htmd.projections.metricrmsd module

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

Bases: htmd.projections.projection.Projection

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

Parameters:
  • refmol (Molecule object) – The reference Molecule to which we want to calculate the RMSD.
  • trajrmsdstr (str) – Atom selection string for the trajectories from which to calculate the RMSD. See more here
  • trajalnstr (str, optional) – Atom selection string for the trajectories from which to align to the reference structure. If None, it defaults to the same as trajrmsdstr. See more here
  • refrmsdstr (str, optional) – Atom selection string for the reference structure from which to calculate the RMSD. If None, it defaults to trajrmsdstr. See more here
  • refalnstr (str, optional) – Atom selection string for the reference structure from which to align to the trajectories. If None, it defaults to trajalnstr. See more here
  • centerstr (str, optional) – Atom selection string around which to center the wrapping of the trajectories. See more here
  • pbc (bool, optional) – Enable or disable simulation wrapping.
copy()

Produces a deep copy of the object

getMapping(mol)

Returns the description of each projected dimension.

Parameters:mol (Molecule object) – 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:np.ndarray