Solvent accessible surface area#

Solvent accessible surface area (SASA), atomic SASA and volumes under the SASA can be calculated.

Module#

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

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. 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 information, use help(SASA) or consult 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#

Solvent accessible surface area 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