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52 Commits

Author SHA1 Message Date
Greg Landrum
d34f3dd6b2 do isotope work relative to the most common isotope 2011-07-01 04:34:14 +00:00
Greg Landrum
9316758cec improved handling of isotope specifications (still definitely not optimal) 2011-07-01 03:42:35 +00:00
Greg Landrum
1df2618213 fix and test issue 3316600 2011-06-15 05:34:15 +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
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
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
4d168b2637 further leak stoppage 2010-06-09 18:30:22 +00:00
Greg Landrum
e4b215a6b0 properly handle quoted NOT atom lists 2010-06-04 10:06:50 +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
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
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
305bf237b4 add the ForwardSDMolSupplier to allow use of gzipped sd files; 
remove the long-obsolete SDFileParser stuff.
 2009-05-14 18:07:57 +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
35de73dff0 prelim parity handling, no testing yet 2009-01-20 06:40:36 +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
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
134a78c700 improve handling of dummies in mol files 2008-08-28 09:28:12 +00:00
Greg Landrum
6e31bd9d73 cleanups 2008-05-16 13:18:44 +00:00
Greg Landrum
eb3d720010 Fixes for sf.net bugs 1942657 : square brackets in smiles allow invalid valences 
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
fab5e54d87 better handling of dummies 2008-04-16 15:40:35 +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
26ee1124b6 test throwing an exception on a missing mol file 2008-04-08 10:21:50 +00:00
Greg Landrum
bc60f17b91 make the next step towards completing feature request (186217); 
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 : 
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
562c18fdfa further progress towards supporting MDL mol file queries (sf.net issue 1756962) 2008-02-26 18:06:20 +00:00
Greg Landrum
f746f26165 remove a compiler warning;stop using sprintf when writing mol files 2008-02-14 07:32:08 +00:00
Greg Landrum
3518e10919 make file parsing more efficient 2007-11-27 18:01:16 +00:00
Greg Landrum
c75aa34b4b - Expand availability of the protrude distance measure. 
- 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
Greg Landrum
3e7dbcf66a start to add better support for MDL mol files. 
this is sf.net issue 1756962: https://sourceforge.net/tracker/?func=detail&atid=814653&aid=1756962&group_id=160139
 2007-07-19 16:41:11 +00:00
Greg Landrum
47c222e3d5 clear up some compiler warnings 2007-05-04 04:59:30 +00:00
Greg Landrum
9bd4c59606 substantial optimization of SD/mol file parsing;some reformattig 2007-03-20 21:06:37 +00:00
Greg Landrum
9d6d55b523 just a backup commit; this isn't quite done yet 2007-03-02 06:21:59 +00:00
Greg Landrum
28c3224c9b MolFileParser: move the chirality setting inside the sanitization test 
FileParsers.vcproj: remove optimization (under vc++) for two files. This is a "fix" for what I believe to be a vc++ compiler bug. See issue 1607290 (http://sourceforge.net/tracker/index.php?func=detail&aid=1607290&group_id=160139&atid=814650)

testMolWriter.cpp: update memory corruption test
 2006-12-21 04:45:37 +00:00
Greg Landrum
cab9793963 small cleanups 2006-12-17 15:00:41 +00:00
Greg Landrum
688ed25c88 fix and test SF.net bug 1603923 
(https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1603923&group_id=160139)
 2006-11-27 17:53:02 +00:00
Greg Landrum
e66c87a322 we shouldn't have been labelling things 'Xe' 2006-10-31 17:47:55 +00:00
Greg Landrum
e56716953d throw an exception with zero-atom molecules; untabify 2006-10-29 07:01:39 +00:00
Greg Landrum
a890611a22 merge back in changes from ChemTransforms (r30:51); 
the makefile for linux is still missing (I have one, I just need to retrieve it)
but otherwise this is in pretty good shape. 
err, I think so at least.
 2006-09-15 16:44:38 +00:00