Greg Landrum
5c21c0ad67
Fixes #1703 ( #1714 )
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* does not actually work
* all tests pass;
Fixes #1703
* make that a bit cleaner
2018-01-08 20:06:42 -05:00
Greg Landrum
ba12d98ad0
Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers ( #1713 )
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* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
* Actually delete atoms and bonds...
* RWMol::clear now calls destroy to handle atom/bond deletion
* Changes broken Atom lookup for windows/gcc
* Adds tests for running with valgrind
* Adds test designed for valgrind and molecule deletions
* Removes RNG, actually tests bond deletions
* update swig wrappers
* deal with most recent changes on the main branch
2018-01-07 14:19:47 -05:00
Greg Landrum
8191fd63fb
Fix for #1478 ( #1486 )
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* Fixes #1478
* minor optimization
2017-07-02 11:31:14 +02:00
Greg Landrum
915cf08faa
run clang-format with c++-11 style over that
2017-04-22 17:19:10 +02:00
Greg Landrum
7c0bb0b743
clang-tidy output
2017-04-22 17:09:24 +02:00
Greg Landrum
7fd991e13d
Fixes #962 ( #1003 )
2016-08-05 07:57:20 -04:00
Greg Landrum
06818ee0ed
improve error reporting for kekulization failures ( #919 )
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* improve error reporting for kekulization failures
Connected to #917
* better phrasing of the message.
2016-05-23 16:10:08 -04:00
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
Greg Landrum
e37296d7c7
post review
2015-11-14 08:08:14 +01:00
Brian Kelley
5f59333a56
Silences unused parameters
2015-10-18 14:02:29 -04:00
Paolo Tosco
5dfbecd6d0
- fixed missed kekulization of aromatic carbocations such as cyclopropenyl
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and tropylium
2015-07-17 01:00:34 +01:00
Greg Landrum
68a8cf4ce8
do not kekulize if there are neither aromatic bonds nor aromatic atoms
2015-04-12 05:59:35 +02:00
Greg Landrum
b072fc4b42
Fixes #141
2013-10-29 05:57:10 +01:00
Greg Landrum
0091417965
Fix #65
2013-07-09 14:54:32 +02:00
Greg Landrum
b4f2ec374e
Fixes : #61
2013-07-04 18:00:09 +02:00
Greg Landrum
0085012701
fix and test issue 3525076
2012-05-10 05:35:20 +00:00
Greg Landrum
de2126b641
optimization work
2012-04-15 06:19:22 +00:00
Greg Landrum
a2b93cf084
pass one: add the basics
2012-02-11 06:41:25 +00:00
Greg Landrum
dad3885839
fix and test sf.net issue 3349243
2011-07-02 04:25:59 +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
2735f51953
fix and test sf.net issue2830244
2009-07-31 10:25:31 +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
0f4bb4dbbc
another correction associated with 2196817 (aromatic dummies)
2008-11-07 06:31:43 +00:00
Greg Landrum
fc6c2b2f9a
fixes to issues 2196817 and 2208994
2008-10-30 06:56:39 +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
cd97b8035b
refactor the new radical-handling code to add a getNumRadicalElectrons()
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method to Atom
2008-09-04 18:09:54 +00:00
Greg Landrum
4702ed3e20
partial fixes (not thoroughly tested, needing more cleanup) for bug 2091839; this mainly has to do with fixing the treatment of radicals
2008-09-04 13:02:07 +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
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
3729140375
additional tests for sf.net bug 1934360.
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fix and test bug 1940646.
a bit of refactoring of the aromaticity code
2008-04-12 13:49:04 +00:00
Greg Landrum
820749851b
clean up the keulization code a bit; more can be done here
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initial fix and test for sf.net bug 1934360. more tests needed,
so this is basically a backup commit
2008-04-11 19:49:31 +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
8b4accb050
improve support for dummy atoms
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this was sf.net feature request 1868217:
https://sourceforge.net/tracker/index.php?func=detail&aid=1868217&group_id=160139&atid=814653
2008-01-10 06:39:33 +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
6615ae5a01
SDMolSupplier: don't throw on errors parsing molecules. This allows the parsing of further mols to continue.
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Conformer.cpp: make sure we don't ask for space for zero atoms.
Kekulize.cpp: don't complain about marked bonds if we aren't removing markers.
molopstest.cpp: bad smiles corrected in one test.exe
ROMol.cpp, RWMol.cpp: extra preconditions added (should have been there all along)
Wrap/MolOps.cpp: docs for replacesubstructs.
2006-09-18 05:21:39 +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
