IMP logo
IMP Reference Guide  2.9.0
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 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 saxs.py.


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