IMP  2.3.1
The Integrative Modeling Platform
kernel/doxygen.h
Go to the documentation of this file.
1 /**
2  * \file IMP/kernel/doxygen.h
3  * \brief Import kernel classes into the IMP scope in docs.
4  *
5  * Copyright 2007-2014 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPKERNEL_DOXYGEN_H
10 #define IMPKERNEL_DOXYGEN_H
11 
12 #include <IMP/kernel.h>
13 
14 #ifdef IMP_DOXYGEN
15 namespace IMP {
16 
17 /** Import IMP::kernel::CommandDispatcher
18  in the IMP namespace.*/
20 /** Import IMP::kernel::Configuration
21  in the IMP namespace.*/
23 /** Import IMP::kernel::ConfigurationSet
24  in the IMP namespace.*/
26 /** Import IMP::kernel::Constraint
27  in the IMP namespace.*/
29 /** Import IMP::kernel::Container
30  in the IMP namespace.*/
32 /** Import IMP::kernel::Decorator
33  in the IMP namespace.*/
35 /** Import IMP::kernel::DependencyGraph
36  in the IMP namespace.*/
38 /** Import IMP::kernel::DerivativeAccumulator
39  in the IMP namespace.*/
41 /** Import IMP::kernel::EvaluationState
42  in the IMP namespace.*/
44 /** Import IMP::kernel::EvaluationStates
45  in the IMP namespace.*/
47 /** Import IMP::kernel::FloatIndex
48  in the IMP namespace.*/
50 /** Import IMP::kernel::FloatIndexes
51  in the IMP namespace.*/
53 /** Import IMP::kernel::FloatKey
54  in the IMP namespace.*/
56 /** Import IMP::kernel::FloatKeys
57  in the IMP namespace.*/
59 /** Import IMP::kernel::IntKey
60  in the IMP namespace.*/
62 /** Import IMP::kernel::IntKeys
63  in the IMP namespace.*/
65 /** Import IMP::kernel::Model
66  in the IMP namespace.*/
68 /** Import IMP::kernel::ModelObject
69  in the IMP namespace.*/
71 /** Import IMP::kernel::ObjectKey
72  in the IMP namespace.*/
74 /** Import IMP::kernel::ObjectKeys
75  in the IMP namespace.*/
77 /** Import IMP::kernel::Optimizer
78  in the IMP namespace.*/
80 /** Import IMP::kernel::OptimizerState
81  in the IMP namespace.*/
83 /** Import IMP::kernel::OptionParser
84  in the IMP namespace.*/
86 /** Import IMP::kernel::PairContainer
87  in the IMP namespace.*/
89 /** Import IMP::kernel::PairModifier
90  in the IMP namespace.*/
92 /** Import IMP::kernel::PairPredicate
93  in the IMP namespace.*/
95 /** Import IMP::kernel::PairScore
96  in the IMP namespace.*/
98 /** Import IMP::kernel::Particle
99  in the IMP namespace.*/
101 /** Import IMP::kernel::ParticleIndex
102  in the IMP namespace.*/
104 /** Import IMP::kernel::ParticleIndexKey
105  in the IMP namespace.*/
107 /** Import IMP::kernel::ParticleIndexKeys
108  in the IMP namespace.*/
110 /** Import IMP::kernel::ParticleIndexPairs
111  in the IMP namespace.*/
113 /** Import IMP::kernel::ParticleIndexQuads
114  in the IMP namespace.*/
116 /** Import IMP::kernel::ParticleIndexTriplets
117  in the IMP namespace.*/
119 /** Import IMP::kernel::ParticleIndexes
120  in the IMP namespace.*/
122 /** Import IMP::kernel::ParticleIndexesKey
123  in the IMP namespace.*/
125 /** Import IMP::kernel::ParticleIndexesKeys
126  in the IMP namespace.*/
128 /** Import IMP::kernel::ParticlePair
129  in the IMP namespace.*/
131 /** Import IMP::kernel::ParticlePairsTemp
132  in the IMP namespace.*/
134 /** Import IMP::kernel::ParticleQuad
135  in the IMP namespace.*/
137 /** Import IMP::kernel::ParticleQuadsTemp
138  in the IMP namespace.*/
140 /** Import IMP::kernel::ParticleTriplet
141  in the IMP namespace.*/
143 /** Import IMP::kernel::ParticleTripletsTemp
144  in the IMP namespace.*/
146 /** Import IMP::kernel::PythonRestraint
147  in the IMP namespace.*/
149 /** Import IMP::kernel::PythonScoreState
150  in the IMP namespace.*/
152 /** Import IMP::kernel::QuadContainer
153  in the IMP namespace.*/
155 /** Import IMP::kernel::QuadModifier
156  in the IMP namespace.*/
158 /** Import IMP::kernel::QuadPredicate
159  in the IMP namespace.*/
161 /** Import IMP::kernel::QuadScore
162  in the IMP namespace.*/
164 /** Import IMP::kernel::Refiner
165  in the IMP namespace.*/
167 /** Import IMP::kernel::Restraint
168  in the IMP namespace.*/
170 /** Import IMP::kernel::RestraintBase
171  in the IMP namespace.*/
173 /** Import IMP::kernel::RestraintSet
174  in the IMP namespace.*/
176 /** Import IMP::kernel::RestraintStatistics
177  in the IMP namespace.*/
179 /** Import IMP::kernel::RestraintStatisticsList
180  in the IMP namespace.*/
182 /** Import IMP::kernel::Sampler
183  in the IMP namespace.*/
185 /** Import IMP::kernel::SaveToConfigurationSetOptimizerState
186  in the IMP namespace.*/
189 /** Import IMP::kernel::ScopedRemoveRestraint
190  in the IMP namespace.*/
192 /** Import IMP::kernel::ScopedRemoveScoreState
193  in the IMP namespace.*/
195 /** Import IMP::kernel::ScopedRestraint
196  in the IMP namespace.*/
198 /** Import IMP::kernel::ScopedScoreState
199  in the IMP namespace.*/
201 /** Import IMP::kernel::ScopedSetFloatAttribute
202  in the IMP namespace.*/
204 /** Import IMP::kernel::ScoreAccumulator
205  in the IMP namespace.*/
207 /** Import IMP::kernel::ScoreAccumulators
208  in the IMP namespace.*/
210 /** Import IMP::kernel::ScoreState
211  in the IMP namespace.*/
213 /** Import IMP::kernel::ScoreStateBase
214  in the IMP namespace.*/
216 /** Import IMP::kernel::ScoringFunction
217  in the IMP namespace.*/
219 /** Import IMP::kernel::SingletonContainer
220  in the IMP namespace.*/
222 /** Import IMP::kernel::SingletonModifier
223  in the IMP namespace.*/
225 /** Import IMP::kernel::SingletonPredicate
226  in the IMP namespace.*/
228 /** Import IMP::kernel::SingletonScore
229  in the IMP namespace.*/
231 /** Import IMP::kernel::StringKey
232  in the IMP namespace.*/
234 /** Import IMP::kernel::StringKeys
235  in the IMP namespace.*/
237 /** Import IMP::kernel::TripletContainer
238  in the IMP namespace.*/
240 /** Import IMP::kernel::TripletModifier
241  in the IMP namespace.*/
243 /** Import IMP::kernel::TripletPredicate
244  in the IMP namespace.*/
246 /** Import IMP::kernel::TripletScore
247  in the IMP namespace.*/
249 /** Import IMP::kernel::UnaryFunction
250  in the IMP namespace.*/
252 /** Import IMP::kernel::build
253  in the IMP namespace.*/
254 using IMP::kernel::build;
255 /** Import IMP::kernel::check_particle
256  in the IMP namespace.*/
257 using IMP::kernel::check_particle;
258 /** Import IMP::kernel::create_decomposition
259  in the IMP namespace.*/
261 /** Import IMP::kernel::get_dependency_graph
262  in the IMP namespace.*/
264 /** Import IMP::kernel::get_dependent_particles
265  in the IMP namespace.*/
267 /** Import IMP::kernel::get_dependent_restraints
268  in the IMP namespace.*/
270 /** Import IMP::kernel::get_dependent_score_states
271  in the IMP namespace.*/
273 /** Import IMP::kernel::get_indexes
274  in the IMP namespace.*/
276 /** Import IMP::kernel::get_input_containers
277  in the IMP namespace.*/
279 /** Import IMP::kernel::get_input_particles
280  in the IMP namespace.*/
282 /** Import IMP::kernel::get_output_containers
283  in the IMP namespace.*/
285 /** Import IMP::kernel::get_output_particles
286  in the IMP namespace.*/
288 /** Import IMP::kernel::get_particle
289  in the IMP namespace.*/
290 using IMP::kernel::get_particle;
291 /** Import IMP::kernel::get_particles
292  in the IMP namespace.*/
294 /** Import IMP::kernel::get_pruned_dependency_graph
295  in the IMP namespace.*/
297 /** Import IMP::kernel::get_required_score_states
298  in the IMP namespace.*/
300 /** Import IMP::kernel::get_restraints
301  in the IMP namespace.*/
302 using IMP::kernel::get_restraints;
303 /** Import IMP::kernel::get_update_order
304  in the IMP namespace.*/
306 /** Import IMP::kernel::get_vertex_index
307  in the IMP namespace.*/
308 using IMP::kernel::get_vertex_index;
309 /** Import IMP::kernel::has_boost_filesystem
310  in the IMP namespace.*/
311 using IMP::kernel::has_boost_filesystem;
312 /** Import IMP::kernel::read_particles_from_buffer
313  in the IMP namespace.*/
315 /** Import IMP::kernel::set_score_state_update_order
316  in the IMP namespace.*/
317 using IMP::kernel::set_score_state_update_order;
318 /** Import IMP::kernel::show_restraint_hierarchy
319  in the IMP namespace.*/
321 /** Import IMP::kernel::write_particles_to_buffer
322  in the IMP namespace.*/
324 } // namespace
325 
326 /** \namespace IMP
327 
328  \brief Synonym for IMP::kernel
329 
330  All \imp code is in the \imp namespace. For convenience and backwards
331  compatibility, the contents of IMP::kernel are hoisted into the \imp
332  namespace itself, in addition to being in the IMP::kernel namespace.
333  For now you should use the IMP namespace versions of the names.
334 */
335 
336 #endif // doxygen
337 #endif /* IMPKERNEL_DOXYGEN_H */
IMP::kernel::EvaluationStates EvaluationStates
Restraints create_decomposition(const RestraintsTemp &rs)
Return the decomposition of a list of restraints.
IMP::kernel::PairModifier PairModifier
A class to store a set of configurations of a model.
ParticleIndexes get_indexes(const ParticlesTemp &ps)
A base class for Keys.
Definition: kernel/Key.h:46
IMP::kernel::ModelObject ModelObject
A shared container for Triplets.
boost::graph DependencyGraph
A directed graph on the interactions between the various objects in the model.
Abstract class for scoring object(s) of type ParticleQuad.
Class for adding derivatives from restraints to the model.
IMP-specific subclass of optparse.OptionParser.
IMP::kernel::ParticleIndexTriplets ParticleIndexTriplets
A base class for modifiers of kernel::ParticleTripletsTemp.
A shared container for Quads.
IMP::kernel::ScoreState ScoreState
ParticlesTemp get_output_particles(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
ScoreStatesTemp get_dependent_score_states(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
IMP::kernel::PairScore PairScore
IMP::kernel::ObjectKey ObjectKey
IMP::kernel::StringKey StringKey
IMP::kernel::CommandDispatcher CommandDispatcher
void show_restraint_hierarchy(ScoringFunctionAdaptor rs, std::ostream &out=std::cout)
Print the hierarchy of restraints.
IMP::kernel::DerivativeAccumulator DerivativeAccumulator
Include all non-deprecated headers in IMP.kernel.
IMP::kernel::ParticleTriplet ParticleTriplet
IMP::kernel::ParticleIndexes ParticleIndexes
IMP::kernel::SingletonContainer SingletonContainer
IMP::kernel::EvaluationState EvaluationState
IMP::kernel::ScopedSetFloatAttribute ScopedSetFloatAttribute
IMP::kernel::Constraint Constraint
IMP::kernel::TripletContainer TripletContainer
IMP::kernel::QuadContainer QuadContainer
Shared optimizer state that is invoked upon commitment of new coordinates.
IMP::kernel::UnaryFunction UnaryFunction
ParticlesTemp get_particles(kernel::Model *m, const ParticleIndexes &ps)
Object used to hold a set of restraints.
IMP::kernel::ParticleIndexPairs ParticleIndexPairs
IMP::kernel::ScoringFunction ScoringFunction
IMP::kernel::StringKeys StringKeys
IMP::kernel::ParticleIndexKey ParticleIndexKey
ContainersTemp get_output_containers(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
IMP::kernel::FloatKeys FloatKeys
IMP::kernel::SingletonPredicate SingletonPredicate
Abstract predicate function.
A shared container for Pairs.
DependencyGraph get_pruned_dependency_graph(kernel::Model *m)
IMP::kernel::QuadScore QuadScore
IMP::kernel::Optimizer Optimizer
ParticlesTemp get_input_particles(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
ParticlesTemp get_dependent_particles(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
IMP::kernel::ParticlePair ParticlePair
IMP::kernel::TripletModifier TripletModifier
IMP::kernel::ScopedRemoveRestraint ScopedRemoveRestraint
IMP::kernel::ObjectKeys ObjectKeys
Represents a scoring function on the model.
IMP::kernel::ParticleQuadsTemp ParticleQuadsTemp
Abstract single variable functor class for score functions.
ScoreStates maintain invariants in the Model.
IMP::kernel::PythonScoreState PythonScoreState
IMP::kernel::ParticleIndexQuads ParticleIndexQuads
IMP::kernel::QuadModifier QuadModifier
IMP::kernel::PythonRestraint PythonRestraint
DependencyGraph get_dependency_graph(kernel::Model *m)
A base class for modifiers of kernel::ParticlesTemp.
Abstract predicate function.
A class to store an fixed array of same-typed values.
Definition: Array.h:33
Abstract class for scoring object(s) of type ParticlePair.
IMP::kernel::Container Container
IMP::kernel::SingletonModifier SingletonModifier
RestraintsTemp get_dependent_restraints(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
void read_particles_from_buffer(const base::Vector< char > &buffer, const ParticlesTemp &particles, const FloatKeys &keys)
load found attributes into the particles
Abstract class for containers of particles.
ContainersTemp get_input_containers(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
IMP::kernel::ScopedRemoveScoreState ScopedRemoveScoreState
IMP::kernel::ParticlePairsTemp ParticlePairsTemp
IMP::kernel::SaveToConfigurationSetOptimizerState SaveToConfigurationSetOptimizerState
base::Vector< char > write_particles_to_buffer(const ParticlesTemp &particles, const FloatKeys &keys)
return a binary buffer with the data
IMP::kernel::Refiner Refiner
IMP::kernel::ScoreAccumulator ScoreAccumulator
IMP::kernel::ScoreStateBase ScoreStateBase
IMP::kernel::Model Model
Class for adding up scores during ScoringFunction evaluation.
A restraint is a term in an IMP ScoringFunction.
IMP::kernel::IntKeys IntKeys
IMP::kernel::QuadPredicate QuadPredicate
IMP::kernel::FloatKey FloatKey
Abstract predicate function.
Class to handle individual model particles.
IMP::kernel::TripletScore TripletScore
IMP::kernel::DependencyGraph DependencyGraph
IMP::kernel::OptionParser OptionParser
A class to store a configuration of a model.
Base class for all optimizers.
Abstract predicate function.
IMP::kernel::Sampler Sampler
IMP::kernel::ParticleIndexKeys ParticleIndexKeys
IMP::kernel::ParticleIndexesKeys ParticleIndexesKeys
Allow applications to easily implement commmands.
IMP::kernel::RestraintStatistics RestraintStatistics
IMP::kernel::Particle Particle
IMP::kernel::PairPredicate PairPredicate
IMP::kernel::ParticleIndexesKey ParticleIndexesKey
Abstract class for scoring object(s) of type Particle.
Base class for all samplers.
IMP::kernel::ParticleQuad ParticleQuad
IMP::kernel::ConfigurationSet ConfigurationSet
IMP::kernel::PairContainer PairContainer
IMP::kernel::ParticleTripletsTemp ParticleTripletsTemp
IMP::kernel::OptimizerState OptimizerState
Implement a constraint on the Model.
IMP::kernel::TripletPredicate TripletPredicate
IMP::kernel::ScopedRestraint ScopedRestraint
IMP::kernel::Decorator Decorator
IMP::kernel::SingletonScore SingletonScore
IMP::kernel::Restraint Restraint
IMP::kernel::ScoreAccumulators ScoreAccumulators
Abstract class to implement hierarchical methods.
IMP::kernel::RestraintStatisticsList RestraintStatisticsList
IMP::kernel::RestraintSet RestraintSet
A base class for modifiers of kernel::ParticleQuadsTemp.
IMP::kernel::ParticleIndex ParticleIndex
IMP::kernel::FloatIndex FloatIndex
Abstract class for scoring object(s) of type ParticleTriplet.
IMP::kernel::ScopedScoreState ScopedScoreState
ScoreStatesTemp get_required_score_states(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
A shared container for Singletons.
IMP::kernel::Configuration Configuration
ScoreStatesTemp get_update_order(ScoreStatesTemp input)
A base class for modifiers of kernel::ParticlePairsTemp.
IMP::kernel::IntKey IntKey
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73
IMP::kernel::RestraintBase RestraintBase
IMP::kernel::FloatIndexes FloatIndexes