Thanks Greg, very helpful!
Can you tell me how should I modify my code to provide the list of
bonds to be highlighted, so I get the image generated by DrawMolecules
looking the same way as produced by DrawMolecule?
On Thu, Sep 14, 2017 at 4:36 PM, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Michal,
>
> There are a couple of things in here.
>
> On Fri, Aug 25, 2017 at 11:42 AM, Michał Nowotka <mmm...@gmail.com> wrote:
>>
>> Hi,
>>
>> I finally decided to try the new C++ drawing code and I found some
>> issues with it. I'll try to descibe my problems.
>>
>> First, lets start with a code that works perfectly:
>>
>> from rdkit import Chem
>> from rdkit.Chem.AllChem import Compute2DCoords
>> from rdkit.Chem.Draw import rdMolDraw2D
>>
>> m = Chem.MolFromSmiles('O=C(C)Oc1ccccc1C(=O)O')
>> Compute2DCoords(m)
>> drawer = rdMolDraw2D.MolDraw2DCairo(500, 500)
>>
>> drawer.DrawMolecule(m,highlightAtoms=m.GetSubstructMatch(Chem.MolFromSmarts('c1ccccc1')))
>> drawer.FinishDrawing()
>> with open('aspirin_a.png','wb') as f:
>> f.write(drawer.GetDrawingText())
>>
>> This code produces the attached 'aspirin_a.png' image, that looks perfect.
>
>
> Yay! :-)
>
>>
>> Now, apart from the `DrawMolecule` there is also `DrawMolecules`
>> function exposed by the `MolDraw2DCairo` module. So what will happen
>> when I use it to render the same molecule?
>>
>> from rdkit import Chem
>> from rdkit.Chem.AllChem import Compute2DCoords
>> from rdkit.Chem.Draw import rdMolDraw2D
>>
>> m = Chem.MolFromSmiles('O=C(C)Oc1ccccc1C(=O)O')
>> Compute2DCoords(m)
>> drawer = rdMolDraw2D.MolDraw2DCairo(500, 500)
>>
>> drawer.DrawMolecules([m],highlightAtoms=[m.GetSubstructMatch(Chem.MolFromSmarts('c1ccccc1'))])
>> drawer.FinishDrawing()
>> with open('aspirin_b.png','wb') as f:
>> f.write(drawer.GetDrawingText())
>>
>>
>> The image is different - only atoms are highlighted, bonds between
>> atoms are not (see the attached 'aspirin_b.png') image.
>
>
> Short answer: DrawMolecules() requires you to provide the list of bonds to
> be highlighted too. This is just a couple of lines of code.
>
>>
>> OK, but who would use `DrawMolecules` to render a single compound
>> anyway? I think it's meant to render multiple compounds at once. The
>> 'old' drawing code has a function called `MolsToGridImage` to do this.
>> And it has a `molsPerRow` parameter which makes it easy to define a
>> shape of the grid. I couldn't find a similar function in the 'new'
>> drawing code so it looks like using `DrawMolecules` is the only way to
>> render multiple mols at once. Let's try that:
>>
>> from rdkit import Chem
>> from rdkit.Chem.AllChem import Compute2DCoords
>> from rdkit.Chem.Draw import rdMolDraw2D
>>
>> m1 = Chem.MolFromSmiles('O=C(C)Oc1ccccc1C(=O)O')
>> Compute2DCoords(m1)
>> m2 = Chem.MolFromSmiles('c1cccnc1O')
>> Compute2DCoords(m2)
>> drawer = rdMolDraw2D.MolDraw2DCairo(500, 500)
>> drawer.DrawMolecules([m1, m2])
>> drawer.FinishDrawing()
>> with open('mols.png','wb') as f:
>> f.write(drawer.GetDrawingText())
>
>
> The MolDraw2D constructors can be called with additional arguments that
> provide the size of the panes used to render grids of molecules.
> For example, here's the code to draw two molecules side by side derived from
> your example:
> from rdkit import Chem
> from rdkit.Chem.Draw import rdMolDraw2D
>
> m1 = Chem.MolFromSmiles('O=C(C)Oc1ccccc1C(=O)O')
> pm1 = rdMolDraw2D.PrepareMolForDrawing(m1)
> m2 = Chem.MolFromSmiles('c1cccnc1O')
> pm2 = rdMolDraw2D.PrepareMolForDrawing(m2)
> drawer = rdMolDraw2D.MolDraw2DCairo(600,300,300,300)
> drawer.DrawMolecules([m1, m2])
> drawer.FinishDrawing()
> with open('mols.png','wb') as f:
> f.write(drawer.GetDrawingText())
>
>
> I've switched to use PrepareMolForDrawing() (because I think it's nice to
> have kekule structures and wedged bonds) and provided a canvas size of
> 600x300 divided into 300x300 panels. The code figures out that this means 2
> mols per row.
>
> It's somewhat curious (and I don't mean that in a good way) that this hasn't
> made it onto the RDKit master yet (instead of using the hack that's
> currently there). I will try to get that done before the next release.
>
> To summarize:
>>
>>
>> - `DrawMolecules` doesn't highlight bonds in the same way as the
>> `DrawMolecule` does
>
>
> correct. That's by design (correct method described above)
>
>> - There is no equivalent of the `MolsToGridImage` where I can define
>> the shape of the grid of molecules at least nothing documented in
>>
>> http://www.rdkit.org/Python_Docs/rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D-class.html
>
>
> Right, it's not documented, but hopefully what I have above helps you see
> how to do it.
>>
>>
>> - `DrawMolecules` does nothing to layout molecules in such a way that
>> they don't obscure each other
>
>
> Correct. It does what you tell it to do, but hopefully the rest of the
> answer tells you how to tell it the right thing.
>
> -greg
>
>
>>
>>
>> Regards,
>>
>> Michał Nowotka
>>
>>
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