Perfect, thank you! On Fri, Sep 15, 2017 at 9:47 AM, Greg Landrum <[email protected]> wrote: > > > On Fri, Sep 15, 2017 at 9:25 AM, Michał Nowotka <[email protected]> wrote: >> >> 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? > > > Sure, here's an example GIST with the code: > https://gist.github.com/greglandrum/431483ac1f9edb03b09c8577031c10e0 > > > -greg > >> On Thu, Sep 14, 2017 at 4:36 PM, Greg Landrum <[email protected]> >> wrote: >> > 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 >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Check out the vibrant tech community on one of the world's most >> >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> _______________________________________________ >> >> Rdkit-discuss mailing list >> >> [email protected] >> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >> > > >
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