ost.mol.alg.dockq Namespace Reference

Functions
def	DockQ

Function Documentation

def ost.mol.alg.dockq.DockQ	(		mdl,
			ref,
			mdl_ch1,
			mdl_ch2,
			ref_ch1,
			ref_ch2,
			ch1_aln = None,
			ch2_aln = None
	)

Computes DockQ for specified interface

DockQ is described in: Sankar Basu and Bjoern Wallner (2016), "DockQ: A
Quality Measure for Protein-Protein Docking Models", PLOS one 

Residues are mapped based on residue numbers by default. If you provide
*ch1_aln* and *ch2_aln* you can enforce an arbitrary mapping.

:param mdl: Model structure
:type mdl: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:param ref: Reference structure, i.e. native structure
:type ref: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
:param mdl_ch1: Specifies chain in model constituting first part of
                interface
:type mdl_ch1: :class:`str`
:param mdl_ch2: Specifies chain in model constituting second part of
                interface
:type mdl_ch2: :class:`str`
:param ref_ch1: ref equivalent of mdl_ch1
:type ref_ch1: :class:`str`
:param ref_ch2: ref equivalent of mdl_ch2
:type ref_ch2: :class:`str`
:param ch1_aln: Alignment with two sequences to map *ref_ch1* and *mdl_ch1*.
                The first sequence must match the sequence in *ref_ch1* and
                the second to *mdl_ch1*.
:type ch1_aln: :class:`ost.seq.AlignmentHandle`
:param ch2_aln: Alignment with two sequences to map *ref_ch2* and *mdl_ch2*.
                The first sequence must match the sequence in *ref_ch2* and
                the second to *mdl_ch2*.
:type ch2_aln: :class:`ost.seq.AlignmentHandle`
:returns: :class:`dict` with keys nnat, nmdl, fnat, fnonnat, irmsd, lrmsd,
          DockQ which corresponds to the equivalent values in the original
          DockQ implementation.

Definition at line 266 of file dockq.py.