v0.3.3 - bugfix cycle detection
Fixes bug that causes small cycles, such as 6-member rings, to be modeled flexibly without glue atoms (e.g. CG0/G0).
Example: O1CC2C(CC1)C1C(C2)CCCC1 sdf
First reported in ccsb-scripps/AutoDock-Vina#106
New feature: support for covalent docking