IMP logo
IMP Reference Guide  develop.cc86c9801d,2022/11/22
The Integrative Modeling Platform
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint Class Reference

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

Inherits RestraintBase.

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

Note
Wraps an IMP::isd::CrossLinkMSRestraint
This class is only available in Python.

Definition at line 40 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.pmi.dof class. More...
 
def get_output
 Get the output of the restraint to be used by the IMP.pmi.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.pmi.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...
 

Constructor & Destructor Documentation

def IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint.__init__ (   self,
  root_hier,
  database = None,
  length = 10.0,
  resolution = None,
  slope = 0.02,
  label = None,
  filelabel = 'None',
  attributes_for_label = None,
  linker = None,
  weight = 1.0 
)

Constructor.

Parameters
root_hierThe canonical hierarchy containing all the states
databaseThe IMP.pmi.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
linkerdescription of the chemistry of the linker itself, as an ihm.ChemDescriptor object (see https://python-ihm.readthedocs.io/en/latest/main.html#ihm.ChemDescriptor). Common cross-linkers can be found in the ihm.cross_linkers module.

Definition at line 64 of file restraints/crosslinking.py.

Member Function Documentation

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

This is called internally.

Creates a nuisance on the data uncertainty

Definition at line 410 of file restraints/crosslinking.py.

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

This is called internally.

Creates a nuisance on the structural uncertainty

Definition at line 382 of file restraints/crosslinking.py.

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

get the hierarchy

Definition at line 345 of file restraints/crosslinking.py.

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

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

Definition at line 466 of file restraints/crosslinking.py.

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

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

Definition at line 434 of file restraints/crosslinking.py.

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

Get a list of tuples containing the particle pairs.

Definition at line 361 of file restraints/crosslinking.py.

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

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

Definition at line 497 of file restraints/crosslinking.py.

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

get the dummy restraints to be displayed in the rmf file

Definition at line 357 of file restraints/crosslinking.py.

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

get the restraint set

Definition at line 349 of file restraints/crosslinking.py.

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

get the restraints in a list

Definition at line 353 of file restraints/crosslinking.py.

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

Set the output level of the output.

Definition at line 370 of file restraints/crosslinking.py.

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

Switch on/off the sampling of psi particles.

Definition at line 374 of file restraints/crosslinking.py.

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

Switch on/off the sampling of sigma particles.

Definition at line 378 of file restraints/crosslinking.py.


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