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| | _SetupFiles (model, reference, chain_mapping) |
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| | _CleanupFiles (dir_name) |
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| | _ParseCADGlobal (lines) |
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| | _ParseCADLocal (lines) |
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| | _ParseVoronotaGlobal (lines) |
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| | _ParseVoronotaLocal (lines) |
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| | _RunCAD (tmp_dir, mode, cad_bin_path, old_regime) |
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| | _HasInsertionCodes (model, reference) |
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| | _MapLabels (model, cad_results, label, chain_mapping) |
| |
| | CADScore (model, reference, mode="voronota", label="localcad", old_regime=False, cad_bin_path=None, chain_mapping=None) |
| |
Wrapper for the CAD score.
References:
Olechnovic K, Kulberkyte E, Venclovas C., CAD-score: A new contact area
difference-based function for evaluation of protein structural models
Proteins. 2012 Aug 30. [Epub ahead of print]
Authors: Valerio Mariani, Alessandro Barbato
| CADScore |
( |
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model, |
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reference, |
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mode = "voronota", |
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label = "localcad", |
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old_regime = False, |
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cad_bin_path = None, |
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chain_mapping = None |
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) |
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Calculates global and local atom-atom (AA) CAD Scores.
You can either access the original implementation available from
https://bitbucket.org/kliment/cadscore/downloads/
or the new implementation which is part of the Voronota package
available from https://bitbucket.org/kliment/voronota/downloads/.
The scores of the two implementations differ but strongly correlate
as the contacts between atoms are estimated differently. When using
the "voronota" *mode* you can minimize those discrepancies by
setting the *old_regime* flag to True.
Furthermore, the "voronota" *mode* generates per-residue scores that
are inverted when compared to the classical implementation
(0.0: bad, 1.0 good).
:param model: The model structure.
:type model: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
:param reference: The reference structure
:type reference: :class:`~ost.mol.EntityView` or
:class:`~ost.mol.EntityHandle`
:param mode: What CAD score implementation to use, must be one in
["classic", "voronota"]
:param label: Local CAD scores will be mapped on residues of model as
float property with this name
:type label: :class:`str`
:param old_regime: Only has an effect if *mode* is "voronota". If set to true,
the discrepancies between the two modes is minimized but
the behaviour of inverted scores persists.
:type old_regime: :class:`bool`
:param cad_bin_path: Path to search for the required executables
(["CADscore_calc.bash",
"CADscore_read_global_scores.bash",
"CADscore_read_local_scores.bash"] for "classic" *mode*
or ["voronota-cadscore"] for "voronota" *mode*). If not
set, the env path is searched.
:type cad_bin_path: :class:`str`
:param chain_mapping: Provide custom chain mapping in case of oligomers
(only supported for "voronota" *mode*). Provided as
:class:`dict` with model chain name as key and target
chain name as value. If set, scoring happens on a
substructure of model that is stripped to chains with
valid mapping.
:type chain_mapping: :class:`dict`
:returns: The result of the CAD score calculation
:rtype: :class:`CADResult`
:raises: :class:`~ost.settings.FileNotFound` if any of the CAD score
executables could not be located.
:raises: :class:`RuntimeError` if the calculation failed
Definition at line 287 of file cadscore.py.
