Thanks, Lukas and Greg, That did the trick. I wrote a couple of functions to encapsulate these ideas and wrote a gist to demonstrate. https://gist.github.com/PatWalters/c4300cd354d4b9c2e87e51ce778a973d
Pat On Thu, May 23, 2019 at 9:42 AM Greg Landrum <greg.land...@gmail.com> wrote: > Thanks for that answer Lukas. > > This is something that's come up before (here's a relatively recent one: > https://sourceforge.net/p/rdkit/mailman/message/35376573/) and it would > probably be worth making this easier. > > rdDepictor.Compute2DCoords takes an optional bondLength argument that > allows you to change the default bond length. We should probably add this > to GenerateDepictionMAtching2DStructure() too. Or would it be more useful > for that that have some (optional) logic that determines the average bond > length in the reference structure and uses that as the default? > > -greg > > On Thu, May 23, 2019 at 3:04 PM Lukas Pravda <lpra...@ebi.ac.uk> wrote: > >> Hi Pat, >> >> >> >> From my experience rdkit uses more or less 1.5 units bond length for 2D >> depictions. So it makes sense if you rescale your template so that the bond >> length is 1.5. >> >> >> >> This is the code snippet I use for the same thing to upscale template >> with bond lengths 1.0 to 1.5 >> >> >> >> import numpy >> >> >> >> factor = 1.5 >> >> >> >> mol = Chem.MolFromMolFile(src, sanitize=True) >> >> matrix = numpy.zeros((4, 4), numpy.float) >> >> >> >> for i in range(3): >> >> matrix[i, i] = factor >> >> matrix[3, 3] = 1 >> >> >> >> AllChem.TransformMol(mol, matrix) >> >> Chem.MolToMolFile(mol, dst) >> >> >> >> Let me know if this is what you were looking for. >> >> >> >> Lukas >> >> *From: *Patrick Walters <wpwalt...@gmail.com> >> *Date: *Thursday, 23 May 2019 at 13:22 >> *To: *RDKIT mailing list <rdkit-discuss@lists.sourceforge.net> >> *Subject: *[Rdkit-discuss] GenerateDepictionMatching2DStructure question >> >> >> >> Hi All, >> >> >> >> I'm trying to align a set of structures to a template that I have as >> molfile. When I call GenerateDepictionMatching2DStructure it appears that >> the coordinate for the template are directly copied. This results in a >> structure like the one below, where the bond lengths for the template are >> different from those in the rest of the molecule. >> >> >> >> [image: image.png] >> >> Is there a way around this so that all of the bond lengths will be the >> same? >> >> >> >> My code is below, thanks in advance, >> >> >> >> Pat >> >> >> >> from rdkit import Chem >> from rdkit.Chem import rdDepictor >> >> >> >> mb = """ >> RDKit 2D >> >> 9 10 0 0 0 0 0 0 0 0999 V2000 >> 2.1845 0.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 1.4701 -0.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 1.4701 -1.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 2.1845 -1.4500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >> 2.8990 -1.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 2.8990 -0.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 >> 3.6836 0.0425 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >> 3.6836 -1.2924 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >> 4.1685 -0.6250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 >> 5 6 1 0 >> 7 9 1 0 >> 6 7 2 0 >> 8 9 1 0 >> 1 6 1 0 >> 1 2 2 0 >> 2 3 1 0 >> 3 4 2 0 >> 4 5 1 0 >> 5 8 2 0 >> M END""" >> >> >> tmplt = Chem.MolFromMolBlock(mb) >> >> smiles = "FC(F)(F)Oc1cccc(-n2nnc3ccc(NC4CCOCC4)nc32)c1" >> mol = Chem.MolFromSmiles(smiles) >> rdDepictor.GenerateDepictionMatching2DStructure(mol, tmplt) >> >> >> >> _______________________________________________ Rdkit-discuss mailing >> list Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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