Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

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

Re: [OpenBabel-Devel] Bzip2 format support

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

Re: [OpenBabel-Devel] Fragmentation

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

Re: [OpenBabel-Devel] [Open Babel] Python test cases (Moving to OpenBabel-dev)

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

Re: [OpenBabel-Devel] possible trojan ?

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

Re: [OpenBabel-Devel] Silicos: Spectrophores ported under OB

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

Re: [OpenBabel-Devel] Silicos: Spectrophores ported under OB

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

Re: [OpenBabel-Devel] segfault on Mac

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

Re: [OpenBabel-Devel] segfault on Mac

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

Re: [OpenBabel-Devel] segfault on Mac

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

Re: [OpenBabel-Devel] segfault on Mac

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