Hi Greg,
I'll see about implementing this. I'll liaise with Ed.
Cheers,
Dave
On Sat, May 20, 2017 at 7:00 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
> 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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>
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--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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