molgemtools 0.0.9

Tools for working with molecular geometry data.

It provides:

• Opening molecular .xyz files.

• Helps generating nicely formatted Molpro or Gaussian input files for quantum chemical calculations.

• Conversion between Cartesian and internal coordinate representations.

• Molecular shape matching based on the Kabsch-Umeyama algorithm.

• Calculating atomic distances, bond angles and dihedral angles.

• Calculating the principal moments of inertia.

• Generating permuted geometries.

• Calculating the Euler angles from 3-dimensional rotation matrices.

• Calculating the molecular adjacency list based on atomic distances.

• Some chemical graph-theoretical tools derived from the adjacency list.

Limitations:

• Only supporting dummy atoms for converting internal coordinate representations (Z-matrices) to Cartesian.

• A Cartesian representation can be converted to Z-matrix if all atoms (with the exception of the first) are connected to at least one atom with an index lower than its own.