Merge pull request #4839 from RosettaCommons/guangfeng/galigdock_genparams
GALigandDock mol2genparams python scripts update.
1. Added a function to rename atom names in mol2 files in order to fix duplicated atom names issue;
2. There is an issue that sometimes NH-CR in (C=O)-NH-CR is incorrectly assigned as a conjugated bond type. In some cases, e.g. APAJIL from CSD, NH-C=O is conjugated but NH-CR is not. To fix this issue, the dihedral angle of the input structure is used as a second check, if the angle (current range is from 40 to 140 degrees) is clearly not planar don't assign it as a conjugated bond.