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
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
