Bugs item #3498131, was opened at 2012-03-06 17:26 Message generated for change (Tracker Item Submitted) made by You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3498131&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: Samuele Sommariva () Assigned to: Nobody/Anonymous (nobody) Summary: Wrong valence for Radicals Initial Comment: I am using Open Babel ver 2.3.1 on a win7 Home machine 64bit It seems that open babel cannot compute the valence of ANY radical carbon. Here is how I found this problem I want to find carbon radicals using SmartsDescriptors. To do that, I added a SmartsDescriptor to plugindefines.txt in my working folder according to daylight http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#RAD I tried with some single-radicals, and the program never found a match for the RandomTest.txt file (see attachment) Trying to understand why, I set these following descriptors (in plugindefines.txt) SmartsDescriptor v4 [v4] Number of atoms with valence of 4 SmartsDescriptor v3 [v3] Number of atoms with valence of 3 #the following copied from Daylight SmartsDescriptor CR [CX3v3+0] C radicals When testing the program I had the following output obabel RandomTest.txt -h -ismi -otxt --append cansmi formula CR V3 V4 I had as output the following cansmi formula CR V3 V4 [CH3] CH3 0 0 1 C[CH2] C2H5 0 0 2 C[CH]C C3H7 0 0 3 C[C](C)C C4H9 0 0 4 C=[CH] C2H3 0 0 2 C[C]=C C3H5 0 0 3 C#[C] C2H 0 0 2 No radicals are found (first numeric column). That’s because no carbon has a valence of 3 (second numeric column): all carbons always have valence of 4 (last column). I expected the "v3" being equal to 1 for all the tested molecules and the V4 being lower by 1. It is not clear to me if this is a bug, an unsupported feature or if I didn't really understand what obabel means with "valence". Am I missing something or this is a bug? Samuele samuele.sommar...@gmail.com ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=428740&aid=3498131&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
