IMP.pmi.restraints.saxs.SAXSRestraint Class Reference

Basic SAXS restraint. More...

Inheritance diagram for IMP.pmi.restraints.saxs.SAXSRestraint:

Detailed Description

Basic SAXS restraint.

Note

This class is only available in Python.

Definition at line 17 of file saxs.py.

Public Member Functions
def	__init__
	Builds the restraint. More...
Public Member Functions inherited from IMP.pmi.restraints.RestraintBase
def	__init__
	Constructor. More...
def	add_to_model
	Add the restraint to the model. More...
def	evaluate
	Evaluate the score of the restraint. More...
def	get_output
	Get outputs to write to stat files. More...
def	get_particles_to_sample
	Get any created particles which should be sampled. More...
def	get_restraint
	Get the primary restraint set. More...
def	get_restraint_for_rmf
	Get the restraint for visualization in an RMF file. More...
def	get_restraint_set
	Get the primary restraint set. More...
def	set_label
	Set the unique label used in outputs and particle/restraint names. More...
def	set_weight
	Set the weight to apply to all internal restraints. More...

Constructor & Destructor Documentation

def IMP.pmi.restraints.saxs.SAXSRestraint.__init__	(		self,
			input_objects,
			saxs_datafile,
			weight = 1.0,
			ff_type = IMP.saxs.HEAVY_ATOMS,
			label = None,
			maxq = 'standard'
	)

Builds the restraint.

Parameters

input_objects	A list of hierarchies or PMI objects that the SAXS restraint will be applied to. This hierarchy MUST be atomic. You can pass a list of CA atom particles to evaluate at residue resolution
saxs_datafile	the SAXS .dat file.
weight	Restraint score coefficient
ff_type	the form factor to use, of the following types: IMP.saxs.HEAVY_ATOMS: use form factors with implicit hydrogens IMP.saxs.ALL_ATOMS: use individual form factors for all atoms. Does not build missing hydrogens. IMP.saxs.CA_ATOMS: use residue based form factors centered at CA atoms
label	Label for the restraint in outputs
maxq	- maximum q value that the restraint will be evaluated at Default vaules for ff_type = ALL_ATOMS : 0.5. HEAVY_ATOMS : 0.4, CA_ATOMS and RESIDUES = 0.15. These values were eyeballed by comparing ALL_ATOM calculated SAXS profiles to those calculated with the reduced representations, so could be improved.

Definition at line 39 of file saxs.py.

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The documentation for this class was generated from the following file:

• saxs.py