On Mar 2, 2017, at 20:34, Craig James wrote:
> Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states that
> the "organic subset" are only allowed outside of brackets if they're in their
> normal lowest-valence state. Actually, now that I read it, it's
On Jan 17, 2013, at 6:20 PM, Kirill Okhotnikov wrote:
I decided to implement bzip2 pack/unpack functionality in open-babel
(#91 bzip2 compression/decompression).
What does the #91 mean? It's not the Open Babel bug id, and a search
of the mailing list finds nothing matching bzip or bzip2.
I do
On Dec 21, 2010, at 10:55 PM, erapp wrote:
I need to be able
to find all unique fragments for a molecule of a given length (i.e. number
of atoms in fragment) and provide information about what makes it unique.
You might be able to adapt some code I wrote a few weeks ago, at
On Nov 11, 2010, at 9:58 PM, Noel O'Boyle replied to Andrew Dalke:
Since I'm not (directly) calling WriteMolecule and since my
test cases don't support the --gen2D or --gen3d flags, this
warning isn't that helpful in a library function.
This is by design (added recently). Up until recently
On Sep 30, 2010, at 2:34 PM, TJ O'Donnell wrote:
I just got an alert from SUPERAntiSpyware that Trojan Downloader-gen/A is in
E:\My Documents\openbabel\openbabel-2.2.3\build\CMakeFiles\CompilerIdC\a.exe
on my computer.
http://www.processlibrary.com/directory/files/a/ says
a.exe is registered
On Jul 6, 2010, at 11:58 AM, Geoffrey Hutchison wrote:
I have some general concerns about using GPLv2 or later with the Silicos
code right now, since it is currently covered by an expiring patent. I
suspect this would be an easy change once the patent expires next year.
I see your point. I
your contribution and make it work
with, under Indigo, which is a relatively recent cheminformatics code
released under GPLv3.
Best regards,
Andrew Dalke
da...@dalkescientific.com
On Apr 12, 2010, at 3:04 AM, Geoffrey Hutchison wrote:
I'd highly suggest using SVN trunk.
Ummm, how?
It looks like the configure-based installation has been removed.
% svn co
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk ob-trunk
% cd ob-trunk/
% find . -name
On Apr 12, 2010, at 9:51 AM, Noel O'Boyle wrote:
There's a memory leak in readstring, at least when used with SMILES
string, even with trunk. There is a filed bug -
http://sourceforge.net/tracker/?func=detailaid=2978796group_id=40728atid=428740.
I didn't think that was the problem because I
On Apr 12, 2010, at 3:04 AM, Geoffrey Hutchison wrote:
You don't mention what version of OB you're using, but imply it's not the
latest development code. I'd highly suggest using SVN trunk.
That fails to work, in a much worse way than before.
After working with Noel to update the build
On Apr 12, 2010, at 9:01 PM, Noel O'Boyle wrote:
SetInFormat should return true for success. Does it?
import openbabel
obc = openbabel.OBConversion()
obc.SetInFormat(smi)
True
mol = openbabel.OBMol()
mol
openbabel.OBMol; proxy of Swig Object of type 'OpenBabel::OBMol *' at
0x1004e5e40
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