moleculekit.projections.metricgyration module#

class moleculekit.projections.metricgyration.MetricGyration(atomsel, refmol=None, trajalnsel=None, refalnsel=None, centersel='protein', pbc=True)#

Bases: Projection

Creates a MetricGyration object that calculates the radius of gyration (ROG) of a molecule.

Parameters:

  • atomsel (str | ndarray | None) – Atom selection for the atoms whose ROG we want to calculate (a selection string, boolean mask, or integer index array). See more here

  • refmol (Molecule | None) – The reference Molecule to which we will align.

  • trajalnsel (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 it’s None and a refmol is passed it will default to ‘protein and name CA’.

  • refalnsel (str | ndarray | None) – Atom selection for refmol 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 trajalnsel.

  • centersel (str | ndarray) – Atom selection around which to wrap the simulation (a selection string, boolean mask, or integer index array). See more here

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

Returns:

metr

Return type:

MetricGyration object

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