ost.bindings.naccess Namespace Reference

Functions
def	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)

Detailed Description

Naccess module

Author: Florian Kiefer, Gerardo Tauriello (cleanup/speedup)

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

CalculateSurfaceArea()

def ost.bindings.naccess.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.


:param entity:              OST entity to calculate surface
:param radius:              Surface probe radius
:param include_hydrogens:   Calculate surface including hydrogens
:param include_hetatm:      Calculate surface including hetatms
:param include_water:       Calculate surface including water
:param selection:           Calculate surface for subset of entity
:param naccess_exe:         naccess executable (full path to executable)
:param naccess_root:        Path to folder containing "accall" binary and
                            files "vdw.radii" and "standard.data". This is the
                            fastest way to call naccess!
:param keep_files:          If True, do not delete temporary files
:param asa_abs:             Attaches per residue absolute SASA to specified
                            FloatProp on residue level
:param asa_rel:             Attaches per residue relative SASA to specified
                            FloatProp on residue level
:param asa_atom:            Attaches per atom SASA to specified FloatProp at
                            atom level
:param scratch_dir:         Scratch directory. A subfolder for temporary files
                            is created in there. If not specified, a default
                            directory is used (see :func:`tempfile.mkdtemp`).
:param 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

Definition at line 230 of file naccess.py.