Pranav Thakur wrote: > I would like to know how I can use OpenBabelGUI to calculate all the > atoms count of a SMILES and number of single bond, double bond and > triple bond present.
> I want output to be something like this: > Number of triple bonds = 3 > Number of double bonds= 2 > Number of rings =1 Sorry not to reply earlier. The GUI does not provide this straight out of the box, but can be extended as shown below, which may also be useful for more complicated queries. For flexibility and beautiful formatting you would need to use scripting - see, for instance, http://openbabel.org/wiki/Python. Paste the following text into the file plugindefines.txt: SmartsDescriptor sbonds *-* Number of single bonds SmartsDescriptor dbonds *=* Number of double bonds #SmartsDescriptor #tbonds #*#* #Number of triple bonds SmartsDescriptor abonds *:* Number of aromatic bonds SmartsDescriptor bonds *~* Number of bonds\n Add or remove hydrogens to count total or bonds between heavy atoms SmartsDescriptor atoms * Number of atoms\n Add or remove hydrogens to count total or heavy atoms When the GUI is restarted the descriptors sbond, dbonds, etc. will be available (see them listed in the menu item Plugins). In the option "Appends properties or descriptors in list to title" enter, for instance: sbonds dbonds On doing a SMILES to SMILES conversion with "Add hydrogens(make explicit)" checked the numbers of bonds will appear after the title, e.g. CC=C propene 7 1 Additionally, entering _Number single,double bonds= into the "Append to title" box gives CC=C propene_Number single,double bonds= 7 1 There is a bug which prevents triple bonds being counted, so the descriptor for it is commented out above. (Which also illustrates what the bug is!) The development code is corrected. ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
