7 Commits

Author SHA1 Message Date
Greg Landrum
da6cd73168 Run clang-format across everything (#7849)
* run clang-format-18 across Code/*.cpp and Code/*.h

* run clang-format-18 across External
2024-09-26 13:39:02 +02:00
Hussein Faara
abe991afda Used const reference to prevent copying in PositionVariationOp::getVariationCounts() (#6906) (#6907) 2023-11-14 12:29:59 +01:00
Greg Landrum
db15b372a1 Fix some problems turned up by ossfuzz (#4927)
* resolves oss-fuzz #24399

* clean up some undefined behavior

* fix some UB in mergeQueryHs

* be more defensive

* defensive programming

* fix a _cxsmilesBondIdx bug

* more defensive programming
2022-01-22 04:30:06 +01:00
Greg Landrum
31f42429ff Fixes #4382 and #4381: two Enumeration related bugs (#4383)
* Fixes #4382

* Fixes #4381
2021-08-05 05:10:53 +02:00
Greg Landrum
2e3f31990d Allow batch editing of molecules: removal only (#3875)
* backup

* simple first pass, passes all tests

* cleanup a bunch of existing uses

* ensure that we can safely add atoms/bonds while in edit mode

* add context manager on python side

* handle exceptions properly in those

* changes in response to review
2021-03-11 05:10:43 +01:00
Greg Landrum
5ab7952303 Fixes #3844: MolEnumerator and link nodes (#3845)
* backup

* Fixes #3844
2021-02-24 05:15:24 +01:00
Greg Landrum
73d26036de Support enumerating some mol file features into MolBundles (#3257)
* backup

* compiles

* progress, but not there yet

* basics now working

* start towards adding another test

* test having two variation points

* add actual enumeration and the corresponding tests

* docs and cleanup

* cleanups to get the mac build working

* attempt to get win32 dll builds to work

* dlls are fun

* Add FixedMolSizeMolBundle class

* changes in response to review

Also: add warnings for bad input in ParseV3000Array

* a bit of refactoring

* additional testing

* does not work, backup

* LINKNODES work now

* cleanup

* allow silencing reaction validation warnings during initialization

* docs

* fix (and test) handling of empty enumerations

* silence warnings when doing alchemy

* first pass at a Python wrapper for the enumerator

* Add Java wrappers for MolBundle and the MolEnumerator

* cleanup some comment formatting
2020-07-11 12:54:23 +02:00