Greg Landrum
50bc499c20
fix for sf.net bug 274
2012-12-15 03:29:03 +00:00
Greg Landrum
5324c9c783
fix and test sf.net issue 272
2012-12-12 04:39:55 +00:00
Greg Landrum
294cb24de4
fix and test issue 266
2012-11-17 07:39:39 +00:00
Greg Landrum
8d9fd053b2
fix and test issue 256;
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this is a change that affects backwards compatibility.
2012-10-08 03:18:05 +00:00
Greg Landrum
6555d2062f
more changes connected to sf.net issue 249
2012-09-16 05:40:17 +00:00
Greg Landrum
b67dd0f437
another bit of fixing sf.net issue 249
2012-09-01 04:06:02 +00:00
Greg Landrum
2d7315e8d4
fix and test sf.net issue 249
2012-08-30 05:45:59 +00:00
Greg Landrum
b5d1ad394e
accelerate FastFindRings
2012-08-29 02:28:03 +00:00
Greg Landrum
14e396c26d
refactoring the SMILES parser to make it more efficient
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NOTE: this changes the ordering of bonds in molecules with branches.
2012-08-28 04:01:49 +00:00
Greg Landrum
f5eb640766
fix and test Issue3549146
2012-07-26 14:34:35 +00:00
Greg Landrum
8690fb99b9
add a test for issue 3526831 (already fixed)
2012-07-02 03:16:15 +00:00
Greg Landrum
ebfe1b1ec8
add a test for issue 3528556 (already fixed)
2012-07-02 03:12:56 +00:00
Greg Landrum
2785c7a251
update expected canonical smiles
2012-06-28 11:21:45 +00:00
Greg Landrum
6157345dde
this version passes the ZINC natural-products torture test
2012-06-28 06:45:42 +00:00
Greg Landrum
0f3b84cd28
backup commit; we are not quite there yet
2012-06-26 06:15:08 +00:00
Greg Landrum
ee43d3e8f8
another step forward
2012-06-13 05:20:39 +00:00
Greg Landrum
a3dc23c43c
more canonicalization improvements
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there are still some problems with double bonds
2012-06-11 03:21:30 +00:00
Greg Landrum
0085012701
fix and test issue 3525076
2012-05-10 05:35:20 +00:00
Greg Landrum
5d48f52545
a quick optimization of the stereochemistry code
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(thanks to Roger Sayle for the suggestion
2012-03-27 10:27:18 +00:00
Greg Landrum
e38ef02346
initial pass at changing atom-atom matching behavior;
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fix for issue 3495370
2012-03-02 07:20:16 +00:00
Greg Landrum
bb4acb5495
merge with the trunk rev1977
2012-02-26 19:19:16 +00:00
Greg Landrum
7ba9571e3c
further refinements
2012-02-26 08:47:14 +00:00
Greg Landrum
813f4863ed
fix and test Issue 3480481
2012-02-18 05:34:34 +00:00
Greg Landrum
fe071d1aa5
fix and test issue 3487473
2012-02-14 17:58:04 +00:00
Greg Landrum
3eeb1bf30c
initial version of a DFS-based ring finder
2012-01-02 15:34:43 +00:00
Greg Landrum
b434870824
tests for the already fixed issue 3415206
2011-09-29 03:59:31 +00:00
Greg Landrum
164a9b19c8
update the way query Hs are merged
2011-09-28 05:24:38 +00:00
Greg Landrum
dad3885839
fix and test sf.net issue 3349243
2011-07-02 04:25:59 +00:00
Greg Landrum
044fda398b
further ring-finding algorithmic changes to fix issue 3185548
2011-02-19 04:35:53 +00:00
Greg Landrum
aa1610797e
initial fix for Issue3184458, more work should still be done here.
2011-02-18 06:31:31 +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
2805355f34
First pass at the rewrite:
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this gets rid of all the "preceding atom" code and passes all tests on linux
builds on other OS's and more extensive regression testing is required
2010-05-31 14:08:11 +00:00
Greg Landrum
ea910aab19
minor cleanup action
2010-04-19 07:47:48 +00:00
Greg Landrum
e2a3aa49ae
fix and test issue 2952255
2010-02-15 19:21:31 +00:00
Greg Landrum
db1f25b16c
chirality support in the fix for issue 2951221
2010-02-14 06:39:51 +00:00
Greg Landrum
8daba8ff30
fix sf.net issue 2951221: note this doesn't add Hs to chiral centers correctly
2010-02-13 14:53:47 +00:00
Greg Landrum
96adbc11ea
remove the deprecated assign{Atom,Bond}ChiralCodes functions
2009-08-02 15:33:08 +00:00
Greg Landrum
2735f51953
fix and test sf.net issue2830244
2009-07-31 10:25:31 +00:00
Greg Landrum
b78abe26d6
fix and test sf.net issue 2787221
2009-05-05 12:54:41 +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
21568e81a4
checkin the tests too
2008-12-10 16:45:46 +00:00
Greg Landrum
c0e1ffdc65
fix and test Issue2313979
2008-12-02 08:50:51 +00:00
Greg Landrum
cb6982e9e0
not done, this is a backup commit
2008-12-02 07:01:46 +00:00
Greg Landrum
0ff9e0a95d
forgot to check in the actual test code with rev885
2008-11-21 05:53:57 +00:00
Greg Landrum
0f4bb4dbbc
another correction associated with 2196817 (aromatic dummies)
2008-11-07 06:31:43 +00:00
Greg Landrum
5eb7c40d21
Fix and test sf.net issue 2219400
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This includes a change to the behavior of MolOps::getShortestPaths()
2008-11-03 20:12:02 +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
023f7b4f0f
Merge changes from the iterative chirality branch:
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https://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/IterativeChirality_20Aug2008
into the trunk.
This covers revs 798-828.
Dependent chirality should now be correctly handled, but the
handling of ring stereochemistry, i.e. things like:
C[C@H]1CC[C@H](C)CC1
is still not 100% correct.
2008-09-19 09:40:15 +00:00
