moleculekit.projections.metricsphericalcoordinate module

class moleculekit.projections.metricsphericalcoordinate.MetricSphericalCoordinate(refmol, targetcom, refcom, trajalnsel='protein and name CA', refalnsel=None, centersel='protein', pbc=True)

Bases: Projection

Creates a MetricSphericalCoordinate object that calculates the spherical coordinates between two centers of masses from a set of trajectories.

Parameters:

• refmol (Molecule) – The reference Molecule to which we will align.

• targetcom (str | ndarray) – Atom selection from which to calculate the target center of mass (a selection string, boolean mask, or integer index array). See more here

• refcom (str | ndarray) – Atom selection from which to calculate the reference center of mass (a selection string, boolean mask, or integer index array). See more here

• trajalnsel (str | ndarray) – Atom selection for the trajectories from which to align to the reference structure (a selection string, boolean mask, or integer index array). See more here

• refalnsel (str | ndarray | None) – Atom selection for refmol from which to align to the reference structure (a selection string, boolean mask, or integer index array). If None, it defaults to the same as trajalnstr. See more here

• centersel (str | ndarray) – Atom selection around which to wrap the simulation (a selection string, boolean mask, or integer index array). See more here

• pbc (bool) – Enable or disable coordinate wrapping based on periodic boundary conditions.

Returns:

metr

Return type:

MetricCoordinate object

getMapping(mol)

Returns the description of each projected dimension.

Parameters:

mol (Molecule) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.

Returns:

map – A DataFrame containing the descriptions of each dimension

Return type:

DataFrame object

project(mol)

Project molecule.

Parameters:

mol (Molecule) – A Molecule object to project.

Returns:

data – An array containing the projected data.

Return type:

ndarray