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IMP Reference Guide  2.11.1
The Integrative Modeling Platform
assignment_tables.h
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1 /**
2  * \file IMP/domino/assignment_tables.h
3  * \brief A Bayesian inference-based sampler.
4  *
5  * Copyright 2007-2019 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPDOMINO_ASSIGNMENT_TABLES_H
10 #define IMPDOMINO_ASSIGNMENT_TABLES_H
11 
12 #include "particle_states.h"
13 #include "subset_filters.h"
14 #include "Assignment.h"
15 #include "Subset.h"
16 #include <IMP/domino/domino_config.h>
17 #include "assignment_containers.h"
18 #include "domino_macros.h"
19 #include <IMP/Sampler.h>
20 #include <IMP/macros.h>
21 #include <boost/unordered_map.hpp>
22 #include <boost/pending/disjoint_sets.hpp>
23 #if BOOST_VERSION > 103900
24 #include <boost/property_map/property_map.hpp>
25 #else
26 #include <boost/property_map.hpp>
27 #endif
28 
29 IMPDOMINO_BEGIN_NAMESPACE
30 class DominoSampler;
31 
32 /** The base class for classes that create Assignments, one per
33  subset. The main method of interest is load_assignments()
34  which enumerates the assignments and loads them into an AssignmentContainer.
35 */
36 class IMPDOMINOEXPORT AssignmentsTable : public IMP::Object {
37  public:
38  AssignmentsTable(std::string name = "AssignmentsTable %1%") : Object(name) {}
39  virtual void load_assignments(const Subset &s,
40  AssignmentContainer *ac) const = 0;
42 };
43 
45 
46 /** The produced states are filtered using the provided
47  SubsetFilterTable objects. The assignments are enumerated
48  and filtered in a straight forward manner.
49 */
50 class IMPDOMINOEXPORT SimpleAssignmentsTable : public AssignmentsTable {
52  SubsetFilterTables sft_;
53  unsigned int max_;
54 
55  public:
58  unsigned int max =
59  std::numeric_limits<unsigned int>::max());
60  virtual void load_assignments(const IMP::domino::Subset &s,
63 };
64 
65 /** The produced states are filtered using the provided
66  SubsetFilterTable objects. The assignments are enumerated
67  and filtered by recursively dividing the subset in half.
68 */
69 class IMPDOMINOEXPORT RecursiveAssignmentsTable : public AssignmentsTable {
71  SubsetFilterTables sft_;
72  unsigned int max_;
73 
74  public:
76  const SubsetFilterTables &sft =
78  unsigned int max =
79  std::numeric_limits<unsigned int>::max());
80  virtual void load_assignments(const IMP::domino::Subset &s,
83 };
84 
85 /** Enumerate states based on provided ParticleStates
86  objects.
87 
88  The produced states are filtered using the provided
89  SubsetFilterTable objects. Branch and bound is used
90  to try to make this process more efficient. To do that
91  the SubsetFilterTable::get_strength() method is used
92  to order the particles from most restricted to least
93  restricted.
94 */
95 class IMPDOMINOEXPORT BranchAndBoundAssignmentsTable : public AssignmentsTable {
96 #if !defined(SWIG) && !defined(IMP_DOXYGEN)
97  /* MSVC/Sun gcc appears confused by a friend class in the anonymous namespace
98  */
99  public:
101  SubsetFilterTables sft_;
102  unsigned int max_;
103 #if IMP_HAS_CHECKS >= IMP_INTERNAL
104  boost::unordered_map<Particle *, ParticlesTemp> rls_;
105 #endif
106 #endif
107  public:
109  const SubsetFilterTables &sft =
111  unsigned int max =
112  std::numeric_limits<unsigned int>::max());
113  virtual void load_assignments(const IMP::domino::Subset &s,
116 };
117 
118 /** Store a map of Assignments objects and return them on demand. This table
119  should be used when each subset is sampled using some other protocol
120  (eg Monte Carlo or molecular dynamics) and those states are then fed
121  in to domino.
122 */
123 class IMPDOMINOEXPORT ListAssignmentsTable : public AssignmentsTable {
124  boost::unordered_map<Subset, IMP::PointerMember<AssignmentContainer> >
125  states_;
126 
127  public:
128  ListAssignmentsTable(std::string name = "ListAssignmentsTable %1%");
129  /** There must not be any duplicates in the list */
131  states_[s] = lsc;
132  }
133  virtual void load_assignments(const IMP::domino::Subset &s,
136 };
137 
138 /** Return the order computed for the particles in the subset to be used for
139  enumeration. This function is there in order to expose internal
140  functionality for easier testing and should not be depended upon.
141 */
142 IMPDOMINOEXPORT ParticlesTemp get_order(const Subset &s,
143  const SubsetFilterTables &sft);
144 
145 IMPDOMINO_END_NAMESPACE
146 
147 #endif /* IMPDOMINO_ASSIGNMENT_TABLES_H */
The base class for containers of assignments.
A Bayesian inference-based sampler.
void set_assignments(const Subset &s, AssignmentContainer *lsc)
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition: object_macros.h:25
A Bayesian inference-based sampler.
Represent a subset of the particles being optimized.
Definition: Subset.h:33
Various general useful macros for IMP.
A more IMP-like version of the std::vector.
Definition: Vector.h:39
A smart pointer to a reference counted object.
Definition: Pointer.h:87
Common base class for heavy weight IMP objects.
Definition: Object.h:106
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
Base class for all samplers.
Various important macros for implementing decorators.
IMP::Vector< IMP::Pointer< SubsetFilterTable > > SubsetFilterTables
A Bayesian inference-based sampler.
#define IMP_OBJECTS(Name, PluralName)
Define the types for storing lists of object pointers.
Definition: object_macros.h:44
Object(std::string name)
Construct an object with the given name.
Container classes to store assignments.
A Bayesian inference-based sampler.
#define IMP_OVERRIDE
Cause a compile error if this method does not override a parent method.