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IMP Reference Guide  develop.af393bce43,2020/02/22
The Integrative Modeling Platform
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 restraints/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_objectsA 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_datafilethe SAXS .dat file.
weightRestraint score coefficient
ff_typethe 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
labelLabel 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 restraints/saxs.py.


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