Solvent accessible surface area¶

Solvent accessible surface area (SASA), atomic SASA, and total volume inside the SASA can be calculated.

Module¶

The SASA class calculates and stores the total and atomic SASA as well as the total volume of the SASA.

Example¶

>>> from morfeus import SASA, read_xyz
>>> elements, coordinates = read_xyz("n-heptane.xyz")
>>> sasa = SASA(elements, coordinates)
>>> print(sasa.atom_areas[1])
18.380429455791376
>>> print(sasa.area)
331.5607124071378
>>> print(sasa.volume)
475.5699458352845

The atom_areas dictionary contains the atomic SASAs indexed from 1. The type of radii can be changed with the keyword argument radii=<str> and custom radii can be supplied with radii=<list>. The probe radius is changed with probe_radius=<float>.

For more detailed information, use help(SASA) or see the API: SASA.

Command line script¶

The command-line script outputs total SASA and volume as well as SASA per atom.

Example¶

$ morfeus sasa PdPMe3.xyz - - print_report
Probe radius (Å): 1.4
Solvent accessible surface area (Å²): 288.3
Volume inside solvent accessible surface (Å³): 410.7
$ morfeus sasa PdPMe3.xyz - - print_report --verbose=True
Probe radius (Å): 1.4
Solvent accessible surface area (Å²): 288.3
Volume inside solvent accessible surface (Å³): 410.7
Symbol    Index     Area (Å²)
Pd        1         91.8
P         2         0.0
C         3         13.4
H         4         18.2
H         5         15.6
H         6         18.2
C         7         13.5
H         8         18.2
H         9         15.6
H         10        18.2
C         11        13.5
H         12        18.2
H         13        18.2
H         14        15.6

Background¶

The solvent accessible surface area (SASA) is a measure of how much of the area of a molecule is available to the solvent. The atomic SASA can be used as a measure of the steric availability of an atom. ᴍᴏʀғᴇᴜs uses a modified version of the method of Shrake and Rupley [1] where a constant surface density of points is used instead of a fixed number of points regardless of the atom area. The atomic SASA and volumes are computed as described by Eisenhaber et al. [2]. ᴍᴏʀғᴇᴜs is not optimized for larger molecules and other programs are recommended for, e.g., proteins.

References