htmd.projections.metricsasa module

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

Bases: htmd.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
  • 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