Greg Landrum
6d3a9f6fb3
Check in a bunch of changes to fix radical handling.
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These are connected to issues 2093420, 2091890, and 2091839
this still needs more testing.
2008-09-23 06:02:02 +00:00
Greg Landrum
76f32244aa
- support splitting a molecule into fragments (in MolOps)
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- expose the calculation of atom CIP ranks
2008-06-27 03:43:42 +00:00
Greg Landrum
6ee3bbc85a
support splitting a molecule into fragments as well as identifying the fragments (feature request 1992648)
2008-06-13 05:48:01 +00:00
Greg Landrum
41fa5fa7b0
The force argument to getExplicitValence and getImplicitValence wasn't doing anything
2008-06-12 05:44:57 +00:00
Greg Landrum
f4374cd520
fix an error in an explanatory comment
2008-05-06 15:52:46 +00:00
Greg Landrum
eb3d720010
Fixes for sf.net bugs 1942657 : square brackets in smiles allow invalid valences
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http://sourceforge.net/tracker/index.php?func=detail&aid=1942657&group_id=160139&atid=814650
This was handled by adding error/consistency checking to Atom.calcExplicitValence()
This includes another pretty big scale modification:
the allowed valence list for atoms (in atomic_data.cpp) can now contain a -1 at the end. If this is the case, the atom will tolerate valences above the ones listed.
This is done to allow "flexible" atoms (i.e. transition metals and the like) to accept arbitrary coordination numbers without generating errors.
2008-04-17 05:09:02 +00:00
Greg Landrum
a788e29511
merge the changes from the CanonicalizerRework30Nov branch in.
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The changes are revs 451:498.
2008-01-30 14:53:04 +00:00
Greg Landrum
ce8d7b9cea
GraphMol/:
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Fix and test sf.net issue 1811276 (http://sourceforge.net/tracker/index.php?func=detail&aid=1811276&group_id=160139&atid=814650 )
2007-10-11 16:50:47 +00:00
Greg Landrum
b6820ed59f
untabify
2007-08-03 16:49:57 +00:00
Greg Landrum
ebb196b8f8
Major thing here: fix and test Issue 1748846 ( https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1748846&group_id=160139 )
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Others:
SmilesParse: clean up some of the smiles generation code
2007-07-06 17:31:58 +00:00
Greg Landrum
5d03333c22
setup svn keywords (should have done this before import... grn)
2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327
initial import
2006-05-06 22:20:08 +00:00
