Energy Minimization scoring module
Module contents
EM scoring module.
This module performs energy minimization and scoring of the models generated in the previous step of the workflow. No restraints are applied during this step.
- class haddock.modules.scoring.emscoring.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.15/x64/lib/python3.10/site-packages/haddock/modules/scoring/emscoring/defaults.yaml'))[source]
Bases:
CNSScoringModuleHADDOCK3 module to perform energy minimization scoring.
Default Parameters
Easy
elecflag
default: True
type: boolean
title: Include electrostatics energy
short description: Include electrostatics energy during the calculations.
long description: Include electrostatics energy during the calculations. If set to false electrostatics will not be considered.
group: force field
explevel: easy
ligand_param_fname
default: ‘’
type: file
title: Custom ligand parameter file
short description: Ligand parameter file in CNS format
long description: Ligand parameter file in CNS format containing all force field parameters (bond, angles, dihedrals, impropers, van der waals) for any ligand not supported by default by HADDOCK
group: force field
explevel: easy
ligand_top_fname
default: ‘’
type: file
title: Custom ligand topology file
short description: Ligand topology file in CNS format
long description: Ligand topology file in CNS format containing the ligand topologies (atoms, masses, charges, bond definitions…) for any ligand not supported by default by HADDOCK
group: force field
explevel: easy
Expert
dielec
default: ‘cdie’
type: string
title: Constant (cdie) or distance-dependent dielectric (rdie) constant.
choices: [‘cdie’, ‘rdie’]
short description: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential.
long description: Use a constant (cdie option) or a distance-dependent dielectric (rdie) constant in the Coulomb potential. A distance dependent dielectric constant will effectively scale down the electrostatic energy by having a 1/r**2 dependency instead of 1/r
group: force field
explevel: expert
dihedflag
default: True
type: boolean
title: No title yet
short description: No short description yet
long description: No long description yet
group: force field
explevel: expert
epsilon
default: 1.0
type: float
title: Dielectric constant
min: 1
max: 78
short description: Dielectric constant for the electrostatic Coulomb energy term.
long description: Dielectric constant for the electrostatic Coulomb energy term.
group: force field
explevel: expert
individualize
default: True
type: boolean
title: Individualise models
short description: Treat each model in the PDB ensemble as a separate entity.
long description: Treat each model in the PDB ensemble as a separate entity. This means that for each a separate topology file will be generated. The models in the ensemble can thus correspond to different molecules.
group: sampling
explevel: expert
nemsteps
default: 50
type: integer
title: Number of EM steps
min: 1
max: 10000
short description: Number of energy minimisation steps to perform.
long description: Number of energy minimisation steps to perform. Note that the effective number might be smaller if the minimisation converges earlier.
group: sampling
explevel: expert
per_interface_scoring
default: False
type: boolean
title: Interchains scoring
short description: Output scores per interface in the PDB header.
long description: With this option true, the interface of all combinations of chains will be analysed and the corresponding HADDOCK scores (without restraints terms) and their components (Eelec, Evdw, Edesol, BSA) will be written to the header of each PDB file.
group: scoring
explevel: expert
tolerance
default: 5
type: integer
title: Failure tolerance percentage
min: 0
max: 99
short description: Percentage of allowed failures for a module to successfully complete
long description: Percentage of allowed failures for a module to successfully complete
group: module
explevel: expert
w_air
default: 0.0
type: float
title: Weight of the distance restraint energy
min: 0
max: 9999
short description: Weight of the distance restraints energy in the scoring function
long description: Weight of the distance restraints energy in the scoring function. Note that this is different from the force constants used during the calculations.
group: scoring
explevel: expert
w_bsa
default: 0.0
type: float
title: Weight of the buried surface area term
min: -9999
max: 9999
short description: Weight of the buried surface area term in the scoring function
long description: Weight of the buried surface area (BSA) term in the scoring function. Note that the BSA is only used for scoring.
group: scoring
explevel: expert
w_cdih
default: 0.0
type: float
title: Weight of the dihedral angle restraint energy
min: 0
max: 9999
short description: Weight of the dihedral angle restraints energy in the scoring function
long description: Weight of the dihedral angle restraints energy in the scoring function. Note that this is different from the force constant used during the calculations.
group: scoring
explevel: expert
w_desolv
default: 1.0
type: float
title: Weight of the desolvation energy term
min: -9999
max: 9999
short description: Weight of the desolvation energy term in the scoring function
long description: Weight of the desolvation energy term in the scoring function. Note that the desolvation energy is only used for scoring.
group: scoring
explevel: expert
w_elec
default: 0.2
type: float
title: Weight of the intermolecular electrostatic energy
min: -9999
max: 9999
short description: Weight of the intermolecular electrostatic energy in the scoring function
long description: Weight of the intermolecular electrostatic energy in the scoring function. Note that this does not affect the electostatic energy during the EM minimization.
group: scoring
explevel: expert
w_vdw
default: 1.0
type: float
title: Weight of the intermolecular van der Waals energy
min: -9999
max: 9999
short description: Weight of the intermolecular van der Waals energy in the scoring function
long description: Weight of the intermolecular van der Waals energy in the scoring function. Note that this does not affect the van der Waals energy during the EM minimization.
group: scoring
explevel: expert
Guru
log_level
default: ‘quiet’
type: string
title: Log level verbosity for CNS
choices: [‘verbose’, ‘normal’, ‘quiet’]
short description: Set the log level verbosity for CNS
long description: CNS, the computational engine used by HADDOCK can generate a lot of output messages. This parameter controls the verbosity of CNS (verbose, normal or quiet)
group: module
explevel: guru