[Open Babel] Question about Conformer Search
Dear users of openbabel, I am trying to generate conformers using openbabel. After trying confab, which takes rather long for large molecules, I tried the genetic algorithm and got really nice results. However, when I was testing different scoring methods I noticed that the results I obtained from "minrmsd" and "minenergy" looked fairly similar to those obtained using "rmsd". Glancing over the source I found "minenergy" and "minrmsd" to be implemented but the respective command-line parameter ignored. Is there any particular reason for this? I am using Open Babel 2.3.90 on a Linux system. On another note: Using the conformer generation, I wanted to change the number of generations without change before convergence is considered to be reached. However, the command-line parameter "--converge #" output by "obabel -L conformer" is ignored since the programme actually looks for "--convergence #". I would suggest to change one of the two to avoid possible further confusion. Best regards and thank you very much in advance Torsten Sachse This message was sent through https://webmail.uni-jena.de -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Two smi conversion problems
I originally used "C=0" but using "[C-]#[O+]" gives the following roundtrip for me: [C-]#[O+] -> SDF -> [C-]#[OH] Since writing the above I tried installing the latest version of Open Babel and using "C=0" now gives an error and using "[C-]#[O+]" gives the correct result. Thanks for the help with this, I think the new version has solved the problem. Best wishes, Scott On 13 March 2014 12:22, Geoffrey Hutchison wrote: > Thanks for the reply, the sdf file was actually produced from a smiles > string using gen3d. > > > OK, I guessed that, but what was the original SMILES? And what version of > Open Babel are you using? The current development code roundtrips: > > [C-]#[O+] -> SDF -> [C-]#[O+] > > Thanks, > -Geoff > -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
