meld.parse.get_rdc_restraints

meld.parse.get_rdc_restraints(system, alignment_index, scaler, ramp=None, quadratic_cut=None, filename=None, content=None, file=None)[source]

Reads restraints from file and returns as RdcRestraint object.

Parameters

  • system (ISystem) – the system object for the restraints to be added to.

  • alignment_index (int) – index of the alignment tensor to use

  • scaler (RestraintScaler) – object to scale the force constant.

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

  • quadratic_cut (Optional[Quantity]) – restraints become linear beyond this deviation, default 999 Hz

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

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

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

Return type

List[RdcRestraint]

Returns

list of restraints from input

Note

The value of kappa is assumed to be in units of Hz \(Angstrom^3\).

Note

All indexing in the input file is assumed to be 1-based.

Note

The expected order of columns in the input file is:

  • residue i

  • atom name i

  • residue j

  • atom name j

  • observed splitting (\(Hz\))

  • experiment (ignored)

  • tolerance (\(Hz\))

  • kappa (\(Hz \AA^3\))

  • force constant (\(kJ mol^{-1} Hz^{-2}\))

  • weight