ost.bindings.msms Namespace Reference

Data Structures
class	MsmsProcessError
	custom exception that substitutes CalledProcessError More...

Functions
def	GetVersion
def	CalculateSurfaceArea
def	CalculateSurface

---

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

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
	)

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.

Parameters:

entity	OST entity to calculate surface
density	Surface point density
radius	Surface probe radius
all_surf	Calculate surface for all cavities (returns multiple surfaces as a list)
no_hydrogens	Calculate surface only for hevy atoms
selection	Calculate surface for subset of entity
msms_exe	msms executable (full path to executable)
msms_env	msms environment variable
keep_files	Do not delete temporary files

Returns:

list of OST SurfaceHandle objects

Definition at line 252 of file msms.py.

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.

Parameters:

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

Returns:

Touplet of lists for (SES, SAS)

Definition at line 169 of file msms.py.

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

Definition at line 41 of file msms.py.