Commit Graph

14 Commits

Author SHA1 Message Date
Greg Landrum
00583fc1ab Fix a couple issues related to atom list handling in V3000 mol blocks (#8824)
Fixes #8820
Fixes #8823
2025-10-09 05:26:01 +02:00
Greg Landrum
86141183c1 Moving towards getting all tests to pass when using the new stereo code (#8409)
* Fixes #8379

* check in some working tests

* test passes

* test passes

* test passes

* test passes

* test passes

* ensure that the invariants flush the streams on failure

* tests pass

* test passes

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* tests pass

* Fixes #8391

* tests pass

* fix a test with legacy
not clear why this was not causing problems before

* make a test work

* Fixes #8396

* gcc builds work

* fingerprint tests pass

* mention backwards incompatible change

* fix a problem with FindMolChiralCenters

* more testing details

* enable the test status output

* Fixes #8432

fix a bug in double-bond stereo handling for template matching

* all depictor tests pass

* use the new-stereo chiral ranks in the depiction code

* always assign new-stereo chiral ranks

* make _ChiralAtomRank a computed property
This is analogous to _CIPRank

* tweak to the way the atom ordering is computed for 2D coordinate generation

* update two expected results

* backup

* response to review

* tests pass

* tests pass

---------

Co-authored-by: = <=>
2025-04-15 14:00:32 +02:00
Greg Landrum
b64aea5082 apply query adjustments when makeAtomsGeneric is enabled (#8315)
* apply query adjustments when makeAtomsGeneric is enabled

* changes in response to review

* I got Python in my C++
2025-03-04 13:50:24 +01:00
Ricardo Rodriguez
5596179c95 Fixes #8256 (#8257)
* add test

* fix
2025-02-12 15:34:28 +01:00
Greg Landrum
2957ab4576 switch to catch2 v3 (#6898)
* switch to catch2 v3
Fixes #6894

* fix a couple of problems noticed in the CI builds

* more warning cleanup

* changes in response to review
2023-11-15 06:45:42 +01:00
Greg Landrum
f0cf0b0f20 Fixes #4789 (#4790) 2021-12-13 14:15:26 +01:00
Ric
8ca62db8a7 Mem leak fixes (#4637)
* fix leaks in tests

* fix leak in smiles parsing error
2021-10-26 05:58:50 +02:00
Greg Landrum
df72c241c5 Improve test coverage and some bug fixes (#4536)
* test getIdOfEntryWithBitId()

* remove unused functions

* improve bv tests in python wrapper

* more UniformGrid tests

* improve deprotect coverage

* improve abbreviations coverage

* add operator!= to DeprotectData

* more testing for adjustQueryProperties

* fix a copy-paste bug

* copy-paste bug

* more testing

* more testing

* more testing

* fix an edge case bug in getValenceContrib

* more bond tests

* add operator!= to StereoInfo
tests StereoInfo::operator==

* make some internal functions testable

* more testing

* minor code cleanup

* fix some bad caching behavior in getDistanceMat() and get3DDistanceMat()

testing

* test FixeMolSizeMolBundle() copy ctor

* deprecate BalabanJ

* more testing

* testing

* mods to get things working for windows DLL builds
(don't bother running some of the tests there)

* fix a typo
2021-09-26 07:45:06 +02:00
Eisuke Kawashima
013ba4f21d Run clang-tidy (modernize-use-override) (#4251) 2021-07-01 05:18:56 +02:00
Eisuke Kawashima
48f4f3ee82 Run clang-tidy (modernize-pass-by-value) (#4224) 2021-06-14 06:57:08 +02:00
Paolo Tosco
7d0d7df5f0 Fixes a number of issues flagged by clang (#3498)
* - fixes a number of issues flagged by clang

* - removed commented line
2020-10-15 15:03:34 +02:00
Greg Landrum
53a1382206 Fixes #3388 (#3389)
* Fixes #3388

* add a test for numradicals too
2020-09-04 12:38:25 -04:00
Greg Landrum
daf78eb62c add test for #3325 (#3331) 2020-08-10 13:17:41 -04:00
Greg Landrum
b55376f284 Adds more options to adjustQueryProperties (#3235)
* add documentation

* backup

* first pass at 5-rings working

* add a static method to initialize an empty parameter object

* expose static method to python

* additional testing

* support the single bond adjustments

* cleanup

* preserve the symbol used in the query from a CTAB

* support the way the MDL code adjusts five-ring aromaticity in query rings

* in-code documentation

* while we're at it, cleanup the way Q and A atoms are handled in the v3k parser

* changes in response to review

* make this C++14 again.

* change in response to review
2020-06-22 09:17:50 -04:00