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OpenStructure
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Inherited by _lDDTGreedySearcher.
Public Member Functions | |
| __init__ (self, target, chem_groups, model, alns, dist_thresh=15.0, dist_diff_thresholds=[0.5, 1.0, 2.0, 4.0]) | |
| trg (self) | |
| mdl (self) | |
| alns (self) | |
| chem_groups (self) | |
| Score (self, mapping, check=True) | |
| FromFlatMapping (self, flat_mapping) | |
Static Public Member Functions | |
| FromMappingResult (mapping_result, dist_thresh=15.0, dist_diff_thresholds=[0.5, 1.0, 2.0, 4.0]) | |
Data Fields | |
| chem_groups | |
Protected Member Functions | |
| _NSCConserved (self, trg_ch, mdl_ch) | |
| _NPairConserved (self, trg_int, mdl_int) | |
| _IndexMapping (self, ch1, ch2) | |
Protected Attributes | |
| _trg | |
| _chem_groups | |
| _mdl | |
| _alns | |
| _dist_diff_thresholds | |
| _dist_thresh | |
| _pairwise_cache | |
| _sc_cache | |
Helper object to compute Backbone only lDDT score
Tightly integrated into the mechanisms from the chain_mapping module.
The prefered way to derive an object of type :class:`BBlDDTScorer` is
through the static constructor: :func:`~FromMappingResult`.
lDDT computation in :func:`BBlDDTScorer.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`
:param dist_thresh: Max distance of a pairwise interaction in target
to be considered as contact in lDDT
:type dist_thresh: :class:`float`
:param dist_diff_thresholds: Distance difference thresholds for
lDDT computations
:type dist_diff_thresholds: :class:`list` of :class:`float`
Definition at line 289 of file bb_lddt.py.
| __init__ | ( | self, | |
| target, | |||
| chem_groups, | |||
| model, | |||
| alns, | |||
dist_thresh = 15.0, |
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dist_diff_thresholds = [0.5, 1.0, 2.0, 4.0] |
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| ) |
Reimplemented in _lDDTGreedySearcher.
Definition at line 323 of file bb_lddt.py.
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protected |
Fetches aln and returns indices of aligned residues returns 2 numpy arrays containing the indices of residues in ch1 and ch2 which are aligned
Definition at line 532 of file bb_lddt.py.
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Definition at line 504 of file bb_lddt.py.
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Definition at line 481 of file bb_lddt.py.
| alns | ( | self | ) |
Alignments between chains in :attr:`~trg` and :attr:`~mdl`
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:`~trg`, second sequence the one from
:attr:`~mdl`.
:type: :class:`dict` with key: :class:`tuple` of :class:`str`, value:
:class:`ost.seq.AlignmentHandle`
Definition at line 398 of file bb_lddt.py.
| chem_groups | ( | self | ) |
Groups of chemically equivalent chains in :attr:`~trg` Provided at object construction :type: :class:`list` of :class:`list` of :class:`str`
Definition at line 412 of file bb_lddt.py.
| 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: :class:`float` representing lDDT
Definition at line 457 of file bb_lddt.py.
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static |
The preferred way to get a :clas:`BBlDDTScorer` 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` :param dist_thresh: The lDDT distance threshold :type dist_thresh: :class:`float` :param dist_diff_thresholds: The lDDT distance difference thresholds :type dist_diff_thresholds: :class:`list` of :class:`float`
Definition at line 361 of file bb_lddt.py.
| mdl | ( | self | ) |
The :class:`BBlDDTEntity` representing model :type: :class:`BBlDDTEntity`
Definition at line 390 of file bb_lddt.py.
| Score | ( | self, | |
| mapping, | |||
check = True |
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| ) |
Computes Backbone lDDT 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: The score
Definition at line 421 of file bb_lddt.py.
| trg | ( | self | ) |
The :class:`BBlDDTEntity` representing target :type: :class:`BBlDDTEntity`
Definition at line 382 of file bb_lddt.py.
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Definition at line 341 of file bb_lddt.py.
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Definition at line 338 of file bb_lddt.py.
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Definition at line 342 of file bb_lddt.py.
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Definition at line 343 of file bb_lddt.py.
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Definition at line 339 of file bb_lddt.py.
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Definition at line 352 of file bb_lddt.py.
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Definition at line 358 of file bb_lddt.py.
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Definition at line 326 of file bb_lddt.py.
| chem_groups |
Definition at line 437 of file bb_lddt.py.
1.9.8