moleculekit.projections.metricsasa module

class moleculekit.projections.metricsasa.MetricSasa(sel='protein', filtersel='all', probeRadius=1.4, numSpherePoints=960, mode='atom')

Bases: moleculekit.projections.projection.Projection

Calculate solvent accessible surface area of a molecule.

Implementation and documentation taken from MDtraj shrake_rupley code.

Parameters:
  • sel (str) – Atom selection string for atoms or residues for which to calculate the SASA. See more here
  • filtersel (str) – Keep only the selected atoms in the system. All other atoms will be removed and will not contribute to the SASA calculation. Keep in mind that the SASA of an atom or residue is affected by the presence of other atoms around it so this will change the SASA of the remaining atoms.
  • probeRadius (float) – The radius of the probe, in Angstrom.
  • numSpherePoints (int) – The number of points representing the surface of each atom, higher values lead to more accuracy.
  • mode (str) – In mode == ‘atom’, the extracted areas are resolved per-atom. In mode == ‘residue’, this is consolidated down to the per-residue SASA by summing over the atoms in each residue.
Returns:

metr

Return type:

MetricSasa 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