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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
pmi1/CompositeRestraint.h
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1 /**
2  * \file IMP/pmi1/CompositeRestraint.h
3  * \brief A restraint for ambiguous cross-linking MS data and multiple
4  * state approach.
5  *
6  * Copyright 2007-2018 IMP Inventors. All rights reserved.
7  *
8  */
9 
10 #ifndef IMPPMI1_COMPOSITE_RESTRAINT_H
11 #define IMPPMI1_COMPOSITE_RESTRAINT_H
12 #include "pmi1_config.h"
13 #include <IMP/Restraint.h>
14 #include <IMP/Particle.h>
15 #include <IMP/tuple_macros.h>
16 //#include <IMP/container/CloseBipartitePairContainer.h>
17 
18 IMPPMI1_BEGIN_NAMESPACE
19 //! A restraint for ambiguous cross-linking MS data and multiple state approach.
20 /** It marginalizes the false positive rate and depends on the expected fpr and
21  an uncertainty parameter beta.
22  */
23 class IMPPMI1EXPORT CompositeRestraint : public Restraint
24 {
25  //particle indexes in the composite
27  ParticleIndexes handle_particle_indexes_;
28  double coffd_;
29  double l_;
30  IMP_NAMED_TUPLE_2(CacheKey, CacheKeys,
31  Int, ipart, Ints, excluded, );
32 
33  IMP_NAMED_TUPLE_2(CacheKeyPot, CacheKeyPots,
34  Int, ipart, Int, kpart, );
35 
36  typedef boost::unordered_map<CacheKey, double> Cache;
37  typedef boost::unordered_map<CacheKeyPot, double> CachePot;
38 
39  //variables needed to tabulate the exponential
40  Floats prob_grid_;
41  double invdx_;
42  double argmax_;
43  double argmin_;
44  bool tabprob_;
45  double plateau_;
46  int exparg_grid_size_;
47 
48  inline double calc_prob (double dist) const{
49  double argvalue=(dist-coffd_)/l_;
50  double prob;
51  if (tabprob_){
52  //this prevents something being below the lower value of the array
53  double maxarg=std::max(argvalue,argmin_);
54  //this prevents something being above the upper value of the array
55  double minarg=std::min(maxarg,argmax_);
56  unsigned k = static_cast<unsigned>( std::floor(minarg*invdx_)+exparg_grid_size_);
57  prob=prob_grid_[k];
58 
59  }
60  else{
61  prob=(1.0-plateau_)/(1.0+std::exp(-argvalue));
62  }
63  return prob;
64  }
65 
66 
67  //boost::unordered_map<std::tuple<unsigned int,unsigned int>,
68  // Pointer<container::CloseBipartitePairContainer>> map_cont_;
69 
70  /* call for probability */
71  double get_probability_per_particle_excluding(unsigned int ipart,
72  Ints excluded_ps, Cache& cache, CachePot& cachepot) const;
73 
74 public:
75 
76 
77  //! Create the restraint.
79  ParticleIndexesAdaptor handle_particle_indexes,
80  double coffd, double l, bool tabprob, double plateau,
81  std::string name="CompositeRestraint%1%");
82 
83  void add_composite_particle(ParticleIndexesAdaptor pi){pis_.push_back(pi);}
84 
85 
86  unsigned int get_number_of_elements() const {return pis_.size();}
87 
88 
89 
90  //double get_probability() const {return 0.0;}
91 
92  virtual double
93  unprotected_evaluate(DerivativeAccumulator *accum) const override;
94  virtual ModelObjectsTemp do_get_inputs() const override;
96 
97  virtual double get_probability() const
98  {
99  return exp(-unprotected_evaluate(nullptr));
100  }
101 
102 
103 };
104 
105 IMPPMI1_END_NAMESPACE
106 
107 #endif /* IMPPMI1_COMPOSITE_RESTRAINT_H */
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition: object_macros.h:25
virtual double unprotected_evaluate(DerivativeAccumulator *da) const
Return the unweighted score for the restraint.
Macros to help in defining tuple classes.
A more IMP-like version of the std::vector.
Definition: Vector.h:42
Take Decorator, Particle or ParticleIndex.
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
A restraint for ambiguous cross-linking MS data and multiple state approach.
Classes to handle individual model particles. (Note that implementation of inline functions is in int...
Abstract base class for all restraints.
int Int
Basic integer value.
Definition: types.h:34
virtual ModelObjectsTemp do_get_inputs() const =0
Class for adding derivatives from restraints to the model.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56