CAPRI Evaluation module

Submodules

haddock.modules.analysis.caprieval.capri module

Module contents

Calculate CAPRI metrics for the input models.

By default the following metrics are calculated:

FNAT (fraction of native contacts), namely the fraction of
intermolecular contacts in the docked complex that are also present in the reference complex.
IRMSD (interface root mean square deviation), namely the RMSD
of the interface of the docked complex with respect to the reference complex.
LRMSD (ligand root mean square deviation), namely the RMSD of the
ligand of the docked complex with respect to the reference complex upon superposition of the receptor.
DOCKQ, a measure of the quality of the docked model obtained
by combining FNAT, IRMSD and LRMSD (see Basu and Wallner 2016, 11 (8), e0161879).
ILRMSD (interface ligand root mean square deviation), the RMSD of the
ligand of the docked complex with respect to the reference complex upon superposition of the interface of the receptor.

The following files are generated:

capri_ss.tsv: a table with the CAPRI metrics for each model.
capri_clt.tsv: a table with the CAPRI metrics for each cluster of models (if clustering information is available).

class haddock.modules.analysis.caprieval.HaddockModule(order: int, path: Path, *ignore: Any, init_params: str | Path = PosixPath('/home/runner/work/haddock3/haddock3/src/haddock/modules/analysis/caprieval/defaults.yaml'), **everything: Any)[source]

Bases: BaseHaddockModule

HADDOCK3 module to calculate the CAPRI metrics.

classmethod confirm_installation() → None[source]: Confirm if contact executable is compiled.

name: str = 'caprieval'

Default Parameters

Easy

alignment_method

default: ‘sequence’
type: string
title: Alignment method used to match the numbering.
choices: [‘structure’, ‘sequence’]
short description: Which alignment method should be used to match the numbering.
long description: Alignment method used to match the numbering. Sequence alignment is haddock3-friendly but might not produce best results for structures that are too different, for that use
group: analysis
explevel: easy

allatoms

default: False
type: boolean
title: Atoms to be considered during the analysis.
short description: Atoms to be considered during the analysis.
long description: Atoms to be considered during the analysis. If false (default), only backbone atoms will be considered, otherwise all the heavy-atoms.
group: analysis
explevel: easy

clt_threshold

default: 4
type: integer
title: Threshold (n) used for the average evaluation in the cluster-based output
min: 1
max: 1000
short description: Threshold (n) used for the average evaluation in the cluster-based output.
long description: Threshold (n) used for the average evaluation in the cluster-based output.
group: analysis
explevel: easy

dockq

default: True
type: boolean
title: Calculate DockQ
short description: Evaluate DockQ.
long description: Evaluate DockQ. A single continuous quality measure for protein docked models based on the CAPRI criteria, a combination of i-RMSD, l-RMSD and FNAT value. For details check the DockQ publication DOI:10.1371/journal.pone.0161879
group: analysis
explevel: easy

fnat

default: True
type: boolean
title: Calculate FNAT
short description: Performs FNAT calculations.
long description: Calculates the Fraction of Native Contacts. This evaluates how many contacts observed in the reference are present in the model. The distance cutoff used to define intermolecular contacts is defined by the fnat_cutoff parameter.
group: analysis
explevel: easy

fnat_cutoff

default: 5.0
type: float
title: Distance cutoff (Å) used to define interface contacts.
min: 3.0
max: 20.0
short description: Distance cutoff (Å) used to define interface contacts between two interacting molecules.
long description: Distance cutoff (Å) used to define interface contacts between two interacting molecules.
group: analysis
explevel: easy

ilrmsd

default: True
type: boolean
title: Calculate I-L-RMSD
short description: Performs Interface Ligand RMSD calculations.
long description: Calculates the Interface Ligand Root Mean Square Deviation. This calculation is done by superimposing the model and the target on the interface backbone atoms of the receptor (defined by the receptor_chain parameter) and calculating the RMSD on all heavy atoms of the ligand (defined by the ligand_chains parameter).
group: analysis
explevel: easy

irmsd

default: True
type: boolean
title: Calculate I-RMSD
short description: Performs Interface RMSD calculations.
long description: Calculates the Interface Root Mean Square Deviation. This calculate the RMSD of interface backbone atoms after fitting on the interface backbone atoms. The interface is idenfied based on intermolecular contacts shorter than the defined irmsd_cutoff.
group: analysis
explevel: easy

irmsd_cutoff

default: 10.0
type: float
title: Distance cutoff (Å) used to define interface residues.
min: 3.0
max: 20.0
short description: Distance cutoff (Å) used to define interface residues based on intermolecular contacts.
long description: Distance cutoff (Å) used to define interface residues based on intermolecular contacts.
group: analysis
explevel: easy

ligand_chains

default: [‘B’]
type: list
title: Ligand ChainIDs
short description: Ligand ChainIDs to be considered for the RMSD calculations.
long description: Ligand ChainIDs to be considered for the RMSD calculations. This determines which chains will be treated as the ligand for the L-RMSD and for I-L-RMSD.
group: analysis
explevel: easy

lovoalign_exec

default: ‘’
type: string
title: Location (path) of the LovoAlign executable
short description: Location (path) of the LovoAlign executable.
long description: Location (path) of the LovoAlign executable.
group: analysis
explevel: easy

lrmsd

default: True
type: boolean
title: Calculate L-RMSD
short description: Performs Ligand RMSD calculations.
long description: Calculates the Ligand Root Mean Square Deviation. This calculation is done by superimposing the receptors (defined by the receptor_chain parameter) and then evaluating the RMSD on the ligands (defined by the ligand_chains parameter). Superposition and RMSD calculations are done on backbone heavy atoms.
group: analysis
explevel: easy

receptor_chain

default: ‘A’
type: string
title: Receptor ChainID
short description: Receptor ChainID to be considered for the RMSD calculations.
long description: Receptor ChainID to be considered for the RMSD calculations. This determines which chain will be treated as the receptor for the L-RMSD and for I-L-RMSD.
group: analysis
explevel: easy

reference_fname

default: ‘’
type: file
title: Reference structure
short description: Structure to be used when calculating the CAPRI metrics.
long description: Reference tructure to be used when calculating the CAPRI metrics. If none is defined then the lowest scoring model is selected by default.
group: analysis
explevel: easy

sort_ascending

default: True
type: boolean
title: Sort in ascending order
short description: Sort in ascending order.
long description: Sort in ascending order.
group: analysis
explevel: easy

sortby

default: ‘score’
type: string
title: Sort the structures/clusters in the output file by this value
choices: [‘score’, ‘irmsd’, ‘lrmsd’, ‘ilrmsd’, ‘fnat’, ‘dockq’]
short description: Which value should be used to sort the output.
long description: Which value should be used to sort the output, the output table will be sorted accordingly.
group: analysis
explevel: easy