IMP  2.4.0
The Integrative Modeling Platform
EnvelopePenetrationRestraint.h
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1 /**
2  * \file IMP/em/EnvelopePenetrationRestraint.h
3  * \brief Score how well a protein is inside its density
4  *
5  * Copyright 2007-2015 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPEM_ENVELOPE_PENETRATION_RESTRAINT_H
10 #define IMPEM_ENVELOPE_PENETRATION_RESTRAINT_H
11 
12 #include <IMP/em/em_config.h>
13 #include "DensityMap.h"
14 #include <IMP/atom/Hierarchy.h>
15 #include <IMP/atom/Atom.h>
16 #include <IMP/atom/Mass.h>
17 #include <IMP/core/XYZR.h>
18 #include <IMP/kernel/Model.h>
19 #include <IMP/kernel/Restraint.h>
20 #include <IMP/Refiner.h>
21 
22 IMPEM_BEGIN_NAMESPACE
23 
24 //! Calculate score based on fit to EM map
25 /** \ingroup exp_restraint
26 
27  */
28 class IMPEMEXPORT EnvelopePenetrationRestraint : public kernel::Restraint {
29  public:
30  //! Constructor
31  /**
32  \param[in] ps The particles participating in the fitting score
33  \param[in] em_map The density map used in the fitting score
34  \param[in] threshold
35 
36  \note kernel::Particles that are rigid-bodies are interpolated and
37  not resampled.
38  This significantly reduces the running time but is less accurate.
39  If the user prefers to get more accurate results, provide
40  its members as input particles and not the rigid body.
41  \todo we currently assume rigid bodies are also molecular hierarchies.
42  */
43  EnvelopePenetrationRestraint(kernel::Particles ps, DensityMap *em_map,
44  Float threshold);
45 
46  virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum)
47  const IMP_OVERRIDE;
48  virtual IMP::kernel::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
49  IMP_OBJECT_METHODS(EnvelopePenetrationRestraint);
50 
51 #ifndef SWIG
52  IMP_LIST(private, Particle, particle, kernel::Particle *, kernel::Particles);
53 #endif
54  private:
55  IMP::base::PointerMember<DensityMap> target_dens_map_;
56  algebra::BoundingBoxD<3> target_bounding_box_;
57  // reference to the IMP environment
58  IMP::core::XYZs xyz_;
59  kernel::Particles ps_;
60  Float threshold_;
61 };
62 
63 IMPEM_END_NAMESPACE
64 
65 #endif /* IMPEM_ENVELOPE_PENETRATION_RESTRAINT_H */
Mass.h
A decorator for particles with mass.
IMP::kernel::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition: kernel/DerivativeAccumulator.h:25
IMP::em::EnvelopePenetrationRestraint
Calculate score based on fit to EM map.
Definition: EnvelopePenetrationRestraint.h:28
IMP::base::PointerMember
A smart pointer to a ref-counted Object that is a class member.
Definition: Pointer.h:147
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.
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:94
Restraint.h
Abstract base class for all restraints.
Refiner.h
Import IMP/kernel/Refiner.h in the namespace.
IMP::kernel::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition: kernel/Restraint.h:52
IMP::kernel::Particle
Class to handle individual model particles.
Definition: kernel/Particle.h:37
Model.h
Storage of a model, its restraints, constraints and particles.
IMP::kernel::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP::Float
double Float
Basic floating-point value (could be float, double...)
Definition: types.h:20
IMP_LIST
#define IMP_LIST(protection, Ucname, lcname, Data, PluralData)
A macro to provide a uniform interface for storing lists of objects.
Definition: kernel/container_macros.h:90
XYZR.h
Decorator for a sphere-like particle.
IMP_OVERRIDE
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.
Definition: compiler_macros.h:75