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ca5edda7fb4ea9fd574d4300a6c4c2c535165aee
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58 Commits

Author SHA1 Message Date
Greg Landrum
ca5edda7fb fix and test problems with reading aromatic Si from smiles 
(github issue 5)
 2013-02-14 03:59:44 +00:00
Greg Landrum
24e269f8ac I *think* that this fixes sf.net issue 40: 
the long-standing problem with ring stereochemistry and canonicalization
 2012-11-02 06:33:11 +00:00
Greg Landrum
5c2a3f12ce fix and test issue 257 
Note that unknown bond types are now written to SMILES as "~" characters.
The smiles parser has been modified to recognize these.
 2012-10-12 08:58:38 +00:00
Greg Landrum
854dde8097 fix and test issue 253 2012-09-21 12:32:35 +00:00
Greg Landrum
14e396c26d refactoring the SMILES parser to make it more efficient 
NOTE: this changes the ordering of bonds in molecules with branches.
 2012-08-28 04:01:49 +00:00
Greg Landrum
f2d9755a65 at this point all tests pass 2012-06-29 03:40:28 +00:00
Greg Landrum
55ae9a6e26 start fixing some tests (note: this is not done) 2012-06-29 02:42:27 +00:00
Greg Landrum
0f3b84cd28 backup commit; we are not quite there yet 2012-06-26 06:15:08 +00:00
Greg Landrum
a3dc23c43c more canonicalization improvements 
there are still some problems with double bonds
 2012-06-11 03:21:30 +00:00
Greg Landrum
086cbd769c fix a bug in MolFragmentToSmiles() without canonicalization 2012-05-23 04:37:03 +00:00
Greg Landrum
efc76f5bd5 clean up an uninitialized variable that was causing problems on the mac 2012-05-20 06:11:48 +00:00
Greg Landrum
700d60c94d left out some tests 2012-05-19 04:34:45 +00:00
Greg Landrum
c293dc23da initial version of MolFragmentToSmiles 2012-05-19 03:50:31 +00:00
Greg Landrum
7495b6248f cleanup + tests for issue 3526815 2012-05-18 09:09:04 +00:00
Greg Landrum
cfc14230e1 fix issues 3525799 and 3526810 
this changes some canonical SMILES
and removes support for "[Xa]" dummy atoms in SMILES
 2012-05-18 05:56:45 +00:00
Greg Landrum
a39187a528 fix and test issue 3526814 2012-05-16 05:29:34 +00:00
Greg Landrum
e77cfcf336 fix and test issue 3525776 2012-05-11 13:02:07 +00:00
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