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
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