Greg Landrum
f762346ced
make the perchlorate cleanup pattern more generic to cover all halogenates;
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Fixes #115
2016-04-01 07:54:32 +02:00
Greg Landrum
cf7ceab383
remove wave of warnings
2016-03-30 13:09:59 +02:00
Greg Landrum
d7d95dd684
an alternate approach to fixing #805
2016-03-13 04:21:36 -07:00
kelley
5dbec2fe85
Adds rdcasts where appropriate
2015-11-29 17:52:27 -05:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Brian Kelley
403a3d6b7c
Suppresses Boost warnings
2015-10-18 13:41:03 -04:00
Riccardo Vianello
78d7f6c1d9
Fix regressions occurring when building with msvc9
2015-10-14 09:43:16 +02:00
Greg Landrum
a7383e7861
first pass at #567
2015-08-21 16:45:00 +02:00
Nadine Schneider
0cf0dd37ce
Bugfix in SmilesWrite and some additional tests for getMolFrags function
2015-04-16 10:53:20 +02:00
Nadine Schneider
0b8b6a3690
Some performance fixes for the new canonicalization
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- handling molecules/proteins with multiple fragments
- add criteria for using special symmetry invariant
2015-04-15 18:42:29 +02:00
Greg Landrum
2f77e5e6cd
Fixes #447
2015-03-19 07:19:47 +01:00
Schneider
5774337c89
MolOps: Add function to get the number of atoms with a distinct property
2014-08-19 13:01:10 +02:00
Greg Landrum
e4cfc340a4
support white and black lists for getMolFragsWithQuery
2014-03-25 08:18:30 -04:00
Greg Landrum
fe07610683
copy over conformers too. Part of #234
2014-03-18 06:06:24 +01:00
Greg Landrum
196c2278fb
Fixes #234
2014-03-17 08:33:07 +01:00
Greg Landrum
f629c1ea6d
Fixes #116
2013-10-06 07:49:54 +02:00
Greg Landrum
7ba9571e3c
further refinements
2012-02-26 08:47:14 +00:00
Greg Landrum
a2b93cf084
pass one: add the basics
2012-02-11 06:41:25 +00:00
Greg Landrum
a99ad44859
clean up some compiler warnings
2011-12-31 15:58:57 +00:00
Greg Landrum
3ba11316b2
initial pass at requiring core-dummy matches in replaceCore; remove an extra header import from MolOps.cpp
2011-03-28 06:13:48 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
214f1c5c20
primarily minor code cleanups.
2010-05-26 18:27:40 +00:00
Greg Landrum
e2a3aa49ae
fix and test issue 2952255
2010-02-15 19:21:31 +00:00
Greg Landrum
83e2637137
remove compiler warnings
2009-09-28 09:52:41 +00:00
Greg Landrum
96adbc11ea
remove the deprecated assign{Atom,Bond}ChiralCodes functions
2009-08-02 15:33:08 +00:00
Greg Landrum
f9c0186515
add some minimal targets; move implementations of a couple functions out of MolOps.h
2009-04-18 13:16:17 +00:00
Greg Landrum
e05580e495
This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties
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instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
2009-02-11 20:19:25 +00:00
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
