Hi Chris, Thanks for your reply!
I've discovered a python package, "mols2grid" that can create a grid of molecular structures. It is based on RDKit: https://github.com/cbouy/mols2grid However, it looks as if it might not be the easiest thing to set up. Recently, I have been working with ChemAxon InstantJChem, and with this I am getting close to the output that I am seeking. Best regards, Rudy On Thu, Mar 31, 2022 at 3:40 PM Christopher Mayer-Bacon <cmaye...@umbc.edu> wrote: > Rudy, > I know RDKit can output molecules as a grid of 2D structures, with several > options for molecule size and stereo information. The functionality isn’t > well-documented though, so I’m not sure if it can do all you described. > The mailing list is usually pretty responsive ( > https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/), so I suggest > asking your question there. > -Chris > > On Thu, Mar 31, 2022 at 3:31 PM Rudy Richardson <rjr...@umich.edu> wrote: > >> Can OpenBabel convert a multi-structure 3D SDF into a table (aka matrix >> or grid) of 2D structures? I would like the 2D structures to convey >> stereochemical information, e.g., via wedge bonds, and to include such >> information for atropisomers (e.g., ortho-substituted biphenyls with >> restricted rotation around the phenyl-phenyl bond). It would also be nice >> to have color options (e.g., oxygen = red, nitrogen = blue, halogens = >> green) and options to include hydrogens on heteroatoms but to exclude >> explicit/implcit hydrogens otherwise. >> >> In addition, I would like to be able to include selected data fields in >> each cell along with the 2D structures (e.g., abbreviated name, MW, >> biological activity). >> >> Each of my SDF files has 90 - 100 structures and each structure has 4 >> data fields. I envision output of up to 5 pages with up to 20 structures >> per page. >> >> Ideally, it would be possible to output a vector-graphics file that could >> either be directly imported into MS Word or PPT. Alternatively, it would be >> good to output something like an SVG file that could be imported into >> Inkscape or Adobe Illustrator for processing and then output in a format >> that could be inserted into MS Word or PPT. If these formats would not be >> possible, then another solution that would work for me would be to export >> the grid as an Adobe PDF file. >> >> I have tried various other programs (e.g., ChemOffice, ChemAxon >> MarvinView, ChemAxon InstantJChem, DataWarrior, Molsoft ICM Browser, MOE, >> and Schrodinger). Some of these come close to what I am seeking, but each >> one has flaws. >> >> Thanks. >> >> Best regards, >> >> Rudy >> >> >> >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > -- > -Christopher Mayer-Bacon (*he/him/his*) > PhD student > Department of Biological Sciences > University of Maryland, Baltimore County >
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