Dear All, Today I have spent some time processing a freely-available SDF that contains many compounds and melting-points / ranges ( http://www.mdpi.org/molmall/mdpi1-51sd.zip). The reason for doing this is that I wanted to implement a melting-point predictor following the work of Andreas Bender (J. Chem. Inf. Model. 2005, 45, 581-590) and more recently Reifeng Liu at AZ (J. Chem. Inf. Model. 2008, 48, 981-987). I have attached the python-script that I have at the moment (a) in case it is of some use to anybody else, (b) in the hope that I can improve my python and rdkit abilities through any suggested alterations (I'm sure there are many!), and (c) to form the basis of a couple of questions. At the moment, the script is just running through each compound; checking if the molecule is valid; and if so, noting how many components, and whether any of the atoms are outside of the desired list. These two results are then written out to a new SDF. I am then using this to make sure my data-set contains only compounds that I would say are 'reasonable' to build a melting-point model with. Now for the questions: 1. In RDKit, has the 'cleaning / washing / salt-stripping' of molecules already been formalised based on a set of rules, etc? 2. When identifying compounds that contain a non-allowed atom-type, why do I find the SMARTS def [!H;!C;!N;!O;!F;!S;!Cl;!Br;!I] gives unexpected results, but [!#1;!#6;!#7;!#8;!#9;!#16;!#17;!#35;!#53] works as I would expect? Kind regards James
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inorg_or_mix.py
Description: inorg_or_mix.py
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