dockq - Evaluate protein-protein interfaces

DockQ(dockq_exec, mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2)

Computes DockQ for specified interface

DockQ is available from https://github.com/bjornwallner/DockQ - For this binding to work, DockQ must be properly installed and its dependencies must be available (numpy, Biopython).

Parameters:

  • dockq_exec (str) – Path to DockQ.py script from DockQ repository

  • mdl (ost.mol.EntityView/ost.mol.EntityHandle) – Model structure

  • ref (ost.mol.EntityView/ost.mol.EntityHandle) – Reference structure, i.e. native structure

  • mdl_ch1 (str/list of str) – Specifies chain(s) in model constituting first part of interface

  • mdl_ch2 (str/list of str) – Specifies chain(s) in model constituting second part of interface

  • ref_ch1 (str/list of str) – ref equivalent of mdl_ch1

  • ref_ch2 (str/list of str) – ref equivalent of mdl_ch2

Returns:

Result object of type DockQResult

class DockQResult(Fnat, Fnonnat, native_contacts, model_contacts, iRMS, LRMS, DockQ)

DockQ result object

property Fnat

DockQ - Fnat output

Type:

float

property Fnonnat

DockQ - Fnonnat output

Type:

float

property native_contacts

DockQ - number native contacts

Type:

int

property model_contacts

DockQ - number model contacts

Type:

int

property iRMS

DockQ - iRMS output

Type:

float

property LRMS

DockQ - LMRS output

Type:

float

property DockQ

DockQ - DockQ output

Type:

float

JSONSummary()

Returns JSON serializable summary

static FromDockQOutput(output)

Static constructor from raw DockQ output

Parameters:

output (str) – Raw output from DockQ executable

Returns:

Object of type DockQResult