Greg Landrum
23076b1cdb
Fixes #298
2014-07-23 05:31:16 +02:00
Greg Landrum
0839cf41ad
Fixes #210
2014-02-03 05:25:27 +01:00
Greg Landrum
9e4ceef1bd
Fixes #206 but more testing is definitely required
2014-01-28 06:44:43 +01:00
Greg Landrum
47afcc1f53
remove some debugging printing
2013-12-31 07:12:40 +01:00
Greg Landrum
0a421d8aa5
Fixes #182
2013-12-31 07:11:31 +01:00
Greg Landrum
158c9b9e45
Fixes #136
2013-10-21 05:55:42 +02:00
Greg Landrum
dccf20b8c7
Fixes #45
2013-06-08 06:01:54 +02:00
Greg Landrum
e9d8cb1b99
fix and test github issue 12
2013-03-19 04:44:24 +00:00
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:
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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
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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
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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
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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
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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);
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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;
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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:
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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
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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
