Bugs item #3496072, was opened at 2012-03-01 12:19 Message generated for change (Tracker Item Submitted) made by You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3496072&group_id=40728
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Command-line Tools Group: 2.3.x Status: Open Resolution: None Priority: 5 Private: No Submitted By: https://www.google.com/accounts () Assigned to: Nobody/Anonymous (nobody) Summary: Smarts and group additivity issue Initial Comment: I am working on command line using obabel ver 2.3.1 on Win 7 machine. I'm working on group additivity calculations (enthalpies). I simply edited the plugindefines.txt adding at the end the definition of my new property (HF_Try) and defined my groups (at the moment: alkanes only) I attached a zip file containig: - plugindefines.txt (last rows are what I edited) - HF_Try.txt (the groups I have added) - HC.txt (input file) There are two main problems: 1 - It looks like when more than 1 H atom is present on the group, multiple (= number of H) matches are found. Using -d or -h combined with --gen2d or --gen3d didn't help. I have inserted in the database only alkanes group, so each attachment will be a saturaded carbon (-[CX4]) I defined the following groups:(HF_Try.txt, attached). First time with SMARTS, to be sure I did it right, I checked them with http://smartsview.zbh.uni-hamburg.de/smartsview/view [CH3](-[CX4]) 11 Primary C [CH2](-[CX4])(-[CX4]) 111 Secondary C [CH](-[CX4])(-[CX4])(-[CX4]) 1111 Tertiary C [C](-[CX4])(-[CX4])(-[CX4])(-[CX4]) 11111 Quaternary C And I tryied with the following Hydrocarbons getting the following results: (C:\Translator>obabel HC.txt -ismi -otxt --append HF_Try) CC 66 CCC 288 CCCC 510 CC(C)C 1210 CCCCC 732 CC(C)CC 1432 CC(C)(C)C 132 Looking at the results the some things seem wrong to me. I figured out how the program gets those results: every time H is present is counted with a "multiplicity" a - Every time there is a match on the methyl group, it is counted 3 times more than expected (CC = 6*11, instead of 2*11) this problem is found also every time a methyl group is present b - Every time a Secondary group is found, it is counted twice (CCC = 2*111 + 6*11, instead of 2*11+111) (CCCC = 4*111 + 6*11, instead of 2*11+2*111) (CCCCC = 6*111+6*11 , instead of 2*11+3*111) c - Tertiary carbons itself seems ok (CC(C)C = 1111 + 9*11 instead 1111 + 3*11, reffers to the (a) in this list) (CC(C)CC = 1111 + 2*111 + 9*11 instead 1111 + 3*11, reffers to (a) and (b) in this list) d - Quaternary carbons are NOT recognized (or multiplyed by 0?) (CC(C)(C)C = 12*11 instead of 11111+4*11) It seems to me that explicit H are somehow bothering the SMILES parser that makes somehow the following multiplication: groupFound*nH. 2 - when a group is NOT present in the database, the program keeps working, while it should probably give me an error message (if not all the atoms have been visited at least one, the calculation should somehow FAIL or warn me, that not all atoms have been visited) Using the same files I submitted C=CC (result: 0) and C=CCC (result: 3*11): the first three carbons have never been evaluated but still there is a result! Thank you for your kind attention, I hope I have been clear enough to help. You are doing a beatyfull job ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3496072&group_id=40728 ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
