morfeus.sasa module#

Solvent accessible surface area code.

class morfeus.sasa.SASA(elements, coordinates, radii=None, radii_type='crc', probe_radius=1.4, density=0.01)[source]#

Bases: object

Performs and stores results of solvent accessible surface area calculations.

Parameters:

  • elements (Iterable[int] | Iterable[str]) – Elements as atomic symbols or numbers

  • coordinates (ArrayLike2D) – Coordinates (Å)

  • radii (ArrayLike1D | None) – VdW radii (Å)

  • radii_type (str) – Choice of vdW radii: ‘bondi’ or ‘crc’ (default)

  • probe_radius (float) – Radius of probe atom (Å)

  • density (float) – Area per point (Ų) on the vdW surface

area#

Area of the solvent accessible surface.

Type:

float

atom_areas#

Atom areas (starting from 1)

Type:

dict[int, float]

atom_volumes#

Atom volumes (starting from 1)

Type:

dict[int, float]

volume#

Volume of the solvent accessible surface

Type:

float

print_report(verbose=False)[source]#

Print report of results.

Parameters:

verbose (bool) – Whether to print atom areas

Return type:

None

morfeus.sasa.cli(file)[source]#

CLI for solvent accessible surface area.

Parameters:

file (str) – Geometry file

Returns:

Partially instantiated class

Return type:

Any