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OpenStructure
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Inherited by _QSScoreGreedySearcher.
Public Member Functions | |
| def | __init__ (self, target, chem_groups, model, alns, contact_d=12.0) |
| def | qsent1 (self) |
| def | chem_groups (self) |
| def | qsent2 (self) |
| def | alns (self) |
| def | Score (self, mapping, check=True) |
| def | ScoreInterface (self, trg_ch1, trg_ch2, mdl_ch1, mdl_ch2) |
| def | FromFlatMapping (self, flat_mapping) |
Static Public Member Functions | |
| def | FromMappingResult (mapping_result) |
Helper object to compute QS-score
Tightly integrated into the mechanisms from the chain_mapping module.
The prefered way to derive an object of type :class:`QSScorer` is through
the static constructor: :func:`~FromMappingResult`. Example score
computation including mapping:
::
from ost.mol.alg.qsscore import QSScorer
from ost.mol.alg.chain_mapping import ChainMapper
ent_1 = io.LoadPDB("path_to_assembly_1.pdb")
ent_2 = io.LoadPDB("path_to_assembly_2.pdb")
chain_mapper = ChainMapper(ent_1)
mapping_result = chain_mapper.GetlDDTMapping(ent_2)
qs_scorer = QSScorer.FromMappingResult(mapping_result)
score_result = qs_scorer.Score(mapping_result.mapping)
print("score:", score_result.QS_global)
QS-score computation in :func:`QSScorer.Score` implements caching.
Repeated computations with alternative chain mappings thus become faster.
:param target: Structure designated as "target". Can be fetched from
:class:`ost.mol.alg.chain_mapping.MappingResult`
:type target: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:param chem_groups: Groups of chemically equivalent chains in *target*.
Can be fetched from
:class:`ost.mol.alg.chain_mapping.MappingResult`
:type chem_groups: :class:`list` of :class:`list` of :class:`str`
:param model: Structure designated as "model". Can be fetched from
:class:`ost.mol.alg.chain_mapping.MappingResult`
:type model: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:param alns: Each alignment is accessible with ``alns[(t_chain,m_chain)]``.
First sequence is the sequence of the respective chain in
:attr:`~qsent1`, second sequence the one from :attr:`~qsent2`.
Can be fetched from
:class:`ost.mol.alg.chain_mapping.MappingResult`
:type alns: :class:`dict` with key: :class:`tuple` of :class:`str`, value:
:class:`ost.seq.AlignmentHandle`
Definition at line 281 of file qsscore.py.
| def __init__ | ( | self, | |
| target, | |||
| chem_groups, | |||
| model, | |||
| alns, | |||
contact_d = 12.0 |
|||
| ) |
Definition at line 324 of file qsscore.py.
| def alns | ( | self | ) |
Alignments between chains in :attr:`~qsent1` and :attr:`~qsent2`
Provided at object construction. Each alignment is accessible with
``alns[(t_chain,m_chain)]``. First sequence is the sequence of the
respective chain in :attr:`~qsent1`, second sequence the one from
:attr:`~qsent2`.
:type: :class:`dict` with key: :class:`tuple` of :class:`str`, value:
:class:`ost.seq.AlignmentHandle`
Definition at line 400 of file qsscore.py.
| def chem_groups | ( | self | ) |
Groups of chemically equivalent chains in *target* Provided at object construction :type: :class:`list` of :class:`list` of :class:`str`
Definition at line 382 of file qsscore.py.
| def FromFlatMapping | ( | self, | |
| flat_mapping | |||
| ) |
Same as :func:`Score` but with flat mapping
:param flat_mapping: Dictionary with target chain names as keys and
the mapped model chain names as value
:type flat_mapping: :class:`dict` with :class:`str` as key and value
:returns: Result object of type :class:`QSScorerResult`
Definition at line 485 of file qsscore.py.
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static |
The preferred way to get a :class:`QSScorer` Static constructor that derives an object of type :class:`QSScorer` using a :class:`ost.mol.alg.chain_mapping.MappingResult` :param mapping_result: Data source :type mapping_result: :class:`ost.mol.alg.chain_mapping.MappingResult`
Definition at line 360 of file qsscore.py.
| def qsent1 | ( | self | ) |
Represents *target* :type: :class:`QSEntity`
Definition at line 374 of file qsscore.py.
| def qsent2 | ( | self | ) |
Represents *model* :type: :class:`QSEntity`
Definition at line 392 of file qsscore.py.
| def Score | ( | self, | |
| mapping, | |||
check = True |
|||
| ) |
Computes QS-score given chain mapping
Again, the preferred way is to get *mapping* is from an object
of type :class:`ost.mol.alg.chain_mapping.MappingResult`.
:param mapping: see
:attr:`ost.mol.alg.chain_mapping.MappingResult.mapping`
:type mapping: :class:`list` of :class:`list` of :class:`str`
:param check: Perform input checks, can be disabled for speed purposes
if you know what you're doing.
:type check: :class:`bool`
:returns: Result object of type :class:`QSScorerResult`
Definition at line 413 of file qsscore.py.
| def ScoreInterface | ( | self, | |
| trg_ch1, | |||
| trg_ch2, | |||
| mdl_ch1, | |||
| mdl_ch2 | |||
| ) |
Computes QS-score only considering one interface
This only works for interfaces that are computed in :func:`Score`, i.e.
interfaces for which the alignments are set up correctly.
:param trg_ch1: Name of first interface chain in target
:type trg_ch1: :class:`str`
:param trg_ch2: Name of second interface chain in target
:type trg_ch2: :class:`str`
:param mdl_ch1: Name of first interface chain in model
:type mdl_ch1: :class:`str`
:param mdl_ch2: Name of second interface chain in model
:type mdl_ch2: :class:`str`
:returns: Result object of type :class:`QSScorerResult`
:raises: :class:`RuntimeError` if no aln for trg_ch1/mdl_ch1 or
trg_ch2/mdl_ch2 is available.
Definition at line 450 of file qsscore.py.
1.9.1