Лаборатория изучения механизмов органических реакций

rotepi

Usage: rotepi -rot=1,2 -angle=90 file.xyz

Dependencies: Grimme's xtb (for -xtb option)

Rotates a fragment of a molecule in xyz format around a given bond.

Options:
-rot=i,j,k  atomic numbers i and j defined the rotatable bond.
            The bond must not be part of a cycle.
            k is optional and may be found automatically.
            -rot does not work when j and k are in the same cycle.
-angle   rotation angle in degrees (default 180).
-reflect reflection of transformed part about ijk plane
         Set -angle=0 for only reflection
-epi=i,j,k  epimerization about i (rotation of a fragment including 
            atoms j and k around the bissector of j-i-k angle.
            j and k are optional and may be found automatically.
            -angle and -reflect work for -epi too.
-xtb=n  Rough optimization with xtb (for linux). 
        This option is useful if the transformation of the molecule 
        results in very close atoms (there will be a warning about this).
        '-xtb' is '-xtb=10' (10 optimization steps).