ost.bindings.naccess Namespace Reference

Functions
def	CalculateSurfaceArea

---

Detailed Description

Naccess module

Author: Florian Kiefer

This module is for calculating surface areas
from OpenStructure using the external program naccess

How To Use This Module:
 1. Import it (e.g. as "from ost.bindings import naccess")
 2. Use it (e.g. as "sasa = naccess.CalculateSurfaceArea(entity)")

Requirement:
 - naccess installed

---

Function Documentation

def ost.bindings.naccess.CalculateSurfaceArea	(		entity,
			radius = 1.4,
			include_hydrogens = False,
			include_hetatm = False,
			include_water = False,
			selection = "",
			naccess_exe = 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 msms executable (full path to executable)
keep_files	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	Directory for temporary files (NACCESS is sensitive to "." in directory names
max_number_of_atoms	Max Number of atoms in the entity (i.e. is limited in the default NACCESS version to 50 000)

Definition at line 200 of file naccess.py.