Hi, sorry to be a pain but I found another few pathetic cases (chemistry has a lot of them). Azulene C10H8 is a merged 5 and 7 ring, purely CH:
% babel -ipdb azulene.pdb -oinchi ---errorlevel 2============================== *** Open Babel Information in NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule azulene.pdb ============================== *** Open Babel Information in NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule azulene.pdb Kekulize: Cannot get an even number of electron for molecule azulene.pdb InChI=1S/C10H8/c1-2-5-9-7-4-8-10(9)6-3-1/h1-8H This is correct. But: % babel -ig09 azulene-g4.log.gz -oinchi ---errorlevel 2============================== *** Open Babel Information in NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule ============================== *** Open Babel Information in NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule Kekulize: Cannot get an even number of electron for molecule InChI=1S/C10H9/c1-2-5-9-7-4-8-10(9)6-3-1/h1-7H,8H2 An additional H is added in the inchi, but not when a pdb or sdf is produced from the gaussian file. This is with development babel version: [artemisia:~/tmp] % babel --version Open Babel 2.3.2 -- Oct 8 2012 -- 09:44:21 Files are at: wget http://folding.bmc.uu.se/azulene.pdb wget http://folding.bmc.uu.se/azulene-g4.log.gz Fulvene C6H6 has a five ring with a doubly bonded CH2 group attached. wget http://folding.bmc.uu.se/fulvene.pdb wget http://folding.bmc.uu.se/fulvene-g4.log.gz Here the pdb input gives the wrong answer too, it adds TWO extra H: % babel -ipdb fulvene.pdb -oinchi ---errorlevel 2 ============================== *** Open Babel Information in NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule fulvene.pdb ============================== *** Open Babel Information in NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule fulvene.pdb Kekulize: Cannot get an even number of electron for molecule fulvene.pdb InChI=1S/C6H8/c1-6-4-2-3-5-6/h2-4H,5H2,1H3 From the gaussian file just one extra H is produced: % babel -ig09 fulvene-g4.log.gz -oinchi ---errorlevel 2 ============================== *** Open Babel Information in NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule ============================== *** Open Babel Information in NewPerceiveKekuleBonds Kekulize: Huckel rule not satisfied for molecule Kekulize: Cannot get an even number of electron for molecule InChI=1S/C6H7/c1-6-4-2-3-5-6/h2,4-5H,1,3H2 Tetracene (C18H12) gives different answers for different gaussian log files: % babel -ig03 tetracene0-opt.log.gz -oinchi InChI=1S/C18H12/c1-2-6-14-10-18-12-16-8-4-3-7-15(16)11-17(18)9-13(14)5-1/h1-12H (correct) % babel -ig03 tetracene-g4.log.gz -oinchi InChI=1S/C18H14/c1-2-6-14-10-18-12-16-8-4-3-7-15(16)11-17(18)9-13(14)5-1/h1-10H,11-12H2 (TWO Hs added) wget http://folding.bmc.uu.se/tetracene0-opt.log.gz wget http://folding.bmc.uu.se/tetracene-g4.log.gz Thanks for reading, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. [email protected] http://folding.bmc.uu.se ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
