Hi Dave,
Thanks for volunteering, but I have already started working on this based
on on some code that Nadine did a while ago. It's probably more efficient
for me to continue on that
-greg
On Wed, May 24, 2017 at 4:38 PM, David Cosgrove <davidacosgrov...@gmail.com>
wrote:
> 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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