molecular_simulations.analysis.sasa module¶

Solvent-Accessible Surface Area (SASA) analysis module.

This module computes SASA using the Shrake-Rupley algorithm, implemented as MDAnalysis AnalysisBase classes for ease of use and built-in parallelism. Adapted from BioPython and MDTraj implementations.

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

Bases: AnalysisBase

Compute solvent-accessible surface area using Shrake-Rupley algorithm.

Implements SASA calculation as an MDAnalysis AnalysisBase instance, supporting ease of deployment and built-in parallelism. Code is adapted from BioPython and MDTraj implementations as well as an unmerged PR from MDAnalysis.

ag¶: The AtomGroup being analyzed.

probe_radius¶: Probe radius for SASA calculation.

n_points¶: Number of points on each atomic sphere.

radii¶: Array of atomic radii (VDW + probe).

max_radii¶: Maximum pairwise radius sum.

results.sasa¶: Per-residue SASA values after run().

Parameters:

ag (AtomGroup) – AtomGroup for which to compute SASA.
probe_radius (float) – Probe radius in Angstroms. Defaults to 1.4 Å (standard water probe).
n_points (int) – Number of points on each sphere. Higher values are more accurate but slower. Defaults to 256.
**kwargs – Additional arguments passed to AnalysisBase.

Raises:

TypeError – If ag is an UpdatingAtomGroup.
ValueError – If the Universe has no ‘elements’ property.

Example

>>> u = mda.Universe("system.prmtop", "traj.dcd")
>>> sasa = SASA(u.select_atoms("protein"))
>>> sasa.run()
>>> print(sasa.results.sasa)

Initialize the SASA analysis.

Parameters:

ag (AtomGroup) – AtomGroup to analyze.
probe_radius (float) – Probe radius in Angstroms.
n_points (int) – Number of sphere points.
**kwargs – Arguments for AnalysisBase.

__init__(ag, probe_radius=1.4, n_points=256, **kwargs)[source]¶

Initialize the SASA analysis.

Parameters:

ag (AtomGroup) – AtomGroup to analyze.
probe_radius (float) – Probe radius in Angstroms.
n_points (int) – Number of sphere points.
**kwargs – Arguments for AnalysisBase.

get_sphere()[source]¶

Generate a Fibonacci unit sphere.

Creates evenly distributed points on a unit sphere using the Fibonacci spiral method.

Return type:: ndarray
Returns:: Array of shape (n_points, 3) with unit sphere coordinates.

measure_sasa(ag)[source]¶

Measure SASA of an AtomGroup in the current frame.

Parameters:: ag (AtomGroup) – MDAnalysis AtomGroup to measure.
Return type:: ndarray
Returns:: Array of per-atom SASA values.

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

Bases: SASA

Compute relative SASA for an AtomGroup.

Relative SASA is defined as measured SASA divided by maximum accessible surface area. For proteins, this is computed in a tripeptide context to avoid overestimating SASA of the amide linkage and its neighbors.

results.sasa¶: Absolute SASA values.

results.relative_area¶: Relative SASA values (0-1 scale).

Parameters:

ag (AtomGroup) – AtomGroup for SASA calculation.
probe_radius (float) – Probe radius in Angstroms. Defaults to 1.4 Å.
n_points (int) – Number of sphere points. Defaults to 256.
**kwargs – Additional arguments for AnalysisBase.

Raises:

ValueError – If the Universe has no ‘bonds’ property.

Example

>>> u = mda.Universe("system.prmtop", "traj.dcd")
>>> rsasa = RelativeSASA(u.select_atoms("protein"))
>>> rsasa.run()
>>> print(rsasa.results.relative_area)

Initialize the RelativeSASA analysis.

Parameters:

ag (AtomGroup) – AtomGroup to analyze.
probe_radius (float) – Probe radius in Angstroms.
n_points (int) – Number of sphere points.
**kwargs – Arguments for AnalysisBase.

__init__(ag, probe_radius=1.4, n_points=256, **kwargs)[source]¶

Initialize the RelativeSASA analysis.

Parameters:

ag (AtomGroup) – AtomGroup to analyze.
probe_radius (float) – Probe radius in Angstroms.
n_points (int) – Number of sphere points.
**kwargs – Arguments for AnalysisBase.