Greg Landrum
9f4471f872
more on #204
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A few other cleanups
2014-02-06 06:43:28 +01:00
Greg Landrum
deed4a9acf
Merge branch 'Issue194_V3000MolWriter'
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Conflicts:
Code/GraphMol/Chirality.cpp
Code/GraphMol/FileParsers/test1.cpp
2014-01-22 07:07:27 +01:00
Greg Landrum
6dbd804121
clean up the way the unicode strings are handled and broaden suport a bit
2013-12-30 16:11:09 +01:00
Greg Landrum
e7ad13929b
Fixes #179
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could be more elegant, but works for MolFromSmiles and MolFromSmarts
2013-12-30 09:02:43 +01:00
Greg Landrum
2ee9f1c02a
add to python wrapper
2013-12-23 06:43:12 +01:00
Greg Landrum
1501af51a5
PDB reader/writer fixes;
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add MolToMolFile() to python API
2013-10-25 05:02:09 +02:00
Greg Landrum
173c53c8e4
integrate Roger's bond-perception/assignment code
2013-09-30 05:11:31 +02:00
Greg Landrum
18724155c8
add pdb writer to wrapper
2013-09-29 16:59:57 +02:00
Greg Landrum
a75b3fe0b3
add PDB input to python wrapper
2013-09-29 16:15:30 +02:00
Greg Landrum
42e140e0c0
make sure that a nonzero atom list is passed to MolFragmentToSmiles
2012-09-27 17:50:35 +00:00
Greg Landrum
c293dc23da
initial version of MolFragmentToSmiles
2012-05-19 03:50:31 +00:00
Greg Landrum
3520c441cb
add allBondsExplicit argument for SMILES writing
2012-03-26 03:12:37 +00:00
Greg Landrum
dbd78604c8
fix and test issue 3477283
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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
53d804a02e
not really working yet; backup commit
2011-11-18 06:55:06 +00:00
Greg Landrum
76e5b8dd9b
show the content of exceptions when parsing mol files instead of just ignoring them
2011-11-03 04:13:51 +00:00
Greg Landrum
c9161554b9
clean up some compiler warnings from clang
2011-05-26 02:36:23 +00:00
Greg Landrum
faab610321
add string replacements to smiles and smarts parsers
2011-05-22 10:45:14 +00:00
Greg Landrum
e977a642f6
add support for writing non-canonical SMILES;
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add support for atom-mapping information in plain SMILES
2010-12-20 03:59:56 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
116c036c07
doc updates for writers to indicate that "-" writes to stdout;
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rename computedProps property to __computedProps
2010-09-19 13:13:10 +00:00
Greg Landrum
5aaad5a680
turn off the compressed suppliers by default since they don't work on windows
2009-06-20 05:53:37 +00:00
Greg Landrum
69d1e777cd
support compressed sd suppliers on the python side as well;
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note: this stuff all still needs to be tested on windows
2009-05-15 04:01:34 +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
cfc3fcbd08
merge sybyl file parsers into trunk. These are revs831:895 from the branch
2008-11-25 06:04:17 +00:00
Greg Landrum
4dc3d63fcd
Update requirements.
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Minor cleanups in some cpps
Finish the changes so that fileparsers don't throw exceptions unless
the file is not found.
2008-08-19 03:05:58 +00:00
Greg Landrum
61b05af6fc
Modify suppliers and parsers so that they don't throw
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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
9f61e71f05
get this compiling on linux
2007-08-12 05:03:38 +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
4e7d182fcc
Support editable molecules in Python.
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This is Feature Request #1764162
http://sourceforge.net/tracker/index.php?func=detail&aid=1764162&group_id=160139&atid=814653
This implementation has been tested on Windows
2007-07-31 05:30:11 +00:00
Greg Landrum
547f71ec7c
further work on the TPL reader/writer
2007-03-04 16:22:11 +00:00
Greg Landrum
804b3dbf88
TPL reading is now getting close to being done
2007-03-03 06:38:03 +00:00
Greg Landrum
81f341882e
try to get ChemTransforms checked in
2006-07-18 05:33:58 +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
