Re: [Open Babel] is there a torsion angle energy minimizer in openbabel?

On 6 July 2012 19:46, Geoff Hutchison wrote: > > Is there an torsion angle energy minimizer in open babel? > > Not per-se. There are multiple general force fields with minimizers, and > you could set up constraints to just minimize torsions and not anything > else. > > Interesting. So, in a nuts

[Open Babel] File format

I am reading molecules from a non-conventional format and I was wondering if someone could tell me if open-babel perhaps already supports it. The format is: t # methane (name of molecule or any other information you want to put such as number of atoms/bonds..etc) v 0 C v 1 C v 2 C u 0 1 1 u 0

[Open Babel] Structure is not tanimoto similar to itself

If I make a file foo.smi with just this in it: [N-]=[N+]=c1c(=O)ccc2=c1c(=O)c1c1c2=O And then make and use an index file: ~/openbabel/bin/obabel foo.smi -ofs ~/openbabel/bin/obabel foo.fs -ocan -sfoo.smi -at5 -aa --title "" I find that the structure is only 0.7 similar to itself. I thoug