Tools to generate and manipulate z-matrices

zmatools is a package for generating and manipulate the z-matrix of a small molecules

Currently it has two tools:

1. Generating the z-matrix from a structure file
2. Producing a trajectory when each dihedral is sampled in a specific range, assuming the rest of the atoms are fixed.

To install this tool, clone or download the git repository. Change to the downloaded directory and install the software with

python setup.py install

To find the available commands

zmat -h

To find the help of individual commands

zmat generate -h

To generate a z-matrix to be used with Gaussian

zmat generate model0.mol2 --gaussian

To obtain verbose information on the z-matrix generation

zmat generate model0.mol2 --verbosity 2

To produce a dihedral trajectory in the range -180 to 180 in 15 degrees increment

zmat traj model0.mol2

the trajectories will be in xyz-formats in model0_dihed_traj4.xyz, model0_dihed_traj5.xyzetc.

To produce a dihedral trajectory in the range -180 to 180 in 30 degrees increment

zmat traj model0.mol2 -d 30