[Open Babel] Segmentation fault in inchi conversion

Hi, I get a segmentation fault when running the following command: obabel -iinchi -:"InChI=1S/2C8H12.Ni/c2*1-2-4-6-8-7-5-3-1;/h2*1-2,7-8H,3-6H2;/b2*2-1-,8-7-;" -osmi I'm running Open Babel 2.3.2 on a MacBook Pro, OSX 10.8.3 (installed via homerbrew). I have also tried it on an Ubuntu box (10.0

Re: [Open Babel] Segmentation fault in inchi conversion

Hi again, Some more information… The InChI "InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-2,7-8H,3-6H2/b2-1-,8-7-" gives the same problem. I have now updated the ubuntu box to also run ob 2.3.2 and it segfaults now as well, so it seems it has something to do with differences between 2.3.1 and 2.3.2. Ki

[Open Babel] Confusion in similarity search

Hi, In a similarity search, obabel consider another molecule than the reference I'm giving. My library being test.smi: C1(=CC2=C(C(C(C2)(C#N)C#N)(CC(=O)C)C#N)C(=O)N)C(=O)NC(=O)S1 A C1(=Cc2c(oc3c(cc(cc3)Br)c2=O)C(=O)N)C(=O)NC(=O)S1B C1(=CC2=C(C(C(C2)(C#N)C#N)(C22=O)C#N)C(=O)N)C(=O)NC(=O

Re: [Open Babel] Confusion in similarity search

> Any ideas apart from shuffling the smiles file? :) At least, for this question, it's ok, I get round the problem to fetch all the values I need. Regards, Pascal -- Precog is a next-generation analytics platform capable

Re: [Open Babel] Confusion in similarity search

On 11/04/2013 15:45, Pascal Muller wrote: > Hi, > > In a similarity search, obabel consider another molecule than the > reference I'm giving. > > My library being test.smi: > > C1(=CC2=C(C(C(C2)(C#N)C#N)(CC(=O)C)C#N)C(=O)N)C(=O)NC(=O)S1 A > C1(=Cc2c(oc3c(cc(cc3)Br)c2=O)C(=O)N)C(=O)NC(=O)S1B >

Re: [Open Babel] Similarity search / Open Babel Warning in ParseSmiles

On 10/04/2013 16:55, Pascal Muller wrote: > Dear all, > > I would like to find similar molecules within library and compute > Tanimoto coefficient. > > I'm right by assuming that, using -at0.0, I should retrieve all molecules? > > obabel library.fs -Smol.smi -ofpt -at0.0 > (version 2.3.2) > > But I

[Open Babel] What's New and Cooking in Open Babel?

I presented a short talk at the recent ACS meeting describing what's new and under development in Open Babel. You can check it out at: http://baoilleach.blogspot.com/2013/04/talk-on-open-babel-at-new-orleans-acs.html Regards, Noel --

Re: [Open Babel] What's New and Cooking in Open Babel?

Nice! Craig On Thu, Apr 11, 2013 at 1:39 PM, Noel O'Boyle wrote: > I presented a short talk at the recent ACS meeting describing what's > new and under development in Open Babel. You can check it out at: > > http://baoilleach.blogspot.com/2013/04/talk-on-open-babel-at-new-orleans-acs.html > > Re

[Open Babel] forcefield setting

Good afternoon, I installed Openbabel on my Windows 7 laptop. I could minimize a molecule by obabel input.sdf -O output.sdf --minimize but when I tried to use a different forcefield by obabel input.sdf -O output.sdf --minimize -ff MMFF94 or "-ff Ghemical" or "-ff MMFF94s" it complains that

Re: [Open Babel] forcefield setting

I just found my answer for the forcefield setting in an earlier post. I should use "--ff" instead of "-ff". But still, if there is a proper way to set up the environment variables, I would be interested to know. LIng -- View this message in context: http://forums.openbabel.org/forcefield-sett