* support tracking where the conformer generation code fails
* less verbose output
* tests now pass
* fix a stupid typo
* fix SWIG wrappers
* changes in response to review
* improvements for smal anr large ring conformer generation
* add documentation and reorder parameters in EmbedParam
* resolve merge conflict due to coordMap null pointer
* minor changes to address merge comments
* reorder variables in EmbedParameters
* add regression test for small ring and macrocycle torsion preferences
* not apply small ring torsions to bridged ring systems
* fix and test for bridged small rings torsion pattern exclusion
* add ETKDGv3 and srETKDGv3 option to keep compatiblity for original ETKDG
* EKTDG version 3 related minor fix
* add reference to doc string
* Java wrapper for ETKDGv3
* fix doc
* change CPCI to shared_ptr, but it seems to be much slower
* minor modifications to small bridged ring systems, and share_ptr from previous commit is fine
* rollback from shared_ptr(map) to just map
* run clang-format
Co-authored-by: Shuzhe Wang <shuwang@eu-login-10.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-14.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-17.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-45.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-05.euler.ethz.ch>
Co-authored-by: Shuzhe Wang <shuwang@eu-login-15.euler.ethz.ch>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* initial version; no actual testing yet
* start on tests
* rename seed->randomSeed; add tests
* add support in java wrapper
* add support in python wrapper
* yapf
* document the parameter object;
introduce pre-defined const objects for ETDG, ETKDG, and KDG
* this is why we write tests
* swig did not like the initialization in the header file
