schrodinger.application.matsci.geometry module¶

Utilities for geometry manipulation or property calculation

schrodinger.application.matsci.geometry.radius_of_gyration(struct, molecule_coms=False)¶

Calculate radius of gyration for a structure

Parameters

struct (structure.Structure) – The structure to calculate RG for
molecule_coms (bool) – Whether to use center of mass of each molecule in the structure for calculating Rg

Return type

float

Returns

The radius of gyration

schrodinger.application.matsci.geometry.fit_structure_to_ellipsoid(struct)¶

Fit the structure to an ellipsoid and return the ellipsoid semi-axes and principal moments of inertia

The method is taken from https://pubs.acs.org/doi/abs/10.1021/jp047138e and uses the following equations to calculate the semi-axes values: I1 = M/5 * (a**2 + b**2) I2 = M/5 * (a**2 + c**2) I3 = M/5 * (b**2 + c**2) Also see https://en.wikipedia.org/wiki/Ellipsoid#Dynamical_properties

Parameters: struct (structure.Structure) – The structure to fit to an ellipsoid
Return type: tuple of (float, float, float, [float, float, float])
Returns: Tuple of semi-axes values in Angstroms and principal moments of inertia in u * A**2