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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
IMP Manual
Reference Guide
Modules
Classes
Examples
include
IMP
isd
CrossLinkMSRestraint.h
Go to the documentation of this file.
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/**
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* \file IMP/isd/CrossLinkMSRestraint.h
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* \brief A pmf based likelihood function
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* with prior knowledge on the false positive rate.
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*
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* Copyright 2007-2016 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPISD_CROSS_LINK_MSRESTRAINT_H
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#define IMPISD_CROSS_LINK_MSRESTRAINT_H
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#include "isd_config.h"
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#include <
IMP/Restraint.h
>
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#include <
IMP/particle_index.h
>
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IMPISD_BEGIN_NAMESPACE
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//! A restraint for ambiguous cross-linking MS data and multiple state approach.
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/** It marginalizes the false positive rate and depends on the expected fpr and
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an uncertainty parameter beta.
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*/
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class
IMPISDEXPORT
CrossLinkMSRestraint
:
public
Restraint
{
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IMP::ParticleIndexPairs
ppis_;
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IMP::ParticleIndexPairs
sigmass_;
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IMP::ParticleIndex
lengthi_;
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IMP::ParticleIndexes
psis_;
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double
length_;
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double
slope_;
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int
constr_;
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bool
get_log_prob_;
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double
sphere_cap(
float
r1,
float
r2,
float
d)
const
;
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public
:
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//! Create the restraint.
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CrossLinkMSRestraint
(
IMP::Model
* m,
double
length,
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bool
get_log_prob =
false
,
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std::string name =
"CrossLinkMSRestraint%1%"
);
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CrossLinkMSRestraint
(
IMP::Model
* m,
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IMP::ParticleIndexAdaptor
lengthi,
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bool
get_log_prob =
false
,
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std::string name =
"CrossLinkMSRestraint%1%"
);
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CrossLinkMSRestraint
(
IMP::Model
* m,
double
length,
double
slope,
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bool
get_log_prob =
false
,
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std::string name =
"CrossLinkMSRestraint%1%"
);
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void
add_contribution(
const
IMP::ParticleIndexPair
& pps,
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const
IMP::ParticleIndexPair
& sigmas,
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IMP::ParticleIndex
psi) {
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ppis_.push_back(pps);
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sigmass_.push_back(sigmas);
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psis_.push_back(psi);
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}
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double
get_probability()
const
;
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unsigned
int
get_number_of_contributions()
const
{
return
ppis_.size(); }
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virtual
double
unprotected_evaluate(
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IMP::DerivativeAccumulator
* accum)
const
IMP_OVERRIDE
;
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virtual
IMP::ModelObjectsTemp
do_get_inputs
()
const
IMP_OVERRIDE
;
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IMP_OBJECT_METHODS
(
CrossLinkMSRestraint
);
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};
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IMPISD_END_NAMESPACE
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#endif
/* IMPISD_CROSS_LINK_MSRESTRAINT_H */
IMP::isd::CrossLinkMSRestraint
A restraint for ambiguous cross-linking MS data and multiple state approach.
Definition:
CrossLinkMSRestraint.h:22
particle_index.h
Various general useful functions for IMP.
IMP::Array
A class to store an fixed array of same-typed values.
Definition:
Array.h:33
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
object_macros.h:25
IMP::ParticleIndexAdaptor
Definition:
particle_index.h:32
IMP::Index< ParticleIndexTag >
IMP::Vector< ParticleIndexPair >
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
Model.h:72
Restraint.h
Abstract base class for all restraints.
IMP::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition:
compiler_macros.h:80
IMP::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition:
DerivativeAccumulator.h:25
IMP::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition:
Restraint.h:52