lddt_deprecated.rst

orphan:

lDDT (deprecated)

Object to compute lDDT scores using :func:`LocalDistDiffTest` as in Mariani et al..

Example usage.

#! /bin/env python
"""Run lDDT from within script."""
from ost.io import LoadPDB
from ost.mol.alg import (CleanlDDTReferences,
                         lDDTSettings, lDDTScorer)

ent_full = LoadPDB('3ia3', remote=True)
model_view = ent_full.Select('cname=A')
references = [ent_full.Select('cname=C')]

#
# Initialize settings with default parameters and print them
settings = lDDTSettings()
settings.PrintParameters()

# Clean up references
CleanlDDTReferences(references)
#
# Calculate lDDT
scorer = lDDTScorer(references=references, model=model_view, settings=settings)
print("Global score:", scorer.global_score)
scorer.PrintPerResidueStats()

param references:	Sets :attr:`references`
param model:	Sets :attr:`model`
param settings:	Sets :attr:`settings`

Object containing enough information to uniquely identify an atom in a structure.

param chain:	A string containing the name of the chain to which the atom belongs
param residue_number:	The number of the residue to which the atom belongs
type residue_number:	:class:`~ost.mol.ResNum`
param residue_name:	A string containing the name of the residue to which the atom belongs
param atom_name:	A string containing the name of the atom

Dictionary-like object containing the list of interatomic distances that originate from a single residue to be checked during a run of the Local Distance Difference Test algorithm (key = pair of :class:`UniqueAtomIdentifier`, value = pair of floats representing min and max distance observed in the structures used to build the map).

Dictionary-like object containing all the :class:`~ost.mol.alg.ResidueRDMap` objects related to all the residues (key = :class:`~ost.mol.ResNum`, value = :class:`ResidueRDMap`).