IMP Reference Guide  develop.cc86c9801d,2022/11/22 The Integrative Modeling Platform

Setup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes' theory of probability. More...

## Detailed Description

Setup cross-link distance restraints at atomic level The "atomic" aspect is that it models the particle uncertainty with a Gaussian The noise in the data and the structural uncertainty of cross-linked amino-acids is inferred using Bayes' theory of probability.

Note
This class is only available in Python.

Definition at line 495 of file /restraints/crosslinking.py.

## Public Member Functions

def __init__
Constructor. More...

def create_restraints_for_rmf
create dummy harmonic restraints for each XL but don't add to model Makes it easy to see each contribution to each XL in RMF More...

def get_best_stats
return the probability, best distance, two coords, and possibly the psi for each xl More...

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

def plot_violations
Create CMM files, one for each state, of all crosslinks. More...

Public Member Functions inherited from IMP.pmi1.restraints.RestraintBase
def __init__
Constructor. More...

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.AtomicCrossLinkMSRestraint.__init__ ( self, root_hier, xldb, atom_type = 'NZ', length = 10.0, slope = 0.01, nstates = None, label = None, nuisances_are_optimized = True, sigma_init = 5.0, psi_init = 0.01, one_psi = True, filelabel = None, weight = 1.0 )

Constructor.

Automatically creates one "sigma" per crosslinked residue and one "psis" per pair. Other nuisance options are available.

ote Will return an error if the data+extra_sel don't specify two particles per XL pair.

Parameters
 root_hier The root hierarchy on which you'll do selection xldb CrossLinkDataBase object atom_type Can either be "NZ" or "CA" length The XL linker length slope Linear term to add to the restraint function to help when far away nstates The number of states to model. Defaults to the number of states in root. label The output label for the restraint nuisances_are_optimized Whether to optimize nuisances sigma_init The initial value for all the sigmas psi_init The initial value for all the psis one_psi Use a single psi for all restraints (if False, creates one per XL) filelabel automatically generated file containing missing/included/excluded cross-links will be labeled using this text weight Weight of restraint

Definition at line 517 of file /restraints/crosslinking.py.

## Member Function Documentation

create dummy harmonic restraints for each XL but don't add to model Makes it easy to see each contribution to each XL in RMF

Definition at line 752 of file /restraints/crosslinking.py.

 def IMP.pmi1.restraints.crosslinking.AtomicCrossLinkMSRestraint.get_best_stats ( self, limit_to_state = None, limit_to_chains = None, exclude_chains = '', use_CA = False )

return the probability, best distance, two coords, and possibly the psi for each xl

Parameters
 limit_to_state Only examine contributions from one state limit_to_chains Returns the particles for certain "easy to visualize" chains exclude_chains Even if you limit, don't let one end be in this list. Only works if you also limit chains use_CA Limit to CA particles

Definition at line 944 of file /restraints/crosslinking.py.

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

Definition at line 777 of file /restraints/crosslinking.py.

This is potentially quite stupid. It's also a hack since the sigmas should be stored in the RMF file. Also, requires one sigma and one psi for ALL XLs.

Definition at line 803 of file /restraints/crosslinking.py.

 def IMP.pmi1.restraints.crosslinking.AtomicCrossLinkMSRestraint.plot_violations ( self, out_prefix, max_prob_for_violation = 0.1, min_dist_for_violation = 1000000000.0, coarsen = False, limit_to_chains = None, exclude_chains = '' )

Create CMM files, one for each state, of all crosslinks.

will draw in GREEN if non-violated in all states (or if only one state) will draw in PURPLE if non-violated only in a subset of states (draws nothing elsewhere) will draw in RED in ALL states if all violated (if only one state, you'll only see green and red)

Parameters
 out_prefix Output xlink files prefix max_prob_for_violation It's a violation if the probability is below this min_dist_for_violation It's a violation if the min dist is above this coarsen Use CA positions limit_to_chains Try to visualize just these chains exclude_to_chains Try to NOT visualize these chains

Definition at line 824 of file /restraints/crosslinking.py.

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