moleculekit.projections.metricrmsd module

class moleculekit.projections.metricrmsd.MetricRmsd(refmol, trajrmsdstr, trajalnstr=None, refrmsdstr=None, refalnstr=None, centerstr='protein', pbc=True)

Bases: Projection

Calculates the RMSD of a set of trajectories to a reference structure

Parameters:

• refmol (Molecule) – The reference Molecule to which we want to calculate the RMSD.

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

• trajalnstr (str | ndarray | None) – Atom selection for the trajectories 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 trajrmsdstr. See more here

• refrmsdstr (str | ndarray | None) – Atom selection for the reference structure from which to calculate the RMSD (a selection string, boolean mask, or integer index array). If None, it defaults to trajrmsdstr. See more here

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

• centerstr (str | ndarray) – Atom selection around which to center the wrapping of the trajectories (a selection string, boolean mask, or integer index array). See more here

• pbc (bool) – Enable or disable simulation wrapping.

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