Hi Chris, Looks as though my previous reply did not reach you before you sent the link to "mols2grid". I discovered this python package recently, and it definitely looks to be of interest (albeit, at first glance, it appears a bit complicated). There is also a KNIME workflow for mols2grid that is available on the KNIME Hub.
However, I think I am getting close to a solution by using teh form view widget in ChemAxon InstantJChem. Thanks! Rudy On Fri, Apr 1, 2022 at 9:26 AM Chris Swain via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.net> wrote: > Hi, > > Might be worth looking at > > https://github.com/cbouy/mols2grid > > Chris > > > Message: 1 > Date: Thu, 31 Mar 2022 15:24:57 -0400 > From: Rudy Richardson <rjr...@umich.edu> > To: babel <openbabel-discuss@lists.sourceforge.net> > Subject: [Open Babel] SDF to Structure Matrix? > Message-ID: > <cacf_hodr0_4wjt4n_aunrmvftaqlqy7qkhyne+0umgkllvf...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 > -------------- next part -------------- > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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