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Public Member Functions | Data Fields
MappedLDDTScorer Class Reference

Inherits object.

Public Member Functions

def __init__
 
def GetPerResidueScores
 

Data Fields

 alignment
 
 calpha_only
 
 settings
 
 lddt_scorer
 
 reference_chain_name
 
 model_chain_name
 

Detailed Description

A simple class to calculate a single-chain lDDT score on a given chain to
chain mapping as extracted from :class:`OligoLDDTScorer`.

:param alignment: Sets :attr:`alignment`
:param calpha_only: Sets :attr:`calpha_only`
:param settings: Sets :attr:`settings`

.. attribute:: alignment

  Alignment with two sequences named according to the mapped chains and with
  views attached to both sequences (e.g. one of the items of
  :attr:`QSscorer.alignments`).

  The first sequence is assumed to be the reference and the second one the
  model. Since the lDDT score is not symmetric (extra residues in model are
  ignored), the order is important.

  :type: :class:`~ost.seq.AlignmentHandle`

.. attribute:: calpha_only

  If True, restricts lDDT score to CA only.

  :type: :class:`bool`

.. attribute:: settings

  Settings to use for lDDT scoring.

  :type: :class:`~ost.mol.alg.lDDTSettings`

.. attribute:: lddt_scorer

  lDDT Scorer object for the given chains.

  :type: :class:`~ost.mol.alg.lDDTScorer`

.. attribute:: reference_chain_name

  Chain name of the reference.

  :type: :class:`str`

.. attribute:: model_chain_name

  Chain name of the model.

  :type: :class:`str`

Definition at line 1286 of file qsscoring.py.

Constructor & Destructor Documentation

def __init__ (   self,
  alignment,
  calpha_only,
  settings 
)

Definition at line 1336 of file qsscoring.py.

Member Function Documentation

def GetPerResidueScores (   self)
:return: Scores for each residue
:rtype:  :class:`list` of :class:`dict` with one item for each residue
     existing in model and reference:

     - "residue_number": Residue number in reference chain
     - "residue_name": Residue name in reference chain
     - "lddt": local lDDT
     - "conserved_contacts": number of conserved contacts
     - "total_contacts": total number of contacts

Definition at line 1349 of file qsscoring.py.

Field Documentation

alignment

Definition at line 1338 of file qsscoring.py.

calpha_only

Definition at line 1339 of file qsscoring.py.

lddt_scorer

Definition at line 1341 of file qsscoring.py.

model_chain_name

Definition at line 1343 of file qsscoring.py.

reference_chain_name

Definition at line 1342 of file qsscoring.py.

settings

Definition at line 1340 of file qsscoring.py.


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