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