Re: [Open Babel] using Open Babel for virtual library generation

2018-02-06 Thread Stefano Forli
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Re: [Open Babel] using Open Babel for virtual library generation

2018-02-03 Thread Noel O'Boyle
;> Chris >> >> On 30 Jan 2018, at 19:45, openbabel-discuss-request@list >> s.sourceforge.net >> <mailto:openbabel-discuss-requ...@lists.sourceforge.net> >> <mailto:openbabel

Re: [Open Babel] using Open Babel for virtual library generation

2018-02-01 Thread Stefano Forli
t <mailto:openbabel-disc...@lists.sf.net> <mailto:openbabel-disc...@lists.sf.net <mailto:openbabel-disc...@lists.sf.net>>"     mailto:openbabel-disc...@lists.sf.net> <mailto:openbabel-disc...@lists.sf.net <mail

Re: [Open Babel] using Open Babel for virtual library generation

2018-02-01 Thread Noel O'Boyle
gt;> generated a 10 million molecule library doing this. >> >> Cheers, >> >> Chris >> >> On 30 Jan 2018, at 19:45, openbabel-discuss-request@list >>> s.sourceforge.net >>> <mailto:openbabel-discuss-requ...@lists.sour

Re: [Open Babel] using Open Babel for virtual library generation

2018-01-31 Thread Stefano Forli
e: 1 Date: Tue, 30 Jan 2018 15:25:38 + (UTC) From: Siavoush Dastmalchi mailto:siavous...@yahoo.com>> To: "openbabel-disc...@lists.sf.net <mailto:openbabel-disc...@lists.sf.net>" mailto:openbabel-disc...@lists.sf.net>> Subject: [Open Babel] using

Re: [Open Babel] using Open Babel for virtual library generation

2018-01-30 Thread Nicolas Cheron
lecule library doing this. > > Cheers, > > Chris > > On 30 Jan 2018, at 19:45, openbabel-discuss-requ...@lists.sourceforge.net > wrote: > > Message: 1 > Date: Tue, 30 Jan 2018 15:25:38 + (UTC) > From: Siavoush Dastmalchi > To: "openbabel-disc...@lists.sf

Re: [Open Babel] using Open Babel for virtual library generation

2018-01-30 Thread Chris Swain
; Message: 1 > Date: Tue, 30 Jan 2018 15:25:38 + (UTC) > From: Siavoush Dastmalchi mailto:siavous...@yahoo.com>> > To: "openbabel-disc...@lists.sf.net <mailto:openbabel-disc...@lists.sf.net>" > mailto:openbabel-disc...@lists.sf.net>> > Subject: [Open

Re: [Open Babel] using Open Babel for virtual library generation

2018-01-30 Thread Noel O'Boyle
Yes - absolutely. Can you provide a specific example? The SMILES syntax "&" is intended for this use. I'm not sure whether that code is in good shape, but this would be a good chance to test it out and get it working if not. - Noel On 30 January 2018 at 15:25, Siavoush Dastmalchi via OpenBabel-di

Re: [Open Babel] using Open Babel for virtual library generation

2018-01-30 Thread Benjamin Bucior
Hi Siavoush, To my understanding, in OBChemTsfm::Init (phmodel.cpp, around line 208), there's only options to delete atoms, change the atomic number or charge, or modify bonds. If your combinations have very simple rules, you might be able to use a workaround in Open Babel to get around these lim

Re: [Open Babel] using Open Babel for virtual library generation

2018-01-30 Thread Stefano Forli
Hi Siavoush, I've tried a few times with OpenBabel, but since there is no support for actual chemical reactions, its essentially impossible to do. At least for me, the best way to handle the problem is to use the RXN format, which can be used to describe any chemical reactions. For that you m

[Open Babel] using Open Babel for virtual library generation

2018-01-30 Thread Siavoush Dastmalchi via OpenBabel-discuss
Dear List, I was wondering if it is possible to use OB for virtual library generation. For example adding building blocks in a file to different sites of a core structure in a combinatorial manner. Many thanks in advance for you help. Cheers,Siavoush --