Greg Landrum
e16b345d8b
fix and test issue 3525673
2012-05-12 05:31:54 +00:00
Greg Landrum
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
162662186d
not working yet
2012-04-19 06:15:40 +00:00
Greg Landrum
207b1c181b
fix and test issue 3482695
2012-02-02 03:28:48 +00:00
Greg Landrum
51991c7619
add line numbers to all error messages/warnings from ctab parsing
2012-01-29 08:41:30 +00:00
Greg Landrum
dbd78604c8
fix and test issue 3477283
...
add a new option for ctab parsing to cause the parser to be less strict about
errors in the file syntax.
2012-01-22 09:40:54 +00:00
Greg Landrum
510f68b102
initial pass at fixing issue 3432136
2011-11-03 04:13:02 +00:00
Greg Landrum
82129c3e13
fix and test Issue3399798
2011-08-30 09:13:07 +00:00
Greg Landrum
59c05266b7
fix and test issue 3392107. Add first pass at being able to write atom list queries to mol files
2011-08-16 06:03:27 +00:00
Eddie Cao
adbd5c7b18
Several InChI generation fixes, including perchloric acid, isotopic property, chirality loss, stereoany
2011-07-25 06:41:47 +00:00
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
