[Rdkit-devel] I found Bug
Open-Source Cheminformatics and Machine Learning
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From: Akihiro Y. <aki...@ya...> - 2009-07-16 12:45:03
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Dear developers, Nice to meet you. I am a japanese researcher for computational chemistry, and I am newly studying programming of cheminformatics. Therefore I am studying RDKit code. I am very impressed by your effective, exciting, and beautiful programs. I hope you go to continue to develop RDKit in a long time. And what I would like to say is I found a bug in RDKit. please see around 203th-line of RDKit_Q22009_1/Code/GraphMol/Depictor/EmbeddedFrag.cpp. ----------Orignal-------------- d_eatoms[aid].nbr1 = nb1; d_eatoms[aid].nbr1 = nb2; ------------------------------- ----------Correct?------------- d_eatoms[aid].nbr1 = nb1; d_eatoms[aid].nbr2 = nb2; ------------------------------- This code makes a bug in case of the following (rare) case. I found it when I am reading RDKitQ1_2009, but I think it is not be fixed yet in RDKitQ2_2009. When 4 atoms(e.g. A, B, C and E below) are already assigned their coordinates, and will add the coordinate of D, RDKit makes invalid results. (This is because nb2 is not changed from nb2=0.) (And I found that you changed the initial value of nb2=0 instead of nb2=-1 in RDKitQ1_2009. I think nb2=-1 is preferred rather than nb2=0) B | | A--E---C | | D Best regard. Akihiro Yokota -------------------------------------- Power up the Internet with Yahoo! Toolbar. http://pr.mail.yahoo.co.jp/toolbar/ |