naccess - Calculate accessible area of a molecule

CalculateSurfaceArea(entity, radius=1.4, include_hydrogens=False, include_hetatm=False, include_water=False, selection='', naccess_exe=None, naccess_root=None, keep_files=False, asa_abs='asaAbs', asa_rel='asaRel', asa_atom='asaAtom', scratch_dir=None, max_number_of_atoms=50000)

Calculates analytical the solvent accessible surface area by using the external naccess program

This method calculates the molecular surface areas by invoking the external program naccess. First, it is checked if the naccess executable is present, then, the necessary files are prepared in a temporary directory and naccess is executed. The last step is to remove the temporary directory.

Parameters:

  • entity – OST entity to calculate surface

  • radius – Surface probe radius

  • include_hydrogens – Calculate surface including hydrogens

  • include_hetatm – Calculate surface including hetatms

  • include_water – Calculate surface including water

  • selection – Calculate surface for subset of entity

  • naccess_exe – naccess executable (full path to executable)

  • naccess_root – Path to folder containing “accall” binary and files “vdw.radii” and “standard.data”. This is the fastest way to call naccess!

  • keep_files – If True, do not delete temporary files

  • asa_abs – Attaches per residue absolute SASA to specified FloatProp on residue level

  • asa_rel – Attaches per residue relative SASA to specified FloatProp on residue level

  • asa_atom – Attaches per atom SASA to specified FloatProp at atom level

  • scratch_dir – Scratch directory. A subfolder for temporary files is created in there. If not specified, a default directory is used (see tempfile.mkdtemp()).

  • max_number_of_atoms – Max Number of atoms in the entity (i.e. is limited in the default NACCESS version to 50 000)

Returns:

absolute SASA calculated using asa_atom