Re: [Open Babel] Generating all-by-all Tanimoto similarity scores in Microsoft GUI

2015-10-21 Thread seanph16
I've been playing around with the open babel python command line now and have been able to generate the Tanimoto coefficient for one molecule compared against all molecules in my set, however can't figure out how to generate the all-by-all comparison. This is what I am inputting: obab

[Open Babel] Endless run for a particular SMILES

2015-10-21 Thread Sebastien Moretti
Hi I try to convert this SMILES string into a png file but openbabel (2.3.2 Linux 64bits) never stops and produces nothing. CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)[C@H]1OP([O-])(=O)OCC(COC(*)=O)OC(*)=O babel -ismiles SMILES_FILE -p 7.3 -opng

[Open Babel] 3D sdf file generation fails

2015-10-21 Thread Kai Bittermann
Dear OpenBabel discussion forum, I would like to raise two questions: 1) I would like to generate 3D structures from a smiles input - but when I try creating imidazole with "Generate 3D coordinates" ticked: c1cnc[nH]1 I only get the attached awkward 3D sdf. The error is reproducable with OpenB

Re: [Open Babel] Endless run for a particular SMILES

2015-10-21 Thread Jeff Janes
On Tue, Oct 20, 2015 at 6:52 AM, Sebastien Moretti < sebastien.more...@unil.ch> wrote: > Hi > > I try to convert this SMILES string into a png file but openbabel (2.3.2 > Linux 64bits) never stops and produces nothing. > > CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@@H]1[C@@H](O)[C@H > ](

Re: [Open Babel] Generating all-by-all Tanimoto similarity scores in Microsoft GUI

2015-10-21 Thread Matthew Baumgartner
Hi, Check out chemfp. It can do efficient all-by-all similarity calculations. http://chemfp.com/ You can read about NxN searches here: https://chemfp.readthedocs.org/en/latest/using-tools.html#nxn-self-similar-searches On 10/21/2015 09:05 AM, seanph16 wrote: > I've been playing around with the o