SimTk/msmbuilder — pull request #203 by vvoelz (2013-05-30 20:26:41+00:00)
Title: Updated dihedral.py and parsers.py to allow user-defined dihedrals.

I've tested this out on my projects and it seems to work well. Perhaps you other developer-types could take a look to confirm. Only minor changes to metrics/dihedral.py and metrics/parsers.py were required. --Vince

$ Cluster.py dihedral -h

...optional arguments:
-h, --help show this help message and exit
-a DIHEDRAL_ANGLES which dihedrals. Choose from phi, psi, chi (to choose
multiple, seperate them with a slash), or user
Default: phi/psi
-f DIHEDRAL_USERFILENAME
filename for dihedral indices, N lines of 4 space-
separated indices (otherwise ignored) Default:
DihedralIndices.dat
-p DIHEDRAL_P p used for metric=minkowski (otherwise ignored)
Default: 2