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
5eadc06bf6
fix and test for issue 3453172
2011-12-30 07:13:33 +00:00
Greg Landrum
2ffaa92cf7
fix and test issue3228150;
...
note that as part of these changes MolToSmiles and MolToSmarts no longer have
side effects on the original molecule.
2011-03-26 06:51:50 +00:00
Greg Landrum
d6741adc22
make some types more explicit in MolOps.h (easier SWIG wrapping)
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support finding non-specfied chiral centers
remove vestigial GetFragmentSmiles() function
additional flexibility in AllChem.TransformMol()
2011-02-24 08:00:39 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
Greg Landrum
006c696067
an inital pass at a solution to adding support for stereochemistry of ring bonds (bug 3139534);
...
this needs a ton more testing, but it is worth getting a "working" version in
2010-12-28 10:38:14 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
80c0a8825e
fix issue 3009836; partial fix for issue 3009911
2010-06-01 17:54:49 +00:00
Greg Landrum
2805355f34
First pass at the rewrite:
...
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
96adbc11ea
remove the deprecated assign{Atom,Bond}ChiralCodes functions
2009-08-02 15:33:08 +00:00
Greg Landrum
268b08ec17
fix and test sf.net issue 2804599
2009-06-11 04:55:44 +00:00
Greg Landrum
e3ebc00ed5
fix and test bug 2762917
2009-04-15 04:39:10 +00:00
Greg Landrum
09455ef42e
resolves issue 2705543
2009-03-28 06:43:04 +00:00
Greg Landrum
a412664c65
just for backup
2009-03-27 16:12:54 +00:00
Greg Landrum
6042af28b9
add removeStereochemistry function to MolOps
2009-03-06 09:55:53 +00:00
Greg Landrum
9ac8b25d4b
make ring stereochemistry in output SMILES at least correct (if not canonical);
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move the incorrectness warning to the SMILES writer
2008-12-06 06:51:52 +00:00
Greg Landrum
ac4eee9115
continuing refinement of issue 1896935
2008-12-03 19:53:51 +00:00
Greg Landrum
a61cc8a07b
fix a ring-stereochem edge case
2008-12-03 17:04:01 +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
148a3a87c4
add getTotalDegree() method to Atom; support generating stereochem information from 3D coords
2008-05-26 14:54:35 +00:00
Greg Landrum
5351f6cd04
test sf.net bug 1942656: five-coordinate carbon left with stereochem
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http://sourceforge.net/tracker/index.php?func=detail&aid=1942656&group_id=160139&atid=814650
2008-04-17 05:04:28 +00:00
Greg Landrum
4ea82818a6
switch away from using the old, unsupported boost::log stuff.
...
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
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
