- Calculation of the constant potential terms at the end of adapted optimization can be optionally eliminated, by the use of the -neglect_frozen flag. This feature allows for less memory and cpu usage in the case of partial optimization of large molecules.
- The corresponding atom symbols, bond symbols, and torsion angles are now printed on a line under the matching smarts pattern.
- Input proteins with only partial information about residues were not handled properly. As a result, none of the side chains which were supposed to be made flexible with the use of an option -sideC were optimized. This problem was fixed.
- A bug causing memory corruption in the case of ligand optimization in partially flexible protein receptor is fixed.
- Residues with non-standard name CYX were not properly handled in the situation when their side chains were included into the flexible part of the protein receptor. This bug has been fixed.