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;
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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:
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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
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
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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);
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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
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.
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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
Greg Landrum
3e7dbcf66a
start to add better support for MDL mol files.
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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
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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
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(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);
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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
Greg Landrum
5d03333c22
setup svn keywords (should have done this before import... grn)
2006-05-06 22:54:39 +00:00
Greg Landrum
75a79b6327
initial import
2006-05-06 22:20:08 +00:00
