ost.bindings.tmtools Namespace Reference

Data Structures
class	TMScoreResult

Functions
	_SetupFiles (models, custom_chain_mapping=None)
	_CleanupFiles (dir_name)
	_ParseTmAlign (lines, lines_matrix)
	_ParseUSAlign (lines, lines_matrix)
	_RunTmAlign (tmalign, tmp_dir)
	_RunUSAlign (usalign, tmp_dir)
	_ParseTmScore (lines)
	_RunTmScore (tmscore, tmp_dir)
	TMAlign (model1, model2, tmalign=None)
	TMScore (model1, model2, tmscore=None)
	USAlign (model1, model2, usalign=None, custom_chain_mapping=None)

Detailed Description

Wrappers for the tmalign and tmscore utilities.

References:

tmscore: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 
tmalign: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9 


Authors: Pascal Benkert, Marco Biasini

Function Documentation

_CleanupFiles()

_CleanupFiles (   dir_name )

protected

Definition at line 54 of file tmtools.py.

_ParseTmAlign()

_ParseTmAlign (   lines,   lines_matrix  )

protected

Definition at line 58 of file tmtools.py.

_ParseTmScore()

_ParseTmScore (   lines )

protected

Definition at line 243 of file tmtools.py.

_ParseUSAlign()

_ParseUSAlign (   lines,   lines_matrix  )

protected

Definition at line 79 of file tmtools.py.

_RunTmAlign()

_RunTmAlign (   tmalign,   tmp_dir  )

protected

Definition at line 163 of file tmtools.py.

_RunTmScore()

_RunTmScore (   tmscore,   tmp_dir  )

protected

Definition at line 260 of file tmtools.py.

_RunUSAlign()

_RunUSAlign (   usalign,   tmp_dir  )

protected

Definition at line 183 of file tmtools.py.

_SetupFiles()

_SetupFiles (   models,   custom_chain_mapping = None  )

protected

Definition at line 35 of file tmtools.py.

TMAlign()

TMAlign	(		model1,
			model2,
			tmalign = None
	)

Performs a sequence independent superposition of model1 onto model2, the 
reference.


: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 tmalign: If not None, the path to the tmalign executable.
:returns: The result of the tmscore superposition
:rtype: :class:`ost.bindings.TMAlignResult`

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

Definition at line 280 of file tmtools.py.

TMScore()

TMScore	(		model1,
			model2,
			tmscore = None
	)

Performs a sequence dependent superposition of model1 onto model2, 
the reference.

: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 tmscore: If not None, the path to the tmscore executable.
:returns: The result of the tmscore superposition
:rtype: :class:`TMScoreResult`

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

Definition at line 304 of file tmtools.py.

USAlign()

USAlign	(		model1,
			model2,
			usalign = None,
			custom_chain_mapping = None
	)

Performs a sequence independent superposition of model1 onto model2, the 
reference. Can deal with multimeric complexes and RNA.

Creates temporary model files on disk and runs USalign with:
``USalign model1.pdb model2.pdb -mm 1 -ter 0 -m rotmat.txt``

: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 usalign: If not None, the path to the USalign executable. Searches
                for executable with name ``USalign`` in PATH if not given.
:param custom_chain_mapping: Custom chain mapping that is passed as -chainmap
                             to USalign executable. Raises an error is this
                             is not supported by the USalign executable you're
                             using (introduced in July 2023).
                             It's a dict with reference chain names as key
                             (model2) and model chain names as values
                             (model1).
:type custom_chain_mapping: :class:`dict`
:returns: The result of the superposition
:rtype: :class:`ost.bindings.MMAlignResult`

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

Definition at line 328 of file tmtools.py.