haddock.modules.analysis.caprifilter package
Submodules
Module contents
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