Greg Landrum
9dcef9ac57
Fixes #607 ( #1075 )
2016-09-23 04:57:07 +02:00
Greg Landrum
91674e6482
Fixes issue #1021 ( #1026 )
...
* Fixes #1021 , kind of.
The test for the bug passes, but there are other failures
* all tests except hanoi pass
* passes all tests
* remove some vestigial code
* remove debug-droppings
* minor documentation
2016-08-30 18:59:10 +02:00
Greg Landrum
7fd991e13d
Fixes #962 ( #1003 )
2016-08-05 07:57:20 -04:00
Greg Landrum
339fa081e5
Merge fix/github908 branch
2016-07-27 04:49:55 +02:00
Greg Landrum
435a34df4f
Expose the aromatizeIfPossible parameter to python ( #991 )
...
- Add tests for that
- Improve the C++ tests for aromatizeIfPossible
2016-07-26 13:17:41 -04:00
Brian Kelley
659ac6cb27
Adds aromatization and reaction options to AdjustQuery ( #965 )
...
* Adds aromatization and reaction options to AdjustQuery
aromatizeIfPossible - checks kekulized queries for
aromatic compatibility
adds IGNORE_MAPPED and IGNORE_ATTACHEDRGROUPS options
to adjustDegree
* Missed return false.
* Removes IGNOREATTACHEDRGROUPS
2016-06-29 05:09:30 +02:00
Greg Landrum
d63f44cc0c
Add cartridge support for adjustQueryProperties() ( #949 )
...
* backup commit
* Change the names and meanings of MolOps::AdjustQueryWhichFlags
What was there before was not flexible enough and was extremely confusing. This should clear that up.
NOTE: this does break backwards compatibility with code that uses this enum, but given that this is new and has not been
widely promoted, I suspect it should not affect that many people. The default behavior of MolOps::adjustQueryProperties()
remains the same.
* adjust to the new AdjustQueryWhichFlags
* add mol_adjust_query_properties tests to the cartridge
2016-06-21 14:38:32 -04:00
Greg Landrum
ca1d3015ef
update a test
2016-06-21 06:25:08 +02:00
Greg Landrum
452ed7156f
Add support for a simplified aromaticity model. ( #942 )
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* first pass
* Fixes #623
* fix a merge problem
* move the aromaticity perception to a helper fn
* python doc update
* replace setSimpleAromaticity() with a parameter to setAromaticity()
* add simple test for the custom aromaticity function
2016-06-17 17:48:20 -04:00
Brian Kelley
45ab3505dc
AddTee is now SetTee ( #930 )
2016-06-01 04:46:27 +02:00
Greg Landrum
e846a96123
Fix github #868 ( #925 )
...
* fix an incorrect status message
* Fixes #868
Switch the warning to only occur if we have a non-negated atomic number query with value=1
2016-05-31 13:23:21 -04:00
Greg Landrum
1c56b07f66
cleanups of RDLog's tee behavior ( #926 )
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- rename RDLog::AddTee()->RDLog::SetTee()
- remove a leak when RDLog::SetTee() (formerly AddTee()) is called twice
- add RDLog::ClearTee() method to allow RDLog::SetTee() to be safely used with a stream that goes out of scope.
2016-05-30 10:04:59 -04:00
Greg Landrum
06818ee0ed
improve error reporting for kekulization failures ( #919 )
...
* improve error reporting for kekulization failures
Connected to #917
* better phrasing of the message.
2016-05-23 16:10:08 -04:00
Greg Landrum
f762346ced
make the perchlorate cleanup pattern more generic to cover all halogenates;
...
Fixes #115
2016-04-01 07:54:32 +02:00
Greg Landrum
6a4a032e92
Fixes #518
2016-03-21 16:57:12 +01:00
Greg Landrum
d7d95dd684
an alternate approach to fixing #805
2016-03-13 04:21:36 -07:00
Greg Landrum
ed7b7b8a37
Fixes #805
2016-03-09 08:47:29 +01:00
Greg Landrum
027d231e38
add a test (still fails)
2016-03-09 07:27:11 +01:00
Greg Landrum
da46a3d80f
Merge remote-tracking branch 'origin/master' into fix/Issue694
2016-02-20 02:35:29 +01:00
Greg Landrum
250a8abbd4
removed a diff-dropping
2016-02-17 05:57:08 +01:00
Greg Landrum
38f8a92d2b
Fixes #754
2016-02-17 05:15:53 +01:00
Greg Landrum
b0b9ed632f
add first test (it fails)
2016-02-17 05:15:30 +01:00
Greg Landrum
0ee4ce4b8c
add a test
2016-02-16 14:02:33 +01:00
bp-kelley
84b4122f6b
Merge pull request #759 from greglandrum/dev/github758
...
Add argument to addHs allowing only certain Hs to be considered
2016-02-12 17:24:08 -05:00
Greg Landrum
4f2aa0f51e
Fixes #758
2016-02-08 16:11:22 +01:00
Juuso Lehtivarjo
2ad2b03c4a
Bug fix to getShortestPath
2016-02-08 11:27:08 +02:00
Greg Landrum
70c2995cf8
Fixes #717
...
This changes the CIPCode and CIPRank atom properties to no longer be computed properties.
Note: under linux I was unable to actually get the bug to manifest (converting the uint property to an int didn't cause problems), but that doesn't mean it shouldn't still be fixed.
2016-01-06 03:45:14 +01:00
Greg Landrum
23d7df99f0
Fixes #678
2015-12-17 04:11:21 +01:00
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
54311dff9c
Suppresses warnings in tests
2015-10-18 16:09:58 -04:00
Greg Landrum
c5a7371202
Fixes #584
2015-08-27 10:00:35 +02:00
Greg Landrum
8596c6f9ad
add support for converting dummies to queries
2015-08-22 05:43:42 +02:00
Greg Landrum
a7383e7861
first pass at #567
2015-08-21 16:45:00 +02:00
Greg Landrum
cf17b14c12
add a couple more test cases that came up independently
2015-07-17 03:40:41 -04:00
Paolo Tosco
5dfbecd6d0
- fixed missed kekulization of aromatic carbocations such as cyclopropenyl
...
and tropylium
2015-07-17 01:00:34 +01:00
Paolo Tosco
48396640c1
- fixed lack of tropylium/ciclopropenyl cation aromaticity perception
...
- added a test for allyl cation conjugation
- added a test for tropylium/ciclopropenyl cation aromaticity
2015-07-16 20:05:46 +01:00
Greg Landrum
a7a2ee9a62
Fixes #526
2015-06-20 04:54:54 +02:00
Greg Landrum
672f8ea200
Fixes #510
2015-05-20 05:19:40 +02:00
Nadine Schneider
0cf0dd37ce
Bugfix in SmilesWrite and some additional tests for getMolFrags function
2015-04-16 10:53:20 +02:00
Greg Landrum
fba1bf24ee
update expected results
2015-04-10 09:44:32 +02:00
Nadine Schneider
5d963846b8
merge
2015-04-10 09:44:18 +02:00
Greg Landrum
ebaf3aff89
additional test related to #432
2015-03-21 07:17:09 +01:00
Greg Landrum
2f77e5e6cd
Fixes #447
2015-03-19 07:19:47 +01:00
Greg Landrum
74125f685c
Fixes #443
2015-03-05 06:38:38 +01:00
Greg Landrum
7932b3d7d8
Fixes #441
2015-03-01 06:56:42 +01:00
Greg Landrum
4363ac9338
Fixes #432
2015-02-21 08:15:58 +01:00
Nadine Schneider
d9fcb23f9a
Fix in molopstest
2015-02-12 09:04:16 +01:00
Greg Landrum
a0a02b4a99
merge on master
2015-02-03 16:41:46 +01:00
Greg Landrum
877d59499c
Fixes #418
2015-01-30 06:34:42 +01:00
