O , 2011-10-11 12:52 -0400, Igor Filippov [Contr] rakstīja:
> First of - congratulations on the paper! This gives us a way to give OB
> developers their due by citing the publication.
>
> I have found a few examples of Substances from Pubchem where OB 2.3.0
> gives segfault - my guess is due to th
O , 2011-10-25 12:58 -0700, Gglumov rakstīja:
> Thanks.
>
> Let's consider a string in PDB record:
> ATOM 1457 NH2 ARG A 193 15.283 34.730 -9.206 1.00 9.14
> N
>
> When I talk about atom's name I mean "NH2". I guess, this name hiding
> somewhere in OBAtom, isn't it?
It is
T , 2011-12-21 01:00 -0500, Geoffrey Hutchison rakstīja:
> This e-mail has been long delayed. As 2011 draws to a close, Open Babel
> is over 10 years old! At this point, it's used by over 40 open source
> projects, downloaded over 200,000 times, and been used in over 400
> academic papers. And of c
T , 2011-12-21 14:04 -0500, Geoffrey Hutchison rakstīja:
> > IMHO, OBv3 goals have been set some time ago and many of them are completed
> > now, so its completion
> > should be pursued first since its easier and faster to work with the
> > existing code, especially when most of the functionality
2011/12/22 Geoffrey Hutchison :
>
> On Dec 21, 2011, at 2:52 PM, My Th wrote:
>
>> My point also was not about version numbering, but rather the project v3
>> which has been documented in OB wiki with its goals. I would like to see
>> them reached.
>
> I think
O , 2012-05-01 17:18 +0100, Scott McKechnie rakstīja:
> To whom it may concern,
>
> I am having problems when trying to convert files. I am trying to convert a
> .sdf file to a gaussian input file .com:
>
> babel opt.sdf opt.com
> babel: cannot write output format!
> Open Babel 2.3.1 -- May 1 20
2012/5/11 Gaudreault, Francis :
> Hi Geoff,
>
> Yes I have my OBConversion object.
> Here is the code that compiles correctly:
>
> OpenBabel::OBConversion conv(&ifs,&ofs);
> if(!conv.SetInAndOutFormats(informat,"mol2")){
> strcpy(error,"ERROR: OpenBabel: Formats not available\n");
> return
S , 2012-05-12 15:04 +, Gaudreault, Francis rakstīja:
> OpenBabel is not installed on the hosts that download the Application
> dynamically linked to libopenbabel.
>
> Format files are compiled within the libopenbabel, do I need to also
> set the BABEL_LIBDIR to point to libopenbabel.
How are
Sv, 2012-05-13 20:49 -0700, inviso rakstīja:
> As a disclaimer, I'm an amazingly poor excuse for a chemist. In this
> case, I'm simply a programming resource in a research project so
> please forgive any amateur mistakes or abuses of terminology. The
> project is being done in Python using pybel.
T , 2012-05-23 16:06 +0200, Hitesh Patel rakstīja:
> How can I join two molecules at specified atoms. These joining atoms might
> have same Index numbers, because two joining atoms are in different
> molecules.
It goes along these lines:
builder = ob.OBBuilder()
# Use ring conformations from exis
O , 2012-06-19 18:38 +0100, ovalerio rakstīja:
> Hi Geoff,
>
> Thanks. I'm aiming to use OpenBabel as a platform to learn about
> parallelization using GPU and multicore CPU. I want also to contribute
> the code I develop to the OpenBabel project. Following Noel suggestion I
> am first looking
O , 2012-07-31 17:12 +0400, Чугунов Антон rakstīja:
> Dear open babel users,
> I'm adding hydrogens in python script
> using pep.OBMol.AddHydrogens(False, True, 7) function (where pep is
> pybel molecule). But after saving this to PDB file I've got a problem:
> all hydrogens are written AFTER all h
Pk, 2012-09-14 14:44 -0500, joaquin peralta rakstīja:
> Hello,
>
>
> I have been working in a format for openbabel. I change the files
> neccesary to compile, like the developers suggest
> here http://openbabel.org/docs/2.3.1/WritePlugins/AddFileFormat.html
>
>
> I can compile and install my pl
Pk, 2012-09-14 17:17 -0500, joaquin peralta rakstīja:
> Hello,
>
> Thanks very much for the answer but the problem looks worse now :( ...
> I assign the environment variable, but still there.
>
>
> I don't have any other version of openbabel in the system, and I'm
> using the last subversion.
Pk, 2012-09-14 18:08 -0500, joaquin peralta rakstīja:
> Hello,
>
>
> Before I put all the text, just allow me to explain :
>
>
> I'm not compiling with my plugin, it is just a clean svn version. I
> tried with make clean and make and the problem still, I just set all
> environment variables and
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