Greg Landrum
67eccc1620
fix and tests Issue3375684
2011-07-23 03:49:36 +00:00
Greg Landrum
951f4b7fd3
fix and tests sf.net issue3375647
2011-07-22 15:53:05 +00:00
Greg Landrum
f61d48cadf
add some of the inchi rules for ignoring mol file stereochemistry
2011-07-22 14:21:39 +00:00
Greg Landrum
10cb677b33
fix and test Issue3374639
2011-07-22 10:55:40 +00:00
Greg Landrum
c7a9903e41
fix and test issue 3359739
2011-07-09 04:46:55 +00:00
Greg Landrum
1df2618213
fix and test issue 3316600
2011-06-15 05:34:15 +00:00
Greg Landrum
f0c0a060a2
fix and test Issue 3313540
2011-06-10 03:27:46 +00:00
Greg Landrum
a7cbd1a818
better fix for sf.net issue 3313539
2011-06-09 05:30:45 +00:00
Greg Landrum
deae1affcb
provisional fix and test sf.net issue 3313539
2011-06-08 05:18:14 +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
5c14f36de7
partial fix for Issue3228150
2011-03-25 03:26:03 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
Greg Landrum
e703428743
canonicalization test connected with issue 3154208
2011-01-11 05:12:19 +00:00
Greg Landrum
5592e31464
initial fix and tests for issue 3154208
2011-01-10 07:11:44 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
5cc9d6ddeb
fixes and tests for two isotope-related problems:
...
1) issue 3073163
2) incorrect calculation of AMW with isotopes present
2010-09-22 13:26:30 +00:00
Greg Landrum
a09fd9f63a
cleanup work on file parsers code; add v3K rxn support
2010-06-03 06:59:48 +00:00
Greg Landrum
e448b5b7a4
expand capabilities of v3k ctab parser
2010-06-02 17:55:35 +00:00
Greg Landrum
80c0a8825e
fix issue 3009836; partial fix for issue 3009911
2010-06-01 17:54:49 +00:00
Greg Landrum
c235b26126
fix and test issues 3009756 and 3009836
2010-06-01 09:39:42 +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
5ac2d19bfa
resolve sf.net issue 2963522
2010-03-10 06:47:33 +00:00
Greg Landrum
9eccc4521d
add more flexibility to the R group labelling from mol files
2010-03-10 05:14:52 +00:00
Greg Landrum
4b3185e330
fix a v3k mol file problem
2010-02-15 12:43:38 +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
d397d7d7ed
preliminary handling of v3000 mol blocks
2009-06-05 06:12:51 +00:00
Greg Landrum
cfc14cbb8e
robustify multiple query handling
2009-05-28 14:14:15 +00:00
Greg Landrum
477a26b84a
better handling of Q, A and * queries from CTABs
...
sf.net issue 2797708
2009-05-28 04:37:12 +00:00
Greg Landrum
6e0d5c0e67
support parsing atom properties; fix ordering "bug" in property parsing
2009-05-11 15:27:39 +00:00
Greg Landrum
71f1a71ca6
make kekulization optional for mol file writing; fix and test issue 2692246
2009-03-18 18:55:46 +00:00
Greg Landrum
30fe77b609
initial commit: passes all tests and seems to be faster than the original code
2009-02-09 16:19:31 +00:00
Greg Landrum
2f3b3e251c
support parity with implicit hs
2009-01-26 05:56:28 +00:00
Greg Landrum
73fccfd26f
add a few simple tests for the mol file parity handling
2009-01-21 06:05:13 +00:00
Greg Landrum
1a186a2d82
fix and test issue2413431
2008-12-10 09:09:02 +00:00
Greg Landrum
bc580ac2e3
fix and test issue 2337369
2008-11-24 07:40:53 +00:00
Greg Landrum
6d3a9f6fb3
Check in a bunch of changes to fix radical handling.
...
These are connected to issues 2093420, 2091890, and 2091839
this still needs more testing.
2008-09-23 06:02:02 +00:00
Greg Landrum
3a040035db
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 09:36:56 +00:00
Greg Landrum
5e9d1e8307
fix and test issue 1965035
2008-05-16 05:35:50 +00:00
Greg Landrum
384bc8a12b
change the way we handle atom-list queries so that they can be properly translated to SMARTS... test that
2008-04-10 19:07:18 +00:00
Greg Landrum
61b05af6fc
Modify suppliers and parsers so that they don't throw
...
exceptions into python when reading a bad molecule. (Feature
request 1932875)
Modify constructors for both suppliers and parsers so that
throw BadFileExceptions if they cannot open the file. (Feature
request 1938303)
2008-04-09 03:33:49 +00:00
Greg Landrum
bc60f17b91
make the next step towards completing feature request (186217);
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display deprecation warnings for [X] dummies, output [*] by default
2008-04-06 10:41:14 +00:00
Greg Landrum
c86ee3fcf6
implement and test feature request 1906758 :
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support dimensionality flag on conformations
https://sourceforge.net/tracker/index.php?func=detail&aid=1906758&group_id=160139&atid=814653
2008-03-04 07:06:26 +00:00
Greg Landrum
75cd5eb0e8
this is partial progress towards feature request 1902466 :
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translate more query information into SMARTS
https://sourceforge.net/tracker/index.php?func=detail&aid=1902466&group_id=160139&atid=814653
This commit adds support for ring bond counts
and unsaturation queries.
2008-03-04 05:34:49 +00:00
Greg Landrum
562c18fdfa
further progress towards supporting MDL mol file queries (sf.net issue 1756962)
2008-02-26 18:06:20 +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
c75aa34b4b
- Expand availability of the protrude distance measure.
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- Remove a few confusing and unnecessary SD file handling functions from FileParsers (better functionality is available in the SDMolSupplier)
- Support not removing Hs in the Mol file handlers (C++ and Python)
2007-08-11 16:22:42 +00:00
Greg Landrum
168d45ebc9
further improvements in handling queries from MDL mol files
2007-08-07 17:32:30 +00:00
Greg Landrum
f56de77b25
cleanups
2007-07-22 15:23:26 +00:00
