OpenStructure
|
Inherits object.
Public Member Functions | |
def | __init__ |
def | GetPerResidueScores |
Data Fields | |
alignment | |
calpha_only | |
settings | |
lddt_scorer | |
reference_chain_name | |
model_chain_name | |
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.
def __init__ | ( | self, | |
alignment, | |||
calpha_only, | |||
settings | |||
) |
Definition at line 1336 of file qsscoring.py.
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.
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.