Greg Landrum
8ffcfd7149
fix and test issue 35525671
2012-05-11 07:13:45 +00:00
Greg Landrum
f2bc7f77d2
fix and test issue 3525669
2012-05-11 06:42:08 +00:00
Greg Landrum
54f861e5ee
fix and test issue 3525668
2012-05-11 06:36:08 +00:00
Greg Landrum
e7d25d7973
tests passing except reactions
2012-04-21 04:40:55 +00:00
Greg Landrum
3520c441cb
add allBondsExplicit argument for SMILES writing
2012-03-26 03:12:37 +00:00
Greg Landrum
813f4863ed
fix and test Issue 3480481
2012-02-18 05:34:34 +00:00
Greg Landrum
d47f423009
support [HH]
2011-12-20 04:12:07 +00:00
Greg Landrum
9316758cec
improved handling of isotope specifications (still definitely not optimal)
2011-07-01 03:42:35 +00:00
Greg Landrum
faab610321
add string replacements to smiles and smarts parsers
2011-05-22 10:45:14 +00:00
Greg Landrum
3b3d44db16
remove exe property from source files
2011-01-13 04:22:56 +00:00
Greg Landrum
c6c7af1e6a
fix and test issue 3152751
2011-01-07 05:04:26 +00:00
Greg Landrum
e269703e0e
some more natural product tests for issue 3139534
2011-01-05 06:30:56 +00:00
Greg Landrum
f4a0012bc6
fix a residual problem with ring stereochem
2011-01-04 04:45:42 +00:00
Greg Landrum
c20376ad15
typo
2010-12-28 17:57:54 +00:00
Greg Landrum
5891b5edc8
further work on bug 3139534
2010-12-28 15:43:20 +00:00
Greg Landrum
006c696067
an inital pass at a solution to adding support for stereochemistry of ring bonds (bug 3139534);
...
this needs a ton more testing, but it is worth getting a "working" version in
2010-12-28 10:38:14 +00:00
Greg Landrum
67dadac26e
fix and test bug 3145697
2010-12-27 07:20:34 +00:00
Greg Landrum
e977a642f6
add support for writing non-canonical SMILES;
...
add support for atom-mapping information in plain SMILES
2010-12-20 03:59:56 +00:00
Greg Landrum
43fdf6db27
fix and test sf.net bug 3127883
2010-12-05 08:35:41 +00:00
Greg Landrum
f3fbef45c5
update copyright statements
2010-09-26 17:04:37 +00:00
Greg Landrum
d23bdac363
fix and test sf.net issue 3018558
2010-06-20 03:46:58 +00:00
Greg Landrum
2805355f34
First pass at the rewrite:
...
this gets rid of all the "preceding atom" code and passes all tests on linux
builds on other OS's and more extensive regression testing is required
2010-05-31 14:08:11 +00:00
Greg Landrum
96adbc11ea
remove the deprecated assign{Atom,Bond}ChiralCodes functions
2009-08-02 15:33:08 +00:00
Greg Landrum
5fe049ad31
fix and test issues 2690982 and 2525792
2009-03-18 05:13:52 +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
...
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
7d8e37a521
add ringStereoWarning prop when questionable ring stereochem is observed
2008-12-02 17:50:32 +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
c9eb4e91e1
merge revs 736:741 from branch http://rdkit.svn.sourceforge.net/svnroot/rdkit/branches/NumPyPort_27June2008
...
This removes the numeric python dependency and switches to relying on numpy.
current status of tests from branch: pass on lin32 and 64 and win32.
2008-07-05 07:42:38 +00:00
Greg Landrum
e6ccdd9b91
improve handling of Hs on smiles output (connected to sf.net
...
bug 1942220
2008-04-16 05:54:05 +00:00
Greg Landrum
4ea82818a6
switch away from using the old, unsupported boost::log stuff.
...
This "lookalike" implementation is much cruder than the real thing and does not really support
enabling and disabling logs, or associating them with files, but those components were not being
particularly used in the RDKit anyway.
2008-04-06 09:12:02 +00:00
Greg Landrum
5400bafb7d
support Se and Te as potentially aromatic atoms
...
(sf.net bug 1932365, http://sourceforge.net/tracker/index.php?func=detail&aid=1932365&group_id=160139&atid=814650 )
2008-04-06 06:11:58 +00:00
Greg Landrum
a788e29511
merge the changes from the CanonicalizerRework30Nov branch in.
...
The changes are revs 451:498.
2008-01-30 14:53:04 +00:00
Greg Landrum
bef62a88f3
dummy atoms expressed as '*' should not need to be in square brackets
2008-01-12 06:37:35 +00:00
Greg Landrum
8b4accb050
improve support for dummy atoms
...
this was sf.net feature request 1868217:
https://sourceforge.net/tracker/index.php?func=detail&aid=1868217&group_id=160139&atid=814653
2008-01-10 06:39:33 +00:00
Greg Landrum
506ae022ae
move GetAtomSmiles/GetAtomSmarts/GetBondSmiles/GetBondSmarts into separate namespaces;
...
a couple of little hacks to cleanup the smiles produced from a substructure query (not guaranteed to be correct, but better);
additional internal consistency checks;
stop throwing an exception from inside the smarts parser... that just screws up later parses (this should be fixed!);
better cleanup from failed parsing;
2007-08-04 05:11:27 +00:00
Greg Landrum
ebb196b8f8
Major thing here: fix and test Issue 1748846 ( https://sourceforge.net/tracker/?func=detail&atid=814650&aid=1748846&group_id=160139 )
...
Others:
SmilesParse: clean up some of the smiles generation code
2007-07-06 17:31:58 +00:00
Greg Landrum
4006f25d58
fix isotope handling in SMILES
2007-02-28 17:51:17 +00:00
Greg Landrum
2c96cd54dd
fix and test SF.net issue 1670149
...
http://sourceforge.net/tracker/index.php?func=detail&aid=1670149&group_id=160139&atid=814650
2007-02-27 18:07:43 +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
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
