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12 Commits

Author SHA1 Message Date
Greg Landrum
ecf5a67acc Fixes #2437 (#2438) 
* Fixes #2437

getting the canonical atom ranking no longer results in molecules have a
RingInfo structure that's been initialized but contains nothing.

* update expected results for the MMPA tests
 2019-05-10 08:25:31 +02:00
Greg Landrum
8d72034367 Add an allowed valence of 3 for Al (#2425) 
Fixes #2423
 2019-05-09 10:49:14 -04:00
Greg Landrum
26c07e67d6 fixes #908 (#2328) 
Code is a mess and really should be refactored
 2019-03-10 21:43:20 -04:00
Ric
be3170d0d5 Mem errors clean up (#2305) 
* fix test leaks

* fix "invalid read" when casting Query to EqualityQuery

* fix error cleanup in SMILES/SMARTS parsers

* SMILES/SMARTS parser fix updated *.cmake

* fix error cleanup in SLN parser

* SLN parser updated *.cmake

* updated suppressions

* update loop in sln bison
 2019-03-08 05:39:59 +01:00
Greg Landrum
334b1558bc Fixes #2258 (#2286) 2019-02-22 07:30:31 -07:00
Greg Landrum
094f65f5f4 Fix #2148 and #2244 (#2275) 
* not quite done yet

* Fixes #2244

* Fixes #2148

This fixes a few of the knock-on effects of the actual fix.

* Test that we still write SMILES properly

* Fixes #2266 (#2269)

* Fixes #2268 (#2270)

* Improve interactivity of output SVG (#2253)

* Add clickable atoms when tagAtoms() is called

* add python tests

* add class tags for atoms and bonds

* add marker to allow easy insertion of extra text
 2019-02-21 08:03:28 -07:00
Greg Landrum
0360a9de84 Fixes #2268 (#2270) 2019-02-15 10:35:35 -05:00
Greg Landrum
069e920645 Fixes #2224 (#2234) 
* Fixes #2224

* test the basics
 2019-01-21 11:31:02 -05:00
Greg Landrum
ba40ecaca1 Fixes #299 (#2100) 
add a fallback for when the original algorithm fails
 2018-10-11 17:24:15 -04:00
Greg Landrum
17323d11bf Modify removeHs so that it does not remove degree 0 atoms (#2089) 
* Modify removeHs so that it does not remove degree 0 atoms
Update the docs at the same time.

* include a warning when not removing some Hs

* clear up a problem with the warning log
 2018-10-05 13:43:09 -04:00
Greg Landrum
ffc123a665 Fixes #2062 (#2079) 2018-10-02 11:41:22 -04:00
Greg Landrum
223513a76e Start to use Catch2 for new tests (#1732) 
* backup

* build works

* works

* builds on linux

* rename the test

* add another test to make sure that works
 2018-09-04 10:32:17 -04:00