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IMP Reference Guide  2.13.0
The Integrative Modeling Platform
EnvelopeFitRestraint.h
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1 /**
2  * \file IMP/em/EnvelopeFitRestraint.h
3  * \brief score envelope fit based on map distance transform
4  *
5  * \authors Dina Schneidman
6  * Copyright 2007-2020 IMP Inventors. All rights reserved.
7  *
8  */
9 
10 #ifndef IMPEM_ENVELOPE_FIT_RESTRAINT_H
11 #define IMPEM_ENVELOPE_FIT_RESTRAINT_H
12 
13 #include <IMP/em/em_config.h>
14 #include <IMP/em/PCAAligner.h>
16 #include <IMP/em/EnvelopeScore.h>
17 #include <IMP/object_macros.h>
18 
19 #include <IMP/Restraint.h>
20 
21 IMPEM_BEGIN_NAMESPACE
22 
23 //! A restraint for envelope-based scoring of particles in the density map
24 /**
25  The restraint fits the particles into the density map by alignment
26  of principal components of the particles with principal components
27  of the map. Therefore, the particle set should comprise all
28  subunits that fill the map. The aligned particles are scored using
29  EnvelopeScore. This is a fast alignment and scoring that can work well
30  for low resolution density maps.
31 
32  \note In most cases it is more appropriate to use isd::GaussianEMRestraint.
33  */
34 class IMPEMEXPORT EnvelopeFitRestraint : public IMP::Restraint {
35  public:
36  //! Constructor
37  /**
38  \param[in] particles The particles participating in the score
39  \param[in] em_map The density map used in the fitting score
40  \param[in] density_threshold Density map threshold
41  \param[in] penetration_threshold A distance for which penetration
42  of particles out of the map envelope (as defined by density_threshold)
43  is allowed. Recommended value is approximately map resolution
44  */
45  EnvelopeFitRestraint(Particles particles, DensityMap *em_map,
46  double density_threshold, double penetration_threshold);
47 
48  double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const;
49 
50  // compute and return best scoring transformation
51  algebra::Transformation3D get_transformation() const {
52  unprotected_evaluate(nullptr);
53  return transformation_;
54  }
55 
56  // compute best scoring transformation and apply it on the particles
57  void apply_transformation();
58 
59  IMP::ModelObjectsTemp do_get_inputs() const { return ps_; }
61 
62  private:
63  Particles ps_;
64  IMP::PointerMember<PCAAligner> pca_aligner_;
65  double penetration_threshold_;
66  IMP::PointerMember<MapDistanceTransform> distance_transform_;
67  IMP::PointerMember<EnvelopeScore> envelope_score_;
68 
69  // best scoring trans from last evaluate
70  IMP::algebra::Transformation3D transformation_;
71 };
72 
73 IMPEM_END_NAMESPACE
74 
75 #endif /* IMPEM_ENVELOPE_FIT_RESTRAINT_H */
Simple 3D transformation class.
Various general useful macros for IMP.
Fast alignment of points to a density map using principal components.
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition: object_macros.h:25
A restraint for envelope-based scoring of particles in the density map.
IMP::ModelObjectsTemp do_get_inputs() const
Class for handling density maps.
Definition: DensityMap.h:93
A smart pointer to a ref-counted Object that is a class member.
Definition: Pointer.h:146
class for envelope based scoring using MapDistanceTransform
Abstract base class for all restraints.
class for computing a distance transform of the density map
Class for adding derivatives from restraints to the model.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54