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* 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>