An issue related to Szybki TK losing information about already perceived
protein residues has been fixed.
Previously, highly clashed protein-ligand systems that were often a result
of docking were not automatically relaxed when using the default
OEOptType.BFGS optimization method.
Users had to explicitly use the OEOptType.SD_BFGS
method. Now, a clash that exceeds 1e6 (kcal/mol)/A on a gradient norm is
detected and 5 steps of steepest descent optimization are automatically
applied before the BFGS optimizer is run.