Commit Graph

4 Commits

Author SHA1 Message Date
Greg Landrum
a9010da8a4 Small bug fixes and cleanups from fuzz testing (#3299)
* fix ossfuzz issue 24074

* fix ossfuzz issue 23896

* switch to throw exceptions when reading ints/floats

* remove extraneous benchmarking code

* change type of AH query

* confirm an invariant while finding rings

* no sense in adding these tests to github

* switch to use fail() instead of failbit
switch to acceptSpaces by default
2020-07-22 16:57:31 +02:00
Greg Landrum
edd922c99c Cleanup warnings from clang-10 (#3238)
* stop returning local memory in exceptions

* remove a couple unnecessary copies in loops

* fix a bug in the way the default MMFF aromatic parameters are constructed

* remove a bunch of loop-variable warnings

* remove a bunch of clang warnings

* disable clang warnings in python wrappers

* remove some warnings when building the python wrappers
2020-06-19 17:16:22 -04:00
Greg Landrum
95613b6279 Allow SubstanceGroups to survive molecule edits (#3170)
* Progress on #3168

* Fixes #3167

* Fixes #3169

* deal with CBONDS too

* test PATOMS

* Fixes #3175

* a bit of code simplification and test updates

still needs more testing

* more testing

* handle s-group hierarchy
also a couple of other changes in response to the review

* add forgotten test file

* changes in response to review
2020-05-19 17:35:08 +02:00
Greg Landrum
5a79190261 rename SGroup -> SubstanceGroup (#2375)
We leave the names of the bit connected with Mol files as SGroups, since that is
appropriate there, but the more generic pieces are renamed
2019-03-30 14:53:24 -04:00