Hi Greg,
Very nice demo! I’d like to ask whether we can set the size of the “elements” in a molecular graph rather than the figure size? It is easy to set the width and height when drawing a compound. But when we set two compounds as the same size, e.g. 200*150, they may be actually in different size from the view of a chemist, because in their mind the size of an element (such as a ring, a bond or the font size of an atom symbol) should be the same. So can we make the size of a molecular graph dynamic and keep their element size the same, which means a complex molecule should have a higher size than a simple one. In this example mentioned by Ken, the TOC in https://pubs.acs.org/doi/full/10.1021/ci300206e, the size of the substitutes might be 100*100 or 100*120, and the scaffolds are about 300*150. I am not sure if it is suitable to ask under this thread, but I think you should consider this to “draw” such R-group tables. Best, Hongbin Yang 杨弘宾, Ph.D. Research: Toxicophore and Chemoinformatics Pharmaceutical Science, School of Pharmacy East China University of Science and Technology On 08/20/2019 17:36，Greg Landrum<greg.land...@gmail.com> wrote： I actually had a bit of inspiration while waiting for a connecting flight and think I will have a little demo of this ready in a day or so. -greg On Tue, 20 Aug 2019 at 03:29, Greg Landrum <greg.land...@gmail.com> wrote: This is a great problem, but it's certainly not a trivial one. It's a bit of a triviality, but here's at least a demo of how to draw the R groups with the dummies as "attachment points": https://gist.github.com/greglandrum/f7e310045542ab71447351a8043bbf3f -greg On Sun, Aug 18, 2019 at 2:43 PM ken <k...@postinbox.com> 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 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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