ost.bindings.msms Namespace Reference

Data Structures
class	MsmsProcessError

Functions
def	GetVersion (msms_exe=None, msms_env=None)
def	CalculateSurfaceArea (entity, density=1.0, radius=1.5, all_surf=False, no_hydrogens=False, no_hetatoms=False, no_waters=False, selection='', msms_exe=None, msms_env=None, keep_files=False, attach_asa=None, attach_esa=None)
def	CalculateSurfaceVolume (entity, density=1.0, radius=1.5, all_surf=False, no_hydrogens=False, no_hetatoms=False, no_waters=False, selection='', msms_exe=None, msms_env=None, keep_files=False, attach_asa=None, attach_esa=None)
def	CalculateSurface (entity, density=1.0, radius=1.5, all_surf=False, no_hydrogens=False, no_hetatoms=False, no_waters=False, selection='', msms_exe=None, msms_env=None, keep_files=False, attach_asa=None, attach_esa=None)

Detailed Description

MSMS module

Author: Tobias Schmidt

This module is for calculating MSMS surfaces as well as surface areas
(SESA, SASA) from OpenStructure using the external program MSMS.

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

Requirement:
 - MSMS installed

Function Documentation

CalculateSurface()

def ost.bindings.msms.CalculateSurface	(		entity,
			density = 1.0,
			radius = 1.5,
			all_surf = False,
			no_hydrogens = False,
			no_hetatoms = False,
			no_waters = False,
			selection = '',
			msms_exe = None,
			msms_env = None,
			keep_files = False,
			attach_asa = None,
			attach_esa = None
	)

Calculates molecular surface by using the external MSMS program

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


:param entity:        Entity for which the surface is to be calculated
:param density:       Surface point density
:param radius:        Surface probe radius
:param all_surf:      Calculate surface for all cavities (returns multiple
                      surfaces as a list)
:param no_hydrogens:  Calculate surface only for heavy atoms
:param selection:     Calculate surface for subset of entity
:param msms_exe:      msms executable (full path to executable)
:param msms_env:      msms environment variable
:param keep_files:    Do not delete temporary files
:param attach_asa:    Attaches per atom SASA to specified FloatProp at atom level
:param attach_esa:    Attaches per atom SESA to specified FloatProp at atom level
:returns:             list of :class:`~ost.mol.SurfaceHandle` objects

Definition at line 332 of file msms.py.

CalculateSurfaceArea()

def ost.bindings.msms.CalculateSurfaceArea	(		entity,
			density = 1.0,
			radius = 1.5,
			all_surf = False,
			no_hydrogens = False,
			no_hetatoms = False,
			no_waters = False,
			selection = '',
			msms_exe = None,
			msms_env = None,
			keep_files = False,
			attach_asa = None,
			attach_esa = None
	)

Calculates analytical solvent excluded and solvent accessible surface
area by using the external MSMS program.

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


:param entity:        OST entity to calculate surface
:param density:       Surface point density
:param radius:       Surface probe radius
:param all_surf:      Calculate surface area for all cavities (returns multiple
    surfaces areas as a list)
:param no_hydrogens:  Calculate surface only for hevy atoms
:param selection:     Calculate surface for subset of entity
:param msms_exe:      msms executable (full path to executable)
:param msms_env:      msms environment variable
:param keep_files:    Do not delete temporary files
:param attach_asa:    Attaches per atom SASA to specified FloatProp at atom level
:param attach_esa:    Attaches per atom SESA to specified FloatProp at atom level
:returns:             Tuple of lists for (SES, SAS)

Definition at line 164 of file msms.py.

CalculateSurfaceVolume()

def ost.bindings.msms.CalculateSurfaceVolume	(		entity,
			density = 1.0,
			radius = 1.5,
			all_surf = False,
			no_hydrogens = False,
			no_hetatoms = False,
			no_waters = False,
			selection = '',
			msms_exe = None,
			msms_env = None,
			keep_files = False,
			attach_asa = None,
			attach_esa = None
	)

Calculates the volume of the solvent excluded surface by using the external MSMS program.

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


:param entity:        OST entity to calculate surface
:param density:       Surface point density
:param radius:       Surface probe radius
:param all_surf:      Calculate surface area for all cavities (returns multiple
    surfaces areas as a list)
:param no_hydrogens:  Calculate surface only for hevy atoms
:param selection:     Calculate surface for subset of entity
:param msms_exe:      msms executable (full path to executable)
:param msms_env:      msms environment variable
:param keep_files:    Do not delete temporary files
:param attach_asa:    Attaches per atom SASA to specified FloatProp at atom level
:param attach_esa:    Attaches per atom SESA to specified FloatProp at atom level
:returns:             Tuple of lists for (SES, SAS)

Definition at line 252 of file msms.py.

GetVersion()

def ost.bindings.msms.GetVersion	(		msms_exe = None,
			msms_env = None
	)

Get version of MSMS executable

Definition at line 40 of file msms.py.