moleculekit.projections.metriccoordinate module

class moleculekit.projections.metriccoordinate.MetricCoordinate(atomsel, refmol=None, trajalnsel=None, refalnsel=None, centersel='protein', pbc=True)

Bases: moleculekit.projections.projection.Projection

Creates a MetricCoordinate object that calculates the atom coordinates from a set of trajectories.

Parameters

  • atomsel (str) – Atom selection string for the atoms whose coordinates we want to calculate. See more here

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

  • trajalnsel (str, optional) – Atom selection string for the trajectories from which to align to the reference structure. If it’s None and a refmol is passed it will default to ‘protein and name CA’.

  • refalnsel (str, optional) – Atom selection string for refmol from which to align to the reference structure. If None, it defaults to the same as trajalnsel.

  • centersel (str, optional) – Atom selection string around which to wrap the simulation. See more here

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

Returns

metr

Return type

MetricCoordinate object

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