Greg Landrum
1b946794f0
replaceBond and generic atoms and bonds in adjustQueryProperties() ( #1141 )
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* first pass at RWMol::replaceBond()
* get ready for the changes
* rename some options
add bond options (not doing anything with them yet)
update tests to reflect new options
* backup
* re-enable the rest of the tests
2016-11-04 12:41:06 +01:00
Michał Nowotka
f70162a53b
Bug when removing stereo info?
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It's very possible, that I don't understand something (apologies) but shouldn't the second loop iterate over vertices adjacent to the second end of the bond being removed?
2016-06-20 16:40:33 +01:00
kelley
5dbec2fe85
Adds rdcasts where appropriate
2015-11-29 17:52:27 -05:00
Greg Landrum
e08e0d16d8
first pass, using google style
2015-11-14 14:58:11 +01:00
Greg Landrum
e37296d7c7
post review
2015-11-14 08:08:14 +01:00
Brian Kelley
fb84c9f0b7
Switches to URANGE_CHECK when appropriate
2015-10-18 21:14:02 -04:00
Brian Kelley
daa7e62258
Fixes signed conversion issues (use rdcast)
2015-10-18 15:16:38 -04:00
Brian Kelley
5f59333a56
Silences unused parameters
2015-10-18 14:02:29 -04:00
Greg Landrum
1a6fafdec3
Fixes #610
2015-09-09 18:39:56 +02:00
Greg Landrum
07c9c10e26
Fixes #608
2015-09-08 09:52:06 +02:00
Greg Landrum
b78bb40ca5
Fixes #384
2015-03-30 07:20:24 +02:00
Greg Landrum
f5cf3322fe
code cleanup: removing compiler warnings
2014-05-08 06:06:07 +02:00
Greg Landrum
387406f657
ongoing optimization work
2014-02-05 04:22:59 +01:00
Greg Landrum
5ee22df4c4
small optimizations for smiles parser
2014-01-27 16:54:32 +01:00
Greg Landrum
9dca8636b7
Fixes #175
2013-12-07 08:26:58 +01:00
Greg Landrum
5ce10116c5
fix an ugly bit in RWMol::removeAtom
2013-07-15 17:14:37 +02:00
Greg Landrum
586e91ba96
Fixes #59
2013-07-04 05:53:16 +02:00
Greg Landrum
c53196e068
Fixes #42
2013-06-05 05:44:03 +02:00
Greg Landrum
0b45f3c320
fix GitHub issue 8
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This breaks the InChI python unit tests, so those need to be cleaned up.
2013-03-01 06:54:33 +00:00
Greg Landrum
be669050a6
fix and test sf.net issue284
2013-01-31 04:03:04 +00:00
Greg Landrum
1b328e3789
fix and test for issue 264
2012-11-12 14:54:18 +00:00
Greg Landrum
cfaea83d7d
optimizations for molecule construction
2012-08-27 04:52:27 +00:00
Greg Landrum
f5eb640766
fix and test Issue3549146
2012-07-26 14:34:35 +00:00
Greg Landrum
93f6445e01
minor cleanup to RWMol::insertMol; add combineMols to ChemTransforms
2012-07-10 04:00:46 +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
214f1c5c20
primarily minor code cleanups.
2010-05-26 18:27:40 +00:00
Greg Landrum
621b99f225
some optimization work
2009-05-10 04:10:29 +00:00
Greg Landrum
e05580e495
This is a sizeable one: change the way BGL is used so that atoms and bonds are stored as bundled properties
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instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
2009-02-11 20:19:25 +00:00
Greg Landrum
8867db464f
check that self bonds are not added
2008-07-16 04:00:54 +00:00
Greg Landrum
95b86eb371
"fix" issue1993296
2008-06-16 05:52:30 +00:00
Greg Landrum
ca0fe086de
Remove some compiler warnings and problems found with msvc-8
2008-02-14 06:44:17 +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
6aeeca797d
fix a small memory leak
2008-01-26 04:34:45 +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
Santosh Putta
3061511f68
All typedefs based on points move to point.h - dependancies updated here
2006-10-19 23:37:59 +00:00
Greg Landrum
6615ae5a01
SDMolSupplier: don't throw on errors parsing molecules. This allows the parsing of further mols to continue.
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Conformer.cpp: make sure we don't ask for space for zero atoms.
Kekulize.cpp: don't complain about marked bonds if we aren't removing markers.
molopstest.cpp: bad smiles corrected in one test.exe
ROMol.cpp, RWMol.cpp: extra preconditions added (should have been there all along)
Wrap/MolOps.cpp: docs for replacesubstructs.
2006-09-18 05:21:39 +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
