Hi Michal,
There are a couple of things in here.
On Fri, Aug 25, 2017 at 11:42 AM, Michał Nowotka <[email protected]> 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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