Is there a later version than 2.3.1.tar.gz that I can download?
From: Noel O'Boyle
Sent: Thursday, April 16, 2020 1:16 PM
To: Bennion, Brian
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: compiling python bindings for obabel 3.0
If yo
I would love to edit the the subject line but outlook online does not offer
that option that I can find so I am starting a new thread.
The issue we have is that unless I want to have my own personally managed and
updated python installation (not using our LC compute clusters) the current
instal
tion (Bakary N'tji Diallo)
--
Message: 1
Date: Tue, 14 Apr 2020 09:53:59 -0400
From: Geoffrey Hutchison
To: "Bennion, Brian"
Cc: "openbabel-discuss@lists.sourceforge.net"
Subject: Re: [Open Babel] Operating on multi molecule sdf files
Message-ID:
Hello
After reading the docs I think that adding individual properties to individual
molecules in a multi molecule sdf files is probably not possible?
I have an sdf file with 500k molecules and I would like to add a little unique
identifier that isn’t a supported descriptor to each molecule and t
this value.
Brian
From: Geoffrey Hutchison
Sent: Monday, November 4, 2019 1:11:02 PM
To: Bennion, Brian
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] issues reading recent gamess output for charge
However, a collaborator sent us source
Hello,
In earlier posts I noted that obabel was segfaulting when trying to read recent
gamess output.
This is still the case.
However, a collaborator sent us source code that for some version of obabel
that actually reads the output
The issue at this point is that it fails to read the char
Hello,
Recently I have tried to convert gamess input and gamess output with obabel has
just resulted in core dumps.
Is there a way to turn on debugging to tell me where the issue might be?
Whether reading or writing or both?
[bennion1@czvnc2 ATBJOBS]$ /usr/gapps/bbs/TOSS-3/bin/obabel -igamess
3
work just fine, though - I use them all the time. But I'll look
into the problem with the test script and sort it out.
Regards,
- Noel
On Thu, 15 Nov 2018 at 15:56, Bennion, Brian
mailto:benni...@llnl.gov>> wrote:
https://github.com/harryjubb/openbabel_python_docker/issues/1
This i
to need to give us more
information about versions of everything. We haven't deprecated Python 2.
Regards,
- Noel
On Thu, 15 Nov 2018 at 01:18, Bennion, Brian via OpenBabel-discuss
mailto:openbabel-discuss@lists.sourceforge.net>>
wrote:
Hello
I tried to compile obabel with python bin
Hello
I tried to compile obabel with python bindings. During testing the last 4 tests
fail. When I searched for the error I found a bug report from June 2018. Has
there been any progress on this since python2 will be deprecated?
Thanks
Brian Bennion
___
Hello
I recently noted with the help of a colleague that atom names were not being
output properly after an OBminimization operation on a pdb file, especially one
that contains a Bromine atom.
The command I use is obminimize -ff UFF -sd -n 5000 -opdb ligand.pdb >
ligandMin.pdb
The input ligand
Hello,
I am curious if there is a way to preserve atom names during conversions when
using obabel. The documentation doesn't explicitly give me any options to this.
Thanks
Brian Bennion
--
Download BIRT iHub F-Type - T
com]
> Sent: Friday, August 23, 2013 12:17 PM
> To: Bennion, Brian
> Cc: openbabel-discuss@lists.sourceforge.net
> Subject: Re: [Open Babel] morpholine moiety protonation state
>
> I don't know if the morpholine should be protonated at not, but if you think
> it should,
Hello,
While trying to prepare a ligand for further calculations I find that one that
contains a morpholine substituent is not protonated properly. At
physiological pH I would expect the nitrogen on the morpholine to be
protonated. Is this incorrect?
The coordinates are given below for the h
Sent: Sunday, January 27, 2013 11:27 AM
To: Bennion, Brian
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] how to turn off gui compilation?
I wanted to check this, so I installed FC 17 64-bit in VMWare. I
installed the packages cmake, libxml2-devel, wxBase and wxGTK and
wxGTK-
dated version on my work fc17 box and see if I can
replicate my problem.
It only has wxGTK.2.8.12 installed.
Brian
From: Noel O'Boyle [baoille...@gmail.com]
Sent: Sunday, January 27, 2013 11:27 AM
To: Bennion, Brian
Cc: openbabel-discuss@lists.sourc
Hello,
While compiling 2.3.2 on x86_64 FC 17 machine I receive the following errors.
I would like to turn off the gui compilation if possible so I can get the code
compiled and working for another program that is dependent upon obabel
libraries.
[ 83%] Building CXX object src/GUI/CMakeFiles/o
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