meld.system.restraints.ConfinementRestraint

class meld.system.restraints.ConfinementRestraint(system, scaler, ramp, atom_index, radius, force_const)[source]

Bases: NonSelectableRestraint

Confinement restraint from origin

Confines an atom to be within radius of the origin. These restraints are typically set to somewhat larger than the expected radius of gyration of the protein and help to keep the structures comapact even when the protein is unfolded. Typically used with a ConstantScaler.

__init__(system, scaler, ramp, atom_index, radius, force_const)[source]

Initialize a ConfinementRestraint

Parameters

  • system (ISystem) – the system that this restraint belongs to

  • scaler (Optional[RestraintScaler]) – scale the force with alpha

  • ramp (Optional[TimeRamp]) – scale the force over time

  • atom_index (AtomIndex) – the index of the restrained atom

  • radius (Quantity) – the distance to confine to

  • force_const (Quantity) – strength of confinement

Methods

__init__(system, scaler, ramp, atom_index, ...)

Initialize a ConfinementRestraint