Interface Ligand RMSD Matrix calculation module

Submodules

Module contents

ilRMSD matrix module.

This module calculates of the interface-ligand RMSD (ilRMSD) matrix between all the models generated in the previous step.

As all the pairwise ilRMSD calculations are independent, the module distributes them over all the available cores in an optimal way.

Once created, the ilRMSD matrix is saved in text form in the current ilrmsdmatrix folder. The path to this file is then shared with the following step of the workflow by means of the json file rmsd_matrix.json.

IMPORTANT: the module assumes coherent numbering for all the receptor and ligand chains, as no alignment is performed. The user must ensure that the numbering is coherent.

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

class haddock.modules.analysis.ilrmsdmatrix.HaddockModule(order, path, *ignore, init_params=PosixPath('/opt/hostedtoolcache/Python/3.10.20/x64/lib/python3.10/site-packages/haddock/modules/analysis/ilrmsdmatrix/defaults.yaml'), **everything)[source]

Bases: BaseHaddockModule

HADDOCK3 module for clustering with RMSD.

classmethod confirm_installation() → None[source]

Confirm if fast-rmsdmatrix is installed and available.

name: str = 'ilrmsdmatrix'

Default Parameters

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

atom_similarity

default: 90.0
type: float
title: Required atom similarity
min: 10.0
max: 100.0
short description: Required similarity (in %) between the number of atoms in the input models.
long description: Required similarity (in %) between the number of atoms in the input models. If the similarity is higher than this value, the RMSD calculation is performed on the common atoms. Otherwise, the calculation is stopped. The lower the value the looser the checks.
group: analysis
explevel: easy

contact_distance_cutoff

default: 5.0
type: float
title: Distance cutoff defining a contact.
min: 0.1
max: 30.0
short description: Cutoff distance (in Angstrom) defining a contact.
long description: Distance (in Angstrom) cutoff defining a contact. Any atoms within this cutoff range will be used to define the interface. Standard values are usually 3.9 A or 5.0 A.
group: analysis
explevel: easy

ligand_chains

default: []
type: list
title: Ligand ChainIDs
short description: Ligand ChainIDs to be considered for the IL-RMSD calculations.
long description: Ligand ChainIDs to be considered for the IL-RMSD calculations. This determines which chains will be treated as the ligand for the IL-RMSD. By default, all chains are considered with the exception of the receptor chain.
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

Guru

max_models

default: 10000
type: integer
title: Maximum number of models
min: 1
max: 20000
short description: Maximum number of models to be considered when calculating the matrix.
long description: Maximum number of models to be considered when calculating the matrix. If the number of models in the input file is larger than this number, the execution will be aborted.
group: analysis
explevel: guru