meld.parse.get_secondary_structure_restraints

meld.parse.get_secondary_structure_restraints(system, scaler, ramp=None, torsion_force_constant=None, distance_force_constant=None, quadratic_cut=None, first_residue=None, min_secondary_match=4, filename=None, content=None, file=None)[source]

Get a list of secondary structure restraints.

Parameters
  • system (ISystem) – the system

  • scaler (RestraintScaler) – the force scaler

  • ramp (Optional[TimeRamp]) – the ramp, default is ConstantRamp

  • torsion_force_constant (Optional[Quantity]) – force constant for torsions, default 2.5e-2 kJ/mol/deg^2

  • distance_force_constant (Optional[Quantity]) – force constant for distances, default 2.5 kJ/mol/nm^2

  • quadratic_cut (Optional[Quantity]) – switch from quadratic to linear beyond this distance, default 0.2 nm

  • min_secondary_match (int) – minimum number of elements to match in secondary structure

  • first_residue (Optional[ResidueIndex]) – residue at which these secondary structure restraints start

  • filename (Optional[str]) – filename to open

  • content (Optional[str]) – contents to process

  • file (Optional[TextIO]) – object to read from

Returns

A list of RestraintGroups

Note

Specify exactly one of filename, contents, file.

Return type

List[RestraintGroup]