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
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
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
ceec61a3a3
fix and test sf.net issue 1968608
2008-05-22 05:53:00 +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
4ea82818a6
switch away from using the old, unsupported boost::log stuff.
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This "lookalike" implementation is much cruder than the real thing and does not really support
enabling and disabling logs, or associating them with files, but those components were not being
particularly used in the RDKit anyway.
2008-04-06 09:12:02 +00:00
Greg Landrum
3c57caabfb
partially tested fix for sf.net bug 1894348
2008-02-15 16:13:12 +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
83a9f21547
catch problems caused by sf.net Issue1836576 and throw an exception instead of an invariant error; this is not a real fix, which will require a re-examination of the ring-finding code.
2007-11-23 06:13:11 +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
75bce74d77
use SmartsWrite namespace
2007-08-04 05:38:48 +00:00
Greg Landrum
c6ad039a2f
fix for sf.net issue 1719053: ring stereochemistry incorrectly removed:
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http://sourceforge.net/tracker/index.php?func=detail&aid=1719053&group_id=160139&atid=814650
This will need more torture testing, but the unit tests here do cover the edge cases I can think of.
2007-05-23 05:17:07 +00:00
Greg Landrum
4fff15fedf
fixes (and tests) for sf.net bug 1694023 ( http://sourceforge.net/tracker/index.php?func=detail&aid=1694023&group_id=160139&atid=814650 )
2007-04-04 06:07:31 +00:00
Greg Landrum
7041ae233e
handle the NoImplicit flag properly
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update aromaticity to require unsaturation at single-atom donors
test the above two things
This is not necessarily completely stable, but all current tests pass
(once obvious changes have been made). We will just have to see where
the aromaticity changes cause trouble going forward.
2006-09-19 20:20:09 +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
