"""Module containing functions for calculating geometrical parameters for molecules"""
from typing import Dict, List, Tuple
import click
from strenum import StrEnum
from tcmu import geometry, molecule
from tcmu.results.read import read
[docs]
class GeometricParameter(StrEnum):
"""Enum class for geometric parameters"""
COORDINATE = "Coordinate"
DISTANCE = "Distance"
ANGLE = "Angle"
DIHEDRAL = "Dihedral"
PYRAMIDAL = "Pyramidal"
SUMOFANGLES = "SumOfAngles"
geometric_character_to_info_mapping: Dict[GeometricParameter, Tuple[str, str, int]] = {
GeometricParameter.COORDINATE: ("Coordinate", "Å", 6),
GeometricParameter.DISTANCE: ("Distance", " Å", 3),
GeometricParameter.ANGLE: ("Angle", "°", 2),
GeometricParameter.DIHEDRAL: ("Dihedral", "°", 2),
GeometricParameter.PYRAMIDAL: ("Pyramidal", "°", 2),
GeometricParameter.SUMOFANGLES: ("SumOfAngles", "°", 2),
}
@click.command("geo")
@click.argument("path", type=click.Path(exists=True))
@click.argument("atom_indices", type=str, nargs=-1)
@click.option("-p", "--pyramidal", is_flag=True, default=False, help="Instead of calculating a dihedral angle, calculate pyramidalisation angle.")
@click.option("-s", "--soa", is_flag=True, default=False, help="Instead of calculating a dihedral angle, calculate sum-of-angles.")
def calculate_geometry_parameter(path: str, atom_indices: List[str], pyramidal: bool, soa: bool) -> None:
"""
Calculate geometrical parameters for atoms at the provided ``ATOM_INDICES``.
``PATH`` should be an ``.xyz``-file or a calculation directory.
\b
For 0 indices we return all coordinates of the molecule in ``PATH``.
For 1 index this program returns the cartesian coordinate for this atom.
For 2 indices return bond length between atoms.
For 3 indices return bond angle, with the second index being the central atom.
For 4 indices return dihedral angle by calculating the angle between normal vectors
described by atoms at indices ``1-2-3`` and indices ``2-3-4``.
\b
If the ``-p``/``--pyramidal`` flag is turned on it calculates ``360° - ang1 - ang2 - ang3``,
where ``ang1``, ``ang2`` and ``ang3`` are the angles described by indices ``2-1-3``, ``3-1-4``
and ``4-1-2`` respectively.
If the ``-s``/``--soa`` flag is turned on it calculates ``ang1 + ang2 + ang3``.
.. note:: Atom counting starts at 1.
"""
try:
mol = molecule.load(path)
except IsADirectoryError:
mol = read(path).molecule.output
assert 0 <= len(atom_indices) <= 4, f"Number of atom indices must be 1, 2, 3 or 4, not {len(atom_indices)}"
if len(atom_indices) == 0:
mol.delete_all_bonds()
print(mol)
return
atom_indices = [int(i) - 1 for i in atom_indices]
atoms = "-".join([f"{mol[i + 1].symbol}{i + 1}" for i in atom_indices])
param_value = geometry.parameter(mol, *atom_indices, pyramidal=pyramidal, sum_of_angles=soa)
if len(atom_indices) == 1:
param_type, unit, precision = geometric_character_to_info_mapping[GeometricParameter.COORDINATE]
param_value = " ".join([f"{x: .{precision}f}" for x in mol[atom_indices[0] + 1].coords])
print(f"{param_type}({atoms}) = {param_value} {unit}")
return
elif len(atom_indices) == 2:
param_type = GeometricParameter.DISTANCE
elif len(atom_indices) == 3:
param_type = GeometricParameter.ANGLE
elif len(atom_indices) == 4:
if pyramidal:
param_type = GeometricParameter.PYRAMIDAL
elif soa:
param_type = GeometricParameter.SUMOFANGLES
else:
param_type = GeometricParameter.DIHEDRAL
else:
raise ValueError("Invalid number of atom indices")
param_type, unit, precision = geometric_character_to_info_mapping[param_type]
print(f"{param_type}({atoms}) = {param_value: .{precision}f}{unit}")
if __name__ == "__main__":
calculate_geometry_parameter()
TCMU