Hi Ken,
I am afraid that you may have underestimated the amount of your demand. At least it includes R group decomposition (and it seems that only two substitutes are considered in your example), drawing molecules, and rendering the “table”. You can use RDKit to decompose the compounds. For example, use maximum common substructure to setup the scaffold, followed by identification of the connecting points by comparing the the compounds and the scaffold. As for drawing molecules, I think RDKit cannot draw the substituent group (I’m not sure) like what ChemDraw does. If you just want to analyse the compounds by R-group decomposition, I believe some kinds of commercial software such as Schrodinger and StarDrap are pretty good. And as for the example in the paper by Gupta-Ostermann et al. I guess that they drew the figures via ChemDraw and Powerpoint rather than scripts. Best regards, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics On 08/18/2019 20:23，ken<[email protected]> wrote： Hello, I am trying to build a 2-D R-group grid (or table, or spreadsheet), where the row headers contain R1 values and the column headers contain R2 values (or vice versa). Compounds that have given R1 and R2 groups would be represented on the table as a filled cell that intersects those R1 and R2. For example, the input could be an SD file containing the following three compounds: The desired output grid from the sd file would look something like this ("Y" can be replaced with cell formatting or some other indicator): The closest thing to this that I have been able to find is the "SAR Matrix" (https://f1000research.com/articles/3-113/v2), but the code that was used to generate the matrices does not appear to be available. Does anyone happen to have such code or know how I can generate it? I imagine the first step would be to perform an R-group decomposition, but I'm not sure what to do from there. I started to see if I could build the program from scratch, but then I thought that someone must've done this before and I shouldn't needlessly reinvent it. I've been (re)learning Python for the past year or so and I think I have a pretty good handle on the language, but I wouldn't mind putting said learning to the test on a "real" project, so if anyone has a solution that outputs something that even vaguely resembles the desired grid/matrix, maybe I can modify it to fit my needs. At some point, I would need the grid to be editable in Word, but I'll cross that bridge when I get to it... Thank you in advance for your help, Ken
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