ost.bindings.ialign Namespace Reference

Data Structures
class	iAlignResult

Functions
	_SetupFiles (models)
	_CleanupFiles (dir_name)
	_ParseiAlign (lines)
	_RuniAlign (ialign, tmp_dir, options={})
	iAlign (model1, model2, ialign=None)

Detailed Description

Wrappers for the iAlign utility.

References:

Mu Gao and Jeffrey Skolnick, 2010. iAlign: a method for the structural comparison
of protein-protein interfaces. Bioinformatics, 26(18):2259-65.
Mu Gao and Jeffrey Skolnick, 2010. Structural space of protein-protein interfaces
is degenerate, close to complete, and highly connected. PNAS 107(52):22517-22.

Authors: Pascal Benkert, Marco Biasini, Martino Bertoni

Function Documentation

_CleanupFiles()

_CleanupFiles (   dir_name )

protected

Definition at line 51 of file ialign.py.

_ParseiAlign()

_ParseiAlign (   lines )

protected

Definition at line 100 of file ialign.py.

_RuniAlign()

_RuniAlign (   ialign,   tmp_dir,   options = {}  )

protected

Definition at line 122 of file ialign.py.

_SetupFiles()

_SetupFiles (   models )

protected

Definition at line 35 of file ialign.py.

iAlign()

iAlign	(		model1,
			model2,
			ialign = None
	)

Compare protein-protein interfaces of the structures of two pairs of
protein complexes and suporpose them.


:param model1: The model structure. If the superposition is successful, will 
               be superposed onto the reference structure
:type model1: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param model2: The reference structure
:type model2: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param ialign: If not None, the path to the ialign executable.
:returns: The result of the tmscore superposition
:rtype: :class:`iAlignResult`

:raises: :class:`~ost.settings.FileNotFound` if tmalign could not be located.
:raises: :class:`RuntimeError` if the superposition failed

Definition at line 156 of file ialign.py.