Inherited by _lDDTGreedySearcher.

Public Member Functions
def	__init__ (self, target, chem_groups, model, alns, dist_thresh=15.0, dist_diff_thresholds=[0.5, 1.0, 2.0, 4.0])

def	trg (self)

def	mdl (self)

def	alns (self)

def	chem_groups (self)

def	Score (self, mapping, check=True)

def	FromFlatMapping (self, flat_mapping)

Static Public Member Functions
def	FromMappingResult (mapping_result, dist_thresh=15.0, dist_diff_thresholds=[0.5, 1.0, 2.0, 4.0])

Detailed Description

 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.

Constructor & Destructor Documentation

◆ init()

def __init__	(	self,
		target,
		chem_groups,
		model,
		alns,
		dist_thresh = `15.0`,
		dist_diff_thresholds = `[0.5, 1.0, 2.0, 4.0]`
	)

Definition at line 323 of file bb_lddt.py.

Member Function Documentation

◆ alns()

def 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()

def 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()

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: :class:`float` representing lDDT

Definition at line 457 of file bb_lddt.py.

◆ FromMappingResult()

def FromMappingResult	(	mapping_result,
		dist_thresh = `15.0`,
		dist_diff_thresholds = `[0.5, 1.0, 2.0, 4.0]`
	)

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()

def mdl ( self )

 The :class:`BBlDDTEntity` representing model

:type: :class:`BBlDDTEntity`

Definition at line 390 of file bb_lddt.py.

◆ Score()

def Score	(	self,
		mapping,
		check = `True`
	)

 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()

def trg ( self )

 The :class:`BBlDDTEntity` representing target

:type: :class:`BBlDDTEntity`

Definition at line 382 of file bb_lddt.py.

The documentation for this class was generated from the following file:

build-dev-doc/stage/lib64/python3.9/site-packages/ost/mol/alg/bb_lddt.py

Public Member Functions

Static Public Member Functions