Hi Hongbin, Thank you for your reply. I will take your suggestions as a good starting point. I too was afraid that I underestimated the difficulty of the task...
That's an interesting point regarding the examples in the recited paper; one of the cited papers (https://pubs.acs.org/doi/10.1021/ci300206e) seemed to suggest that the matrices were made "with aid of RDKit," but I may have read too much into that. I did know that StarDrop could produce such tables, but it has some limitations (with respect to my specific needs) that motivated me to try to devise a more customized solution. I just learned (like an hour ago) that my organization has a license to this software, so I will see if I can live with its limitations in the short term while I work on my own solution. Thanks again! Ken On Sun, Aug 18, 2019, at 11:27 AM, Hongbin Yang wrote: > > 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<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 > > *Attachments:* > * r_matrix example01.png > * r_matrix example02.png
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