Re: [Open Babel] add hydrogens appropriate for pH

The (de)protonation rules are stored as a list of transformation using SMARTS format in a file called /phmodel.txt/inside the /data/ directory. Such file is editable but as Geoff suggested is not trivial to carefully enumerate all the potential transformations for many functional groups and substru

Re: [Open Babel] ANNOUNCE: Open Babel 2.4.0 Released

That's great Geoff! Thank you for the info and congrats again for the new OB version! Gio -- View this message in context: http://forums.openbabel.org/ANNOUNCE-Open-Babel-2-4-0-Released-tp4659490p4659505.html Sent from the General discussion mailing list archive at Nabble.com.

Re: [Open Babel] ANNOUNCE: Open Babel 2.4.0 Released

Wonderful news! It seems a big step forward. Congrats to you all guys! I would have a question about it. In the SourceForge page one of the reported new feature/improvment is: '3D generation: "--gen3d", allow user to specify the desired speed/quality' I would be interested in exploring such a pos

Re: [Open Babel] How to enumerate all possible stereoisomers of a molecule with a not defined stereocenter?

Thank you so much Stefano. You are very kind. I will give a try to the script, keeping an eye on the structures as you suggested. I appreciated it very much. -- View this message in context: http://forums.openbabel.org/How-to-enumerate-all-possible-stereoisomers-of-a-molecule-with-a-not-defined

[Open Babel] How to enumerate all possible stereoisomers of a molecule with a not defined stereocenter?

Hi everybody, Starting from a certain molecule with possibly undefined sp3 stereocenters (R/S) is it possible to enumerate with OpenBabel all the possible stereisomers as different molecules? Any help is appreciated. Thanks Gio -- View this message in context: http://forums.openbabel.org/How-to

Re: [Open Babel] Generate SMILES with stereocenters defined only for sdf constrained centers

That is exactly what I want. Thank you so much Noel! Giovanni -- View this message in context: http://forums.openbabel.org/Generate-SMILES-with-stereocenters-defined-only-for-sdf-constrained-centers-tp4656565p4656574.html Sent from the General discussion mailing list archive at Nabble.com. -

[Open Babel] Generate SMILES with stereocenters defined only for sdf constrained centers

Hello everybody, When a canonical SMILES is generated from a 2D structure (sdf format) the stereocenters are defined as expected only for those centers which are constrained (with sdf stereo flags) in the input file. Conversely when a canonical SMILES is generated from a 3D structure (sdf format)

Re: [Open Babel] Calculating partial charges with openbabel of a positively charged molecule

Hi Christos, Please, can you tell us if you're using the tag "--partialcharge gasteiger" or not, in your calculation? I was having the same problem with many charged molecules. I noticed that if you do NOT use that tag, obabel correctly calculate the partial charges. For example if you're calcula

Re: [Open Babel] one input file - multiple output files

Hi, Sure! This is as easy as digit: obabel -ipdb input.pdb -ocan -m -O output.smi Where for each molecule contained in input.pdb it will output a file called output[serial_number].smi being the first output1.smi This can be obtained for different input and output formats. Cheers, green69 201

Re: [Open Babel] ANNOUNCE: Open Babel 2.3.1 Release

Congratulation to everybody guys!!! 2011/10/17 Geoffrey Hutchison > I am very happy to finally announce the release of Open Babel 2.3.1, a > major update release of the open source chemistry toolbox. > > Open Babel has been downloaded nearly 200,000 times and is used in over 45 > projects and ov

Re: [Open Babel] Open Babel Paper Published in J Cheminf

Congratulation to everybody! 2011/10/7 Geoffrey Hutchison > I'm glad to announce that after 10 years, we finally got around to > publishing a paper on Open Babel. :-) > > Noel M. O’Boyle , Michael Banck , Craig A. James , Chris Morley , Tim > Vandermeersch, Geoffrey R. Hutchison. “Open Babel: A