Greg Landrum
d0ed0e900c
Fixes #803
2016-03-09 05:05:33 +01:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Greg Landrum
acf69ea1b8
Fixes #553
2015-08-09 07:19:46 +02:00
Nadine Schneider
47dbaf2304
Fix: ring stereo chemistry was swapped incorrectly
2015-02-11 18:21:15 +01:00
Greg Landrum
2d9f809770
fix some broken tests; pyDistGeom is still failing
2015-01-23 06:43:12 -05:00
Greg Landrum
6d7b2b0914
merge with master
2015-01-22 06:30:51 -05:00
Brian Kelley
95a92282d1
Dictionary access is saniztized and optimized.
...
o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
2015-01-15 12:23:29 -05:00
Greg Landrum
9f36ec2534
now testChirality passes
2014-12-29 07:26:25 +00:00
Greg Landrum
9d55833ec1
testChirality passes with the exception of the one test that is commented out
...
(testIssue2705543)
2014-12-24 06:16:20 +00:00
Greg Landrum
ab0f1dcf60
rename to new_canon (probably should come up with a better name, but this will do for now)
2014-12-22 07:56:26 +00:00
Greg Landrum
e17d93078f
remove most everything from RankAtoms.h; remove RankAtoms.cpp from the files included in the build.
...
This compiles, but has yet to be tested.
NOTE that there are untested mods in testChirality.cpp that may not work
2014-12-22 06:58:54 +00:00
Greg Landrum
bc96ccdf1b
Merge with master
2014-12-21 07:36:24 +01:00
Greg Landrum
b640be11d9
some cleanup
2014-12-19 13:49:16 +01:00
Greg Landrum
7fb24da423
merge with master
2014-09-21 21:06:40 +02:00
Greg Landrum
a94ce46a43
smiles tests now pass as well
2014-08-27 22:32:49 +02:00
Greg Landrum
e170195421
backup commit; this does not completely work yet
2014-08-03 08:01:58 +02:00
Greg Landrum
6f909ed449
switch chirality to using unsigned ints
2014-07-27 08:09:00 +02:00
Greg Landrum
0839cf41ad
Fixes #210
2014-02-03 05:25:27 +01:00
Greg Landrum
c95d57aa54
add in-place form of addHs()
2013-10-04 07:58:53 +02:00
Greg Landrum
c82e1151b3
Fixes #90
2013-08-23 12:58:41 +02:00
Greg Landrum
40ab2c06e3
Fixes #87
2013-08-21 08:20:19 +02:00
Greg Landrum
24e269f8ac
I *think* that this fixes sf.net issue 40:
...
the long-standing problem with ring stereochemistry and canonicalization
2012-11-02 06:33:11 +00:00
Greg Landrum
b96cff10e8
fix and test sf.net issue 254
2012-09-23 10:13:46 +00:00
Greg Landrum
3a3b582d28
clean up + add support for D and T in molecular formula
2012-07-27 06:16:45 +00:00
Greg Landrum
a3dc23c43c
more canonicalization improvements
...
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)
...
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);
...
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:
...
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
...
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.
...
The changes are revs 451:498.
2008-01-30 14:53:04 +00:00
