Gyration analysis code

For source code refer to github repository

Module documentation

Module to calculate gyaration and inertial information from coordinates.

Currently only .xyz file input is supported.

To use:

1) import the module in your python script with (script must be in same directory as this file)

import get_gyr as gyr

2) read .xyz file

molecule = gyr.GyrationMolecule("./molecules/water.xyz")

3) call appropriate variable, e.g.

print("Relative shape anisotropy is: ", molecule.Rel_anis)

for detailed information see test_gyr.py script

Classes

GyrationMolecule

Class containing gyration/inertia information for given molecule

Attributes:

Name Type Description
Rx2 float

Radius of gyration squared in first principal direction
Ry2 float

Radius of gyration squared in second principal direction
Rz2 float

Radius of gyration squared in third principal direction
Rg float

Radius of gyration for molecule
Rel_anis float

Relative shape anisotropy, 0 for perfectly spherical arangement 1 for perfectly linear arangement
Ix float

Moment of inertia in first principal direction
Iy float

Moment of inertia in first principal direction
Iz float

Moment of inertia in first principal direction
Methods
__init__(self, fname, flag_xyz=1, flag_periodic=0) special

Calculate gyration properties from given file

Parameters:

Name Type Description Default
fname str

Filename of coordinates, xyz file or simple list of coordinates

 required
flag_xyz int

1 if using xyz file, 0 if using simple list of coordinates

 1
flag_periodic int

1 if using periodic system (not yet supported)

 0
Source code in Gyration-from-coordinates/get_gyr.py 
def __init__(self, fname: str, flag_xyz: int=1, flag_periodic: int=0):
    """Calculate gyration properties from given file

        Arguments:
            fname: Filename of coordinates, xyz file or simple list of coordinates
            flag_xyz: 1 if using xyz file, 0 if using simple list of coordinates
            flag_periodic: 1 if using periodic system (not yet supported)
    """
    if flag_xyz:
        self.name = fname.split('.xyz')[0]

        # Gyration parameters
        self.__coords = self.__xyz_to_coords(fname)
        self.Rx2, self.Ry2, self.Rz2, = self.__calc_evals_gyr(self.__coords)
        self.Rg = np.sqrt(self.Rx2 + self.Ry2 + self.Rz2)
        self.Rel_anis = (1.5 * (self.Rx2**2 + self.Ry2**2 + self.Rz2**2)
                         / (self.Rx2 + self.Ry2 + self.Rz2)**2 - 0.5)

        # Inertia parametrs
        self.Ix, self.Iy, self.Iz, = self.__calc_evals_inertia(self.__coords)
    else:
        print("Not yet implemented")
        quit()