rmgpy.qm.symmetry¶

class rmgpy.qm.symmetry.PointGroup(point_group, symmetry_number, chiral)¶

A symmetry Point Group.

Attributes are:

point_group

symmetry_number

chiral

linear

class rmgpy.qm.symmetry.PointGroupCalculator(settings, unique_id, qm_data)¶

Wrapper type to determine molecular symmetry point groups based on 3D coords information.

Will point to a specific algorithm, like SYMMETRY that is able to do this.

class rmgpy.qm.symmetry.SymmetryJob(settings, unique_id, qm_data)¶

Determine the point group using the SYMMETRY program

(Originally http://www.cobalt.chem.ucalgary.ca/ps/symmetry/: now mirrored at https://github.com/nquesada/symmetry).

Required input is a line with number of atoms followed by lines for each atom including: 1) atom number 2) x,y,z coordinates

finalTol determines how loose the point group criteria are; values are comparable to those specified in the GaussView point group interface

calculate()¶

Do the entire point group calculation.

This writes the input file, then tries several times to run ‘symmetry’ with different parameters, until a point group is found and returned.

parse(output)¶: Check the output string and extract the resulting point group, which is returned.

run(command)¶: Run the command, wait for it to finish, and return the stdout.

unique_id¶: The object that holds information from a previous QM Job on 3D coords, molecule etc…