molecular_simulations.analysis.sasa module

class molecular_simulations.analysis.sasa.RelativeSASA(ag, probe_radius=1.4, n_points=256, **kwargs)

Bases: SASA

Computese Relative SASA for a specified atomgroup. Relative SASA is defined by the measured SASA divided by the maximum accessible surface area and for proteins we define this as within a tripeptide context so as to not overestimate SASA of the amide linkage and its neighbors.

Parameters:

  • ag (mda.AtomGroup) – AtomGroup for which to perform SASA.

  • probe_radius (float) – Defaults to 1.4Å. This is pretty standard and should not be altered in most cases.

  • n_points (int) – Defaults to 256. Number of points to place on each sphere, where a higher number is more costly but accurate.

class molecular_simulations.analysis.sasa.SASA(ag, probe_radius=1.4, n_points=256, **kwargs)

Bases: AnalysisBase

Computes solvent-accessible surface area using the Shrake-Rupley algorithm. Code is adapted from the biopython and mdtraj implementations as well as an unmerged PR from MDAnalysis. Implemented as an instance of AnalysisBase to support ease of deployment and baked-in parallelism.

Parameters:

  • ag (mda.AtomGroup) – AtomGroup for which to perform SASA.

  • probe_radius (float) – Defaults to 1.4Å. This is pretty standard and should not be altered in most cases.

  • n_points (int) – Defaults to 256. Number of points to place on each sphere, where a higher number is more costly but accurate.

get_sphere()

Returns a fibonacci unit sphere for a given number of points.

Returns:

Array of points in fibonacci sphere.

Return type:

(np.ndarray)

measure_sasa(ag)

Measures the SASA of input atomgroup.

Parameters:

ag (mda.AtomGroup) – MDAnalysis AtomGroup.

Returns:

SASA value.

Return type:

(float)