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IMP Reference Guide
2.20.2
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
include
IMP
em
version 2.20.2
EnvelopePenetrationRestraint.h
Go to the documentation of this file.
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/**
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* \file IMP/em/EnvelopePenetrationRestraint.h
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* \brief Score how well a protein is inside its density
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*
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* Copyright 2007-2022 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPEM_ENVELOPE_PENETRATION_RESTRAINT_H
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#define IMPEM_ENVELOPE_PENETRATION_RESTRAINT_H
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#include <IMP/em/em_config.h>
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#include "
DensityMap.h
"
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#include <
IMP/atom/Hierarchy.h
>
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#include <
IMP/atom/Atom.h
>
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#include <
IMP/atom/Mass.h
>
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#include <
IMP/core/XYZR.h
>
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#include <
IMP/Model.h
>
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#include <
IMP/Restraint.h
>
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#include <
IMP/Refiner.h
>
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IMPEM_BEGIN_NAMESPACE
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//! Calculate score based on fit to EM map
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/** \ingroup exp_restraint
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*/
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class
IMPEMEXPORT
EnvelopePenetrationRestraint
:
public
Restraint
{
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public
:
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//! Constructor
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/**
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\param[in] ps The particles participating in the fitting score
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\param[in] em_map The density map used in the fitting score
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\param[in] threshold
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\note Particles that are rigid-bodies are interpolated and
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not resampled.
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This significantly reduces the running time but is less accurate.
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If the user prefers to get more accurate results, provide
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its members as input particles and not the rigid body.
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\todo we currently assume rigid bodies are also molecular hierarchies.
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*/
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EnvelopePenetrationRestraint
(
Particles
ps,
DensityMap
*em_map,
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Float
threshold);
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virtual
double
unprotected_evaluate
(
IMP::DerivativeAccumulator
*accum)
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const override
;
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virtual
IMP::ModelObjectsTemp
do_get_inputs
()
const override
;
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IMP_OBJECT_METHODS
(
EnvelopePenetrationRestraint
);
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#ifndef SWIG
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IMP_LIST
(
private
,
Particle
, particle,
Particle
*,
Particles
);
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#endif
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private
:
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IMP::PointerMember<DensityMap>
target_dens_map_;
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algebra::BoundingBoxD<3>
target_bounding_box_;
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// reference to the IMP environment
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IMP::core::XYZs
xyz_;
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Particles
ps_;
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Float
threshold_;
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};
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IMPEM_END_NAMESPACE
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#endif
/* IMPEM_ENVELOPE_PENETRATION_RESTRAINT_H */
Mass.h
A decorator for particles with mass.
IMP::em::EnvelopePenetrationRestraint
Calculate score based on fit to EM map.
Definition:
EnvelopePenetrationRestraint.h:28
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition:
object_macros.h:25
Atom.h
Simple atom decorator.
Model.h
Storage of a model, its restraints, constraints and particles.
IMP::Restraint::unprotected_evaluate
virtual double unprotected_evaluate(DerivativeAccumulator *da) const
Return the unweighted score for the restraint.
IMP::Vector< Pointer< Particle > >
IMP_LIST
#define IMP_LIST(protection, Ucname, lcname, Data, PluralData)
A macro to provide a uniform interface for storing lists of objects.
Definition:
container_macros.h:127
DensityMap.h
Class for handling density maps.
Hierarchy.h
Decorator for helping deal with a hierarchy of molecules.
IMP::em::DensityMap
Class for handling density maps.
Definition:
DensityMap.h:95
Refiner.h
Refine a particle into a list of particles.
IMP::PointerMember
A smart pointer to a ref-counted Object that is a class member.
Definition:
Pointer.h:143
IMP::algebra::BoundingBoxD< 3 >
IMP::Float
double Float
Basic floating-point value (could be float, double...)
Definition:
types.h:19
IMP::Particle
Class to handle individual particles of a Model object.
Definition:
Particle.h:43
Restraint.h
Abstract base class for all restraints.
XYZR.h
Decorator for a sphere-like particle.
IMP::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition:
DerivativeAccumulator.h:24
IMP::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition:
Restraint.h:56