PrepareMolForDrawing(rxn)
> drawer2.DrawMolecule(rc)
>
>
>
>
>
>
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