ost.bindings.tmtools Namespace Reference

Data Structures
class	TMScoreResult

Functions
def	TMAlign (model1, model2, tmalign=None)
def	TMScore (model1, model2, tmscore=None)
def	USAlign (model1, model2, usalign=None, custom_chain_mapping=None)

Function Documentation

TMAlign()

def ost.bindings.tmtools.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()

def ost.bindings.tmtools.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()

def ost.bindings.tmtools.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.