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