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IMP Reference Guide  develop.cc86c9801d,2022/11/22
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IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint Class Reference

Setup cross-link distance restraints from mass spectrometry data. More...

+ Inheritance diagram for IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint:

Detailed Description

Setup cross-link distance restraints from mass spectrometry data.

The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes theory of probability

ote Wraps an IMP::isd::CrossLinkMSRestraint

Note
This class is only available in Python.

Definition at line 24 of file /restraints/crosslinking.py.

Public Member Functions

def __init__
 Constructor. More...
 
def create_psi
 This is called internally. More...
 
def create_sigma
 This is called internally. More...
 
def get_hierarchies
 get the hierarchy More...
 
def get_movers
 Get all need data to construct a mover in IMP.pmi1.dof class. More...
 
def get_output
 Get the output of the restraint to be used by the IMP.pmi1.output object. More...
 
def get_particle_pairs
 Get a list of tuples containing the particle pairs. More...
 
def get_particles_to_sample
 Get the particles to be sampled by the IMP.pmi1.sampler object. More...
 
def get_restraint_for_rmf
 get the dummy restraints to be displayed in the rmf file More...
 
def get_restraint_sets
 get the restraint set More...
 
def get_restraints
 get the restraints in a list More...
 
def set_output_level
 Set the output level of the output. More...
 
def set_psi_is_sampled
 Switch on/off the sampling of psi particles. More...
 
def set_sigma_is_sampled
 Switch on/off the sampling of sigma particles. More...
 
- Public Member Functions inherited from IMP.pmi1.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.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.__init__ (   self,
  representation = None,
  root_hier = None,
  CrossLinkDataBase = None,
  length = 10.0,
  resolution = None,
  slope = 0.02,
  label = None,
  filelabel = 'None',
  attributes_for_label = None,
  weight = 1.0 
)

Constructor.

Parameters
representationDEPRECATED The IMP.pmi1.representation.Representation object that contain the molecular system
root_hierThe canonical hierarchy containing all the states
CrossLinkDataBaseThe IMP.pmi1.io.crosslink.CrossLinkDataBase object that contains the cross-link dataset
lengthmaximal cross-linker length (including the residue sidechains)
resolutionwhat representation resolution should the cross-link restraint be applied to.
slopeThe slope of a distance-linear scoring function that funnels the score when the particles are too far away. Suggested value 0.02.
labelthe extra text to label the restraint so that it is searchable in the output
filelabelautomatically generated file containing missing/included/excluded cross-links will be labeled using this text
attributes_for_label
weightWeight of restraint

Definition at line 43 of file /restraints/crosslinking.py.

Member Function Documentation

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.create_psi (   self,
  name 
)

This is called internally.

Creates a nuisance on the data uncertainty

Definition at line 387 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.create_sigma (   self,
  name 
)

This is called internally.

Creates a nuisance on the structural uncertainty

Definition at line 360 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_hierarchies (   self)

get the hierarchy

Definition at line 322 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_movers (   self)

Get all need data to construct a mover in IMP.pmi1.dof class.

Definition at line 450 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_output (   self)

Get the output of the restraint to be used by the IMP.pmi1.output object.

Definition at line 418 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_particle_pairs (   self)

Get a list of tuples containing the particle pairs.

Definition at line 338 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_particles_to_sample (   self)

Get the particles to be sampled by the IMP.pmi1.sampler object.

Definition at line 476 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_restraint_for_rmf (   self)

get the dummy restraints to be displayed in the rmf file

Definition at line 334 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_restraint_sets (   self)

get the restraint set

Definition at line 326 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.get_restraints (   self)

get the restraints in a list

Definition at line 330 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.set_output_level (   self,
  level = 'low' 
)

Set the output level of the output.

Definition at line 347 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.set_psi_is_sampled (   self,
  is_sampled = True 
)

Switch on/off the sampling of psi particles.

Definition at line 351 of file /restraints/crosslinking.py.

def IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.set_sigma_is_sampled (   self,
  is_sampled = True 
)

Switch on/off the sampling of sigma particles.

Definition at line 355 of file /restraints/crosslinking.py.


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