haddock.modules.analysis.caprifilter package

Submodules

Module contents

Filter models by any combination of CAPRI metrics computed against a reference structure.

The user specifies a list of metrics via filter_by (e.g. ['irmsd', 'fnat']). For each metric, a per-metric cutoff and filter direction are set independently:

  • {metric}_filter_cutoff: the numerical threshold.

  • {metric}_filter_out: above removes models where value > cutoff (keep ≤); below removes models where value < cutoff (keep ≥).

All active filters are applied simultaneously (AND logic), a model must pass every filter to be kept. The following metrics are supported:

  • RMSD

  • iRMSD (interface RMSD)

  • lRMSD (ligand RMSD)

  • ilRMSD (interface ligand RMSD)

  • FNAT (fraction of native contacts)

  • DOCKQ

The following files are generated:

  • caprifilter.tsv: kept models with score and the user-requested metric columns only.

  • caprifilter_all_models.tsv: all input models, user-requested metrics, and a status column (kept / filtered). Written only when caprifilter_full = true.

  • caprifilter_ss.tsv: caprieval-style ranked table of all models.

  • caprifilter_multiref.tsv: when multiple references are provided, one row per (model, reference) pair.

For more details about this module, please refer to the haddock3 user manual

class haddock.modules.analysis.caprifilter.HaddockModule(order: int, path: Path, init_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/haddock/modules/analysis/caprifilter/defaults.yaml'))[source]

Bases: BaseHaddockModule

HADDOCK3 module to filter models by CAPRI metrics.

classmethod confirm_installation() → None[source]

Confirm if module is installed.

static is_nested(models: list[PDBFile | list[PDBFile]]) → bool[source]
name: str = 'caprifilter'

Default Parameters

Easy

alignment_method

default: ‘sequence’
type: string
title: Alignment method
choices: [‘structure’, ‘sequence’]
short description: Alignment method used to match residue numbering.
long description: Alignment method used to match residue numbering between model and reference. Sequence alignment is the default. Structure alignment requires LovoAlign.
group: analysis
explevel: easy

allatoms

default: False
type: boolean
title: Use all heavy atoms
short description: Use all heavy atoms (including side chains).
long description: If false (default), only backbone atoms are used. If true, all heavy atoms.
group: analysis
explevel: easy

caprifilter_full

default: False
type: boolean
title: Write all-models table
short description: Write caprifilter_all_models.tsv with all models, status (kept/filtered) and requested metrics.
long description: Write caprifilter_all_models.tsv with all models, status (kept/filtered) and requested metrics.
group: analysis
explevel: easy

dockq_filter_cutoff

default: 0.23
type: float
title: DockQ filter cutoff.
min: 0.0
max: 1.0
short description: Filtering threshold for DockQ.
long description: Filtering threshold for DockQ.
group: analysis
explevel: easy

dockq_filter_out

default: ‘below’
type: string
title: DockQ filtering direction.
choices: [‘above’, ‘below’]
short description: Filter out models with DockQ above or below the cutoff.
long description: if ‘above’ - filter out models that are over the cutoff value (dockq_filter_cutoff). if ‘below’ - filter out models with DockQ under the cutoff value (dockq_filter_cutoff).
group: analysis
explevel: easy

filter_by

default: [‘rmsd’]
type: list
title: Metrics to filter by.
short description: List of CAPRI metrics to use for filtering.
long description: List of CAPRI metrics to filter on. Valid values are rmsd, irmsd, lrmsd, ilrmsd, fnat, dockq. Each metric must have its corresponding {metric}_filter_cutoff and {metric}_filter_out parameters set. All filters are applied simultaneously (AND logic), so a model must pass every active filter to be kept.
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.
long description: Distance cutoff (Å) used to define interface contacts between two interacting molecules.
group: analysis
explevel: easy

fnat_filter_cutoff

default: 0.3
type: float
title: FNAT filter cutoff.
min: 0.0
max: 1.0
short description: Filtering threshold for fraction of native contacts.
long description: Filtering threshold for fraction of native contacts.
group: analysis
explevel: easy

fnat_filter_out

default: ‘below’
type: string
title: FNAT filtering direction.
choices: [‘above’, ‘below’]
short description: Filter out models with FNAT above or below the cutoff.
long description: if ‘above’ - filter out models that are over the cutoff value (fnat_filter_cutoff). if ‘below’ - filter out models with FNAT under the cutoff value (fnat_filter_cutoff).
group: analysis
explevel: easy

ilrmsd_filter_cutoff

default: 10.0
type: float
title: ilRMSD filter cutoff (Å).
min: 0.0
max: 99999.99
short description: Filtering threshold for interface-ligand-RMSD.
long description: Filtering threshold for interface-ligand-RMSD.
group: analysis
explevel: easy

ilrmsd_filter_out

default: ‘above’
type: string
title: ilRMSD filtering direction.
choices: [‘above’, ‘below’]
short description: Filter out models with ilRMSD above or below the cutoff.
long description: if ‘above’ - filter out models that are over the cutoff value (ilrmsd_filter_cutoff). if ‘below’ - filter out models with ilRMSD under the cutoff value (ilrmsd_filter_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.
long description: Distance cutoff (Å) used to define interface residues based on intermolecular contacts.
group: analysis
explevel: easy

irmsd_filter_cutoff

default: 5.0
type: float
title: iRMSD filter cutoff (Å).
min: 0.0
max: 99999.99
short description: Filtering threshold for interface-RMSD.
long description: Filtering threshold for interface-RMSD.
group: analysis
explevel: easy

irmsd_filter_out

default: ‘above’
type: string
title: iRMSD filtering direction.
choices: [‘above’, ‘below’]
short description: Filter out models with iRMSD above or below the cutoff.
long description: if ‘above’ - filter out models that are over the cutoff value (irmsd_filter_cutoff). if ‘below’ - filter out models with irmsd under the cutoff value (irmsd_filter_cutoff).
group: analysis
explevel: easy

keep_hetatm

default: False
type: boolean
title: Consider HETATM records
short description: Include HETATM atoms from the reference.
long description: If false (default), only ATOM lines are used. If true, HETATM from the reference are also included.
group: analysis
explevel: easy

ligand_chains

default: []
type: list
title: Ligand ChainIDs
short description: Ligand ChainIDs for RMSD calculations.
long description: Ligand ChainIDs to be considered for the lRMSD and ilRMSD calculations.
group: analysis
explevel: easy

lovoalign_exec

default: ‘’
type: string
title: LovoAlign executable path
short description: Path to the LovoAlign executable.
long description: Path to the LovoAlign executable. Only required when alignment_method=structure.
group: analysis
explevel: easy

lrmsd_filter_cutoff

default: 10.0
type: float
title: lRMSD filter cutoff (Å).
min: 0.0
max: 99999.99
short description: Filtering threshold for ligand-RMSD
long description: Filtering threshold for ligand-RMSD.
group: analysis
explevel: easy

lrmsd_filter_out

default: ‘above’
type: string
title: lRMSD filtering direction.
choices: [‘above’, ‘below’]
short description: Filter out models with lRMSD above or below the cutoff.
long description: if ‘above’ - filter out models that are over the cutoff value (lrmsd_filter_cutoff). if ‘below’ - filter out models with lRMSD under the cutoff value (lrmsd_filter_cutoff).
group: analysis
explevel: easy

receptor_chain

default: ‘A’
type: string
title: Receptor ChainID
short description: Receptor ChainID for RMSD calculations.
long description: Receptor ChainID to be considered for the lRMSD and ilRMSD calculations.
group: analysis
explevel: easy

reference_fname

default: ‘’
type: file
title: Reference structure
short description: Reference structure for CAPRI metric calculation.
long description: Path to the reference PDB structure used to calculate CAPRI metrics. This parameter is mandatory, the module will stop with an error if reference not found.
group: analysis
explevel: easy

rmsd_filter_cutoff

default: 10.0
type: float
title: RMSD filter cutoff (Å).
min: 0.0
max: 99999.99
short description: Filtering threshold for RMSD.
long description: Filtering threshold for RMSD.
group: analysis
explevel: easy

rmsd_filter_out

default: ‘above’
type: string
title: RMSD filtering direction.
choices: [‘above’, ‘below’]
short description: Filter out models with RMSD above or below the cutoff.
long description: if ‘above’ - filter out models that are over the cutoff value (rmsd_filter_cutoff). if ‘below’ - filter out models with rmsd under the cutoff value (rmsd_filter_cutoff).
group: analysis
explevel: easy

sort_ascending

default: True
type: boolean
title: Sort in ascending order
short description: Sort models in ascending order.
long description: Sort models in ascending order inside the output file caprifilter.tsv.
group: analysis
explevel: easy

sortby

default: ‘score’
type: string
title: Sort the output file by this value
choices: [‘score’, ‘irmsd’, ‘lrmsd’, ‘ilrmsd’, ‘fnat’, ‘dockq’, ‘rmsd’]
short description: Which value should be used to sort the output.
long description: Which value should be used to sort the output caprifilter.tsv.
group: analysis
explevel: easy