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IMP Reference Guide  develop.27926d84dc,2024/04/20
The Integrative Modeling Platform
PairContainer.h
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1 // Autogenerated by ../../../../tmp/nightly-build-73208/imp-20240420.develop.27926d84dc/tools/build/make_containers.py
2 // from ../../../../tmp/nightly-build-73208/imp-20240420.develop.27926d84dc/tools/build/container_templates/kernel/ClassnameContainer.h
3 // Do not edit - any changes will be lost!
4 
5 /**
6  * \file IMP/PairContainer.h
7  * \brief A container for Pairs.
8  *
9  * Copyright 2007-2022 IMP Inventors. All rights reserved.
10  */
11 
12 #ifndef IMPKERNEL_PAIR_CONTAINER_H
13 #define IMPKERNEL_PAIR_CONTAINER_H
14 
15 #include <IMP/kernel_config.h>
16 #include "internal/IndexingIterator.h"
17 #include "Particle.h"
18 #include "container_base.h"
19 #include "internal/container_helpers.h"
20 #include "DerivativeAccumulator.h"
21 #include "base_types.h"
22 #include <IMP/ref_counted_macros.h>
23 #include <IMP/check_macros.h>
24 #include <IMP/Pointer.h>
25 #include <IMP/InputAdaptor.h>
26 #include <IMP/utility_macros.h>
27 #include <IMP/deprecation_macros.h>
28 #include <algorithm>
29 #include <cereal/access.hpp>
30 #include <cereal/types/base_class.hpp>
31 
32 IMPKERNEL_BEGIN_NAMESPACE
33 class PairModifier;
34 class PairScore;
35 
36 //! A shared container for Pairs
37 /** Stores a shared collection of Pairs.
38  */
39 class IMPKERNELEXPORT PairContainer : public Container {
40  public:
45  typedef PairModifier Modifier;
47 
48  //! Just use apply() in the base class
49  void apply_generic(const PairModifier *m) const;
50 
51  //! Just use apply_moved() in the base class
52  void apply_generic_moved(const PairModifier *m,
53  const ParticleIndexes &moved_pis,
54  const ParticleIndexes &reset_pis) const;
55 
56  //! Apply a PairModifier to the contents
57  void apply(const PairModifier *sm) const;
58 
59  //! Apply a PairModifier to the contents
60  void apply_moved(const PairModifier *sm,
61  const ParticleIndexes &moved_pis,
62  const ParticleIndexes &reset_pis) const;
63 
64  /** Get all the indexes that might possibly be contained in the
65  container, useful with dynamic containers. For example,
66  with a container::ClosePairContainer, this is the list
67  of all pairs taken from the input list (those that are far apart
68  in addition to those that are close).
69  */
70  virtual ParticleIndexPairs get_range_indexes() const = 0;
71 
72  const ParticleIndexPairs &get_contents() const {
73  if (get_provides_access())
74  return get_access();
75  else {
76  std::size_t nhash = get_contents_hash();
77  if (contents_hash_ != nhash || !cache_initialized_) {
78  contents_hash_ = nhash;
79  cache_initialized_ = true;
80  get_indexes_in_place(contents_cache_); // inheriting class could implement this faster than get_indexes()
81  }
82  return contents_cache_;
83  }
84  }
85 
86  /** Get all the indexes contained in the container.
87 
88  This should be protected but isn't for compatibility reasons.
89 
90  External callers should use get_contents().
91  */
92  virtual ParticleIndexPairs get_indexes() const = 0;
93 
94 
95 #ifndef IMP_DOXYGEN
96 
97  ParticlePairsTemp get() const {
98  return IMP::internal::get_particle(get_model(), get_indexes());
99  }
100 
101  ParticlePair get(unsigned int i) const {
102  return IMP::internal::get_particle(get_model(), get_indexes()[i]);
103  }
104 
105  //! Return size of current container content
106  //! Note that this may be expensive since it may involve
107  //! refreshing of the container
108  unsigned int get_number() const { return get_indexes().size(); }
109 #ifndef SWIG
110  bool get_provides_access() const;
111  virtual const ParticleIndexPairs &get_access() const {
112  IMP_THROW("Object not implemented properly.", IndexException);
113  }
114 
115  template <class Functor>
116  Functor for_each(Functor f) {
118  // use boost range instead
119  return std::for_each(vs.begin(), vs.end(), f);
120  }
121 
122 #endif
123 #endif
124 
125  protected:
126  PairContainer(Model *m,
127  std::string name = "PairContainer %1%");
128  PairContainer() {}
129 
130  virtual void do_apply(const PairModifier *sm) const = 0;
131  virtual void do_apply_moved(const PairModifier *sm,
132  const ParticleIndexes &moved_pis,
133  const ParticleIndexes &reset_pis) const {
134  IMP_UNUSED(moved_pis);
135  IMP_UNUSED(reset_pis);
136  do_apply(sm);
137  }
138  virtual bool do_get_provides_access() const { return false; }
139 
140 #if !defined(SWIG) && !defined(IMP_DOXYGEN)
141  //! Insert the contents of the container into output
142  //! Could be reimplemented to save time in terms of e.g. memory
143  //! allocation compared with calling get_indexes()
144  virtual void get_indexes_in_place(ParticleIndexPairs& output) const{
145  output= get_indexes();
146  }
147 #endif
148 
150 
151  private:
152  mutable std::size_t contents_hash_;
153  mutable ParticleIndexPairs contents_cache_;
154  mutable bool cache_initialized_;
155 
156  friend class cereal::access;
157 
158  template<class Archive> void serialize(Archive &ar) {
159  ar(cereal::base_class<Container>(this));
160  // clear cache on read
161  if (std::is_base_of<cereal::detail::InputArchiveBase, Archive>::value) {
162  contents_hash_ = -1;
163  cache_initialized_ = false;
164  }
165  }
166 
167 };
168 
169 /** This class allows either a list or a container to be
170  accepted as input.
171 */
172 class IMPKERNELEXPORT PairContainerAdaptor :
173 #if !defined(SWIG) && !defined(IMP_DOXYGEN)
174  public Pointer<PairContainer>
175 #else
176  public InputAdaptor
177 #endif
178  {
179  typedef Pointer<PairContainer> P;
180 
181  public:
183 
184  /**
185  Constructs the adaptor pointing to c (so if the contents of c are changed
186  dynamically, so do the contents of the adaptor, and vice versa)
187  */
189 
190  /**
191  Constructs the adaptor pointing to c (so if the contents of c are changed
192  dynamically, so do the contents of the adaptor, and vice versa)
193  */
194  template <class C>
195  PairContainerAdaptor(IMP::internal::PointerBase<C> c)
196  : P(c) {}
197 
198  /**
199  Adapts the non-empty list t to PairContainer
200 
201  @param t a non-empty list of ParticlePairsTemp
202  */
204 
205  /** Set the name of the resulting container if it is currently the
206  default value. */
207  void set_name_if_default(std::string name);
208 };
209 
210 IMPKERNEL_END_NAMESPACE
211 
212 #endif /* IMPKERNEL_PAIR_CONTAINER_H */
A shared container for Pairs.
Definition: PairContainer.h:39
Control display of deprecation information.
Macros to help with reference counting.
Basic types used by IMP.
A class to store a fixed array of same-typed values.
Definition: Array.h:40
Class for adding derivatives from restraints to the model.
std::size_t get_contents_hash() const
A smart pointer to a reference counted object.
Definition: Pointer.h:87
A base class for modifiers of ParticlePairsTemp.
Definition: PairModifier.h:32
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
Convenience class to accept multiple input types.
#define IMP_UNUSED(variable)
Various general useful macros for IMP.
An exception for a request for an invalid member of a container.
Definition: exception.h:156
Classes to handle individual model particles. (Note that implementation of inline functions is in int...
Abstract base class for containers of particles.
#define IMP_THROW(message, exception_name)
Throw an exception with a message.
Definition: check_macros.h:50
A nullptr-initialized pointer to an IMP Object.
Helper macros for throwing and handling exceptions.
#define IMP_REF_COUNTED_NONTRIVIAL_DESTRUCTOR(Name)
Convenience class to accept multiple input types.
Definition: InputAdaptor.h:25
ParticleIndexes get_indexes(const ParticlesTemp &ps)
Get the indexes from a list of particles.
Abstract class for containers of particles.
PairContainerAdaptor(IMP::internal::PointerBase< C > c)