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IMP Reference Guide  develop.031dafb4d2,2024/05/21
The Integrative Modeling Platform
IMP.pmi.restraints.saxs.SAXSRestraint Class Reference

Basic SAXS restraint. More...

Inherits RestraintBase.

Detailed Description

Basic SAXS restraint.

Note
This class is only available in Python.

Definition at line 23 of file restraints/saxs.py.

Public Member Functions

def __init__
 Builds the restraint. 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 unless ff_type=IMP.saxs.RESIDUES is used.
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
  • IMP.saxs.RESIDUES: use residue based form factors using per-residue beads
labelLabel for the restraint in outputs
maxqMaximum q value that the restraint will be evaluated at. If set to 'standard' (the default), the following values will be used (these values were eyeballed by comparing ALL_ATOM calculated SAXS profiles to those calculated with the reduced representations, so could be improved):
  • For ff_type = ALL_ATOMS: 0.5
  • HEAVY_ATOMS: 0.4
  • CA_ATOMS and RESIDUES: 0.15

Definition at line 48 of file restraints/saxs.py.


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