IMP  2.3.0
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.*/
19 typedef IMP::kernel::CommandDispatcher CommandDispatcher;
20 /** Import IMP::kernel::Configuration
21  in the IMP namespace.*/
22 typedef IMP::kernel::Configuration Configuration;
23 /** Import IMP::kernel::ConfigurationSet
24  in the IMP namespace.*/
25 typedef IMP::kernel::ConfigurationSet ConfigurationSet;
26 /** Import IMP::kernel::Constraint
27  in the IMP namespace.*/
28 typedef IMP::kernel::Constraint Constraint;
29 /** Import IMP::kernel::Container
30  in the IMP namespace.*/
31 typedef IMP::kernel::Container Container;
32 /** Import IMP::kernel::Decorator
33  in the IMP namespace.*/
34 typedef IMP::kernel::Decorator Decorator;
35 /** Import IMP::kernel::DependencyGraph
36  in the IMP namespace.*/
37 typedef IMP::kernel::DependencyGraph DependencyGraph;
38 /** Import IMP::kernel::DerivativeAccumulator
39  in the IMP namespace.*/
40 typedef IMP::kernel::DerivativeAccumulator DerivativeAccumulator;
41 /** Import IMP::kernel::EvaluationState
42  in the IMP namespace.*/
43 typedef IMP::kernel::EvaluationState EvaluationState;
44 /** Import IMP::kernel::EvaluationStates
45  in the IMP namespace.*/
46 typedef IMP::kernel::EvaluationStates EvaluationStates;
47 /** Import IMP::kernel::FloatIndex
48  in the IMP namespace.*/
49 typedef IMP::kernel::FloatIndex FloatIndex;
50 /** Import IMP::kernel::FloatIndexes
51  in the IMP namespace.*/
52 typedef IMP::kernel::FloatIndexes FloatIndexes;
53 /** Import IMP::kernel::FloatKey
54  in the IMP namespace.*/
55 typedef IMP::kernel::FloatKey FloatKey;
56 /** Import IMP::kernel::FloatKeys
57  in the IMP namespace.*/
58 typedef IMP::kernel::FloatKeys FloatKeys;
59 /** Import IMP::kernel::IntKey
60  in the IMP namespace.*/
61 typedef IMP::kernel::IntKey IntKey;
62 /** Import IMP::kernel::IntKeys
63  in the IMP namespace.*/
64 typedef IMP::kernel::IntKeys IntKeys;
65 /** Import IMP::kernel::Model
66  in the IMP namespace.*/
67 typedef IMP::kernel::Model Model;
68 /** Import IMP::kernel::ModelObject
69  in the IMP namespace.*/
70 typedef IMP::kernel::ModelObject ModelObject;
71 /** Import IMP::kernel::ObjectKey
72  in the IMP namespace.*/
73 typedef IMP::kernel::ObjectKey ObjectKey;
74 /** Import IMP::kernel::ObjectKeys
75  in the IMP namespace.*/
76 typedef IMP::kernel::ObjectKeys ObjectKeys;
77 /** Import IMP::kernel::Optimizer
78  in the IMP namespace.*/
79 typedef IMP::kernel::Optimizer Optimizer;
80 /** Import IMP::kernel::OptimizerState
81  in the IMP namespace.*/
82 typedef IMP::kernel::OptimizerState OptimizerState;
83 /** Import IMP::kernel::OptionParser
84  in the IMP namespace.*/
85 typedef IMP::kernel::OptionParser OptionParser;
86 /** Import IMP::kernel::PairContainer
87  in the IMP namespace.*/
88 typedef IMP::kernel::PairContainer PairContainer;
89 /** Import IMP::kernel::PairModifier
90  in the IMP namespace.*/
91 typedef IMP::kernel::PairModifier PairModifier;
92 /** Import IMP::kernel::PairPredicate
93  in the IMP namespace.*/
94 typedef IMP::kernel::PairPredicate PairPredicate;
95 /** Import IMP::kernel::PairScore
96  in the IMP namespace.*/
97 typedef IMP::kernel::PairScore PairScore;
98 /** Import IMP::kernel::Particle
99  in the IMP namespace.*/
100 typedef IMP::kernel::Particle Particle;
101 /** Import IMP::kernel::ParticleIndex
102  in the IMP namespace.*/
103 typedef IMP::kernel::ParticleIndex ParticleIndex;
104 /** Import IMP::kernel::ParticleIndexKey
105  in the IMP namespace.*/
106 typedef IMP::kernel::ParticleIndexKey ParticleIndexKey;
107 /** Import IMP::kernel::ParticleIndexKeys
108  in the IMP namespace.*/
109 typedef IMP::kernel::ParticleIndexKeys ParticleIndexKeys;
110 /** Import IMP::kernel::ParticleIndexPairs
111  in the IMP namespace.*/
112 typedef IMP::kernel::ParticleIndexPairs ParticleIndexPairs;
113 /** Import IMP::kernel::ParticleIndexQuads
114  in the IMP namespace.*/
115 typedef IMP::kernel::ParticleIndexQuads ParticleIndexQuads;
116 /** Import IMP::kernel::ParticleIndexTriplets
117  in the IMP namespace.*/
118 typedef IMP::kernel::ParticleIndexTriplets ParticleIndexTriplets;
119 /** Import IMP::kernel::ParticleIndexes
120  in the IMP namespace.*/
121 typedef IMP::kernel::ParticleIndexes ParticleIndexes;
122 /** Import IMP::kernel::ParticleIndexesKey
123  in the IMP namespace.*/
124 typedef IMP::kernel::ParticleIndexesKey ParticleIndexesKey;
125 /** Import IMP::kernel::ParticleIndexesKeys
126  in the IMP namespace.*/
127 typedef IMP::kernel::ParticleIndexesKeys ParticleIndexesKeys;
128 /** Import IMP::kernel::ParticlePair
129  in the IMP namespace.*/
130 typedef IMP::kernel::ParticlePair ParticlePair;
131 /** Import IMP::kernel::ParticlePairsTemp
132  in the IMP namespace.*/
133 typedef IMP::kernel::ParticlePairsTemp ParticlePairsTemp;
134 /** Import IMP::kernel::ParticleQuad
135  in the IMP namespace.*/
136 typedef IMP::kernel::ParticleQuad ParticleQuad;
137 /** Import IMP::kernel::ParticleQuadsTemp
138  in the IMP namespace.*/
139 typedef IMP::kernel::ParticleQuadsTemp ParticleQuadsTemp;
140 /** Import IMP::kernel::ParticleTriplet
141  in the IMP namespace.*/
142 typedef IMP::kernel::ParticleTriplet ParticleTriplet;
143 /** Import IMP::kernel::ParticleTripletsTemp
144  in the IMP namespace.*/
145 typedef IMP::kernel::ParticleTripletsTemp ParticleTripletsTemp;
146 /** Import IMP::kernel::PythonRestraint
147  in the IMP namespace.*/
148 typedef IMP::kernel::PythonRestraint PythonRestraint;
149 /** Import IMP::kernel::PythonScoreState
150  in the IMP namespace.*/
151 typedef IMP::kernel::PythonScoreState PythonScoreState;
152 /** Import IMP::kernel::QuadContainer
153  in the IMP namespace.*/
154 typedef IMP::kernel::QuadContainer QuadContainer;
155 /** Import IMP::kernel::QuadModifier
156  in the IMP namespace.*/
157 typedef IMP::kernel::QuadModifier QuadModifier;
158 /** Import IMP::kernel::QuadPredicate
159  in the IMP namespace.*/
160 typedef IMP::kernel::QuadPredicate QuadPredicate;
161 /** Import IMP::kernel::QuadScore
162  in the IMP namespace.*/
163 typedef IMP::kernel::QuadScore QuadScore;
164 /** Import IMP::kernel::Refiner
165  in the IMP namespace.*/
166 typedef IMP::kernel::Refiner Refiner;
167 /** Import IMP::kernel::Restraint
168  in the IMP namespace.*/
169 typedef IMP::kernel::Restraint Restraint;
170 /** Import IMP::kernel::RestraintBase
171  in the IMP namespace.*/
172 typedef IMP::kernel::RestraintBase RestraintBase;
173 /** Import IMP::kernel::RestraintSet
174  in the IMP namespace.*/
175 typedef IMP::kernel::RestraintSet RestraintSet;
176 /** Import IMP::kernel::RestraintStatistics
177  in the IMP namespace.*/
178 typedef IMP::kernel::RestraintStatistics RestraintStatistics;
179 /** Import IMP::kernel::RestraintStatisticsList
180  in the IMP namespace.*/
181 typedef IMP::kernel::RestraintStatisticsList RestraintStatisticsList;
182 /** Import IMP::kernel::Sampler
183  in the IMP namespace.*/
184 typedef IMP::kernel::Sampler Sampler;
185 /** Import IMP::kernel::SaveToConfigurationSetOptimizerState
186  in the IMP namespace.*/
187 typedef IMP::kernel::SaveToConfigurationSetOptimizerState
188  SaveToConfigurationSetOptimizerState;
189 /** Import IMP::kernel::ScopedRemoveRestraint
190  in the IMP namespace.*/
191 typedef IMP::kernel::ScopedRemoveRestraint ScopedRemoveRestraint;
192 /** Import IMP::kernel::ScopedRemoveScoreState
193  in the IMP namespace.*/
194 typedef IMP::kernel::ScopedRemoveScoreState ScopedRemoveScoreState;
195 /** Import IMP::kernel::ScopedRestraint
196  in the IMP namespace.*/
197 typedef IMP::kernel::ScopedRestraint ScopedRestraint;
198 /** Import IMP::kernel::ScopedScoreState
199  in the IMP namespace.*/
200 typedef IMP::kernel::ScopedScoreState ScopedScoreState;
201 /** Import IMP::kernel::ScopedSetFloatAttribute
202  in the IMP namespace.*/
203 typedef IMP::kernel::ScopedSetFloatAttribute ScopedSetFloatAttribute;
204 /** Import IMP::kernel::ScoreAccumulator
205  in the IMP namespace.*/
206 typedef IMP::kernel::ScoreAccumulator ScoreAccumulator;
207 /** Import IMP::kernel::ScoreAccumulators
208  in the IMP namespace.*/
209 typedef IMP::kernel::ScoreAccumulators ScoreAccumulators;
210 /** Import IMP::kernel::ScoreState
211  in the IMP namespace.*/
212 typedef IMP::kernel::ScoreState ScoreState;
213 /** Import IMP::kernel::ScoreStateBase
214  in the IMP namespace.*/
215 typedef IMP::kernel::ScoreStateBase ScoreStateBase;
216 /** Import IMP::kernel::ScoringFunction
217  in the IMP namespace.*/
218 typedef IMP::kernel::ScoringFunction ScoringFunction;
219 /** Import IMP::kernel::SingletonContainer
220  in the IMP namespace.*/
221 typedef IMP::kernel::SingletonContainer SingletonContainer;
222 /** Import IMP::kernel::SingletonModifier
223  in the IMP namespace.*/
224 typedef IMP::kernel::SingletonModifier SingletonModifier;
225 /** Import IMP::kernel::SingletonPredicate
226  in the IMP namespace.*/
227 typedef IMP::kernel::SingletonPredicate SingletonPredicate;
228 /** Import IMP::kernel::SingletonScore
229  in the IMP namespace.*/
230 typedef IMP::kernel::SingletonScore SingletonScore;
231 /** Import IMP::kernel::StringKey
232  in the IMP namespace.*/
233 typedef IMP::kernel::StringKey StringKey;
234 /** Import IMP::kernel::StringKeys
235  in the IMP namespace.*/
236 typedef IMP::kernel::StringKeys StringKeys;
237 /** Import IMP::kernel::TripletContainer
238  in the IMP namespace.*/
239 typedef IMP::kernel::TripletContainer TripletContainer;
240 /** Import IMP::kernel::TripletModifier
241  in the IMP namespace.*/
242 typedef IMP::kernel::TripletModifier TripletModifier;
243 /** Import IMP::kernel::TripletPredicate
244  in the IMP namespace.*/
245 typedef IMP::kernel::TripletPredicate TripletPredicate;
246 /** Import IMP::kernel::TripletScore
247  in the IMP namespace.*/
248 typedef IMP::kernel::TripletScore TripletScore;
249 /** Import IMP::kernel::UnaryFunction
250  in the IMP namespace.*/
251 typedef IMP::kernel::UnaryFunction UnaryFunction;
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.*/
260 using IMP::kernel::create_decomposition;
261 /** Import IMP::kernel::get_dependency_graph
262  in the IMP namespace.*/
263 using IMP::kernel::get_dependency_graph;
264 /** Import IMP::kernel::get_dependent_particles
265  in the IMP namespace.*/
266 using IMP::kernel::get_dependent_particles;
267 /** Import IMP::kernel::get_dependent_restraints
268  in the IMP namespace.*/
269 using IMP::kernel::get_dependent_restraints;
270 /** Import IMP::kernel::get_dependent_score_states
271  in the IMP namespace.*/
272 using IMP::kernel::get_dependent_score_states;
273 /** Import IMP::kernel::get_indexes
274  in the IMP namespace.*/
275 using IMP::kernel::get_indexes;
276 /** Import IMP::kernel::get_input_containers
277  in the IMP namespace.*/
278 using IMP::kernel::get_input_containers;
279 /** Import IMP::kernel::get_input_particles
280  in the IMP namespace.*/
281 using IMP::kernel::get_input_particles;
282 /** Import IMP::kernel::get_output_containers
283  in the IMP namespace.*/
284 using IMP::kernel::get_output_containers;
285 /** Import IMP::kernel::get_output_particles
286  in the IMP namespace.*/
287 using IMP::kernel::get_output_particles;
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.*/
293 using IMP::kernel::get_particles;
294 /** Import IMP::kernel::get_pruned_dependency_graph
295  in the IMP namespace.*/
296 using IMP::kernel::get_pruned_dependency_graph;
297 /** Import IMP::kernel::get_required_score_states
298  in the IMP namespace.*/
299 using IMP::kernel::get_required_score_states;
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.*/
305 using IMP::kernel::get_update_order;
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.*/
314 using IMP::kernel::read_particles_from_buffer;
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.*/
320 using IMP::kernel::show_restraint_hierarchy;
321 /** Import IMP::kernel::write_particles_to_buffer
322  in the IMP namespace.*/
323 using IMP::kernel::write_particles_to_buffer;
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::EvaluationStates
IMP::kernel::EvaluationStates EvaluationStates
Definition: kernel/doxygen.h:46
IMP::kernel::create_decomposition
Restraints create_decomposition(const RestraintsTemp &rs)
Return the decomposition of a list of restraints.
IMP::PairModifier
IMP::kernel::PairModifier PairModifier
Definition: kernel/doxygen.h:91
IMP::kernel::ConfigurationSet
A class to store a set of configurations of a model.
Definition: kernel/ConfigurationSet.h:28
IMP::kernel::get_indexes
ParticleIndexes get_indexes(const ParticlesTemp &ps)
IMP::kernel::Key
A base class for Keys.
Definition: kernel/Key.h:46
IMP::ModelObject
IMP::kernel::ModelObject ModelObject
Definition: kernel/doxygen.h:70
IMP::kernel::TripletContainer
A shared container for Triplets.
Definition: kernel/TripletContainer.h:37
IMP::kernel::DependencyGraph
boost::graph DependencyGraph
A directed graph on the interactions between the various objects in the model.
Definition: kernel/dependency_graph.h:37
IMP::kernel::QuadScore
Abstract class for scoring object(s) of type ParticleQuad.
Definition: kernel/QuadScore.h:38
IMP::kernel::DerivativeAccumulator
Class for adding derivatives from restraints to the model.
Definition: kernel/DerivativeAccumulator.h:25
IMP::kernel.OptionParser
IMP-specific subclass of optparse.OptionParser.
Definition: kernel/__init__.py:7206
IMP::ParticleIndexTriplets
IMP::kernel::ParticleIndexTriplets ParticleIndexTriplets
Definition: kernel/doxygen.h:118
IMP::kernel::TripletModifier
A base class for modifiers of kernel::ParticleTripletsTemp.
Definition: kernel/TripletModifier.h:33
IMP::kernel::QuadContainer
A shared container for Quads.
Definition: kernel/QuadContainer.h:37
IMP::ScoreState
IMP::kernel::ScoreState ScoreState
Definition: kernel/doxygen.h:212
IMP::kernel::get_output_particles
ParticlesTemp get_output_particles(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
IMP::kernel::get_dependent_score_states
ScoreStatesTemp get_dependent_score_states(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
IMP::PairScore
IMP::kernel::PairScore PairScore
Definition: kernel/doxygen.h:97
IMP::ObjectKey
IMP::kernel::ObjectKey ObjectKey
Definition: kernel/doxygen.h:73
IMP::StringKey
IMP::kernel::StringKey StringKey
Definition: kernel/doxygen.h:233
IMP::CommandDispatcher
IMP::kernel::CommandDispatcher CommandDispatcher
Definition: kernel/doxygen.h:19
IMP::kernel::show_restraint_hierarchy
void show_restraint_hierarchy(ScoringFunctionAdaptor rs, std::ostream &out=std::cout)
Print the hierarchy of restraints.
IMP::DerivativeAccumulator
IMP::kernel::DerivativeAccumulator DerivativeAccumulator
Definition: kernel/doxygen.h:40
kernel.h
Include all non-deprecated headers in IMP.kernel.
IMP::ParticleTriplet
IMP::kernel::ParticleTriplet ParticleTriplet
Definition: kernel/doxygen.h:142
IMP::ParticleIndexes
IMP::kernel::ParticleIndexes ParticleIndexes
Definition: kernel/doxygen.h:121
IMP::SingletonContainer
IMP::kernel::SingletonContainer SingletonContainer
Definition: kernel/doxygen.h:221
IMP::EvaluationState
IMP::kernel::EvaluationState EvaluationState
Definition: kernel/doxygen.h:43
IMP::ScopedSetFloatAttribute
IMP::kernel::ScopedSetFloatAttribute ScopedSetFloatAttribute
Definition: kernel/doxygen.h:203
IMP::Constraint
IMP::kernel::Constraint Constraint
Definition: kernel/doxygen.h:28
IMP::TripletContainer
IMP::kernel::TripletContainer TripletContainer
Definition: kernel/doxygen.h:239
IMP::QuadContainer
IMP::kernel::QuadContainer QuadContainer
Definition: kernel/doxygen.h:154
IMP::kernel::OptimizerState
Shared optimizer state that is invoked upon commitment of new coordinates.
Definition: kernel/OptimizerState.h:43
IMP::UnaryFunction
IMP::kernel::UnaryFunction UnaryFunction
Definition: kernel/doxygen.h:251
IMP::kernel::get_particles
ParticlesTemp get_particles(kernel::Model *m, const ParticleIndexes &ps)
IMP::kernel::RestraintSet
Object used to hold a set of restraints.
Definition: kernel/RestraintSet.h:36
IMP::ParticleIndexPairs
IMP::kernel::ParticleIndexPairs ParticleIndexPairs
Definition: kernel/doxygen.h:112
IMP::ScoringFunction
IMP::kernel::ScoringFunction ScoringFunction
Definition: kernel/doxygen.h:218
IMP::StringKeys
IMP::kernel::StringKeys StringKeys
Definition: kernel/doxygen.h:236
IMP::ParticleIndexKey
IMP::kernel::ParticleIndexKey ParticleIndexKey
Definition: kernel/doxygen.h:106
IMP::kernel::get_output_containers
ContainersTemp get_output_containers(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
IMP::FloatKeys
IMP::kernel::FloatKeys FloatKeys
Definition: kernel/doxygen.h:58
IMP::SingletonPredicate
IMP::kernel::SingletonPredicate SingletonPredicate
Definition: kernel/doxygen.h:227
IMP::kernel::QuadPredicate
Abstract predicate function.
Definition: kernel/QuadPredicate.h:32
IMP::kernel::PairContainer
A shared container for Pairs.
Definition: kernel/PairContainer.h:37
IMP::kernel::get_pruned_dependency_graph
DependencyGraph get_pruned_dependency_graph(kernel::Model *m)
IMP::QuadScore
IMP::kernel::QuadScore QuadScore
Definition: kernel/doxygen.h:163
IMP::Optimizer
IMP::kernel::Optimizer Optimizer
Definition: kernel/doxygen.h:79
IMP::kernel::get_input_particles
ParticlesTemp get_input_particles(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
IMP::kernel::get_dependent_particles
ParticlesTemp get_dependent_particles(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
IMP::ParticlePair
IMP::kernel::ParticlePair ParticlePair
Definition: kernel/doxygen.h:130
IMP::TripletModifier
IMP::kernel::TripletModifier TripletModifier
Definition: kernel/doxygen.h:242
IMP::ScopedRemoveRestraint
IMP::kernel::ScopedRemoveRestraint ScopedRemoveRestraint
Definition: kernel/doxygen.h:191
IMP::ObjectKeys
IMP::kernel::ObjectKeys ObjectKeys
Definition: kernel/doxygen.h:76
IMP::kernel::ScoringFunction
Represents a scoring function on the model.
Definition: kernel/ScoringFunction.h:44
IMP::ParticleQuadsTemp
IMP::kernel::ParticleQuadsTemp ParticleQuadsTemp
Definition: kernel/doxygen.h:139
IMP::kernel::UnaryFunction
Abstract single variable functor class for score functions.
Definition: kernel/UnaryFunction.h:25
IMP::kernel::ScoreState
ScoreStates maintain invariants in the Model.
Definition: kernel/ScoreState.h:53
IMP::PythonScoreState
IMP::kernel::PythonScoreState PythonScoreState
Definition: kernel/doxygen.h:151
IMP::ParticleIndexQuads
IMP::kernel::ParticleIndexQuads ParticleIndexQuads
Definition: kernel/doxygen.h:115
IMP::QuadModifier
IMP::kernel::QuadModifier QuadModifier
Definition: kernel/doxygen.h:157
IMP::PythonRestraint
IMP::kernel::PythonRestraint PythonRestraint
Definition: kernel/doxygen.h:148
IMP::kernel::get_dependency_graph
DependencyGraph get_dependency_graph(kernel::Model *m)
IMP::kernel::SingletonModifier
A base class for modifiers of kernel::ParticlesTemp.
Definition: kernel/SingletonModifier.h:33
IMP::kernel::TripletPredicate
Abstract predicate function.
Definition: kernel/TripletPredicate.h:32
IMP::base::Array
A class to store an fixed array of same-typed values.
Definition: Array.h:33
IMP::kernel::PairScore
Abstract class for scoring object(s) of type ParticlePair.
Definition: kernel/PairScore.h:38
IMP::Container
IMP::kernel::Container Container
Definition: kernel/doxygen.h:31
IMP::SingletonModifier
IMP::kernel::SingletonModifier SingletonModifier
Definition: kernel/doxygen.h:224
IMP::kernel::get_dependent_restraints
RestraintsTemp get_dependent_restraints(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
IMP::kernel::read_particles_from_buffer
void read_particles_from_buffer(const base::Vector< char > &buffer, const ParticlesTemp &particles, const FloatKeys &keys)
load found attributes into the particles
IMP::kernel::Container
Abstract class for containers of particles.
Definition: kernel/container_base.h:44
IMP::kernel::get_input_containers
ContainersTemp get_input_containers(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
IMP::ScopedRemoveScoreState
IMP::kernel::ScopedRemoveScoreState ScopedRemoveScoreState
Definition: kernel/doxygen.h:194
IMP::ParticlePairsTemp
IMP::kernel::ParticlePairsTemp ParticlePairsTemp
Definition: kernel/doxygen.h:133
IMP::SaveToConfigurationSetOptimizerState
IMP::kernel::SaveToConfigurationSetOptimizerState SaveToConfigurationSetOptimizerState
Definition: kernel/doxygen.h:188
IMP::kernel::write_particles_to_buffer
base::Vector< char > write_particles_to_buffer(const ParticlesTemp &particles, const FloatKeys &keys)
return a binary buffer with the data
IMP::Refiner
IMP::kernel::Refiner Refiner
Definition: kernel/doxygen.h:166
IMP::ScoreAccumulator
IMP::kernel::ScoreAccumulator ScoreAccumulator
Definition: kernel/doxygen.h:206
IMP::ScoreStateBase
IMP::kernel::ScoreStateBase ScoreStateBase
Definition: kernel/doxygen.h:215
IMP::Model
IMP::kernel::Model Model
Definition: kernel/doxygen.h:67
IMP::kernel::ScoreAccumulator
Class for adding up scores during ScoringFunction evaluation.
Definition: kernel/ScoreAccumulator.h:46
IMP::kernel::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition: kernel/Restraint.h:52
IMP::IntKeys
IMP::kernel::IntKeys IntKeys
Definition: kernel/doxygen.h:64
IMP::QuadPredicate
IMP::kernel::QuadPredicate QuadPredicate
Definition: kernel/doxygen.h:160
IMP::FloatKey
IMP::kernel::FloatKey FloatKey
Definition: kernel/doxygen.h:55
IMP::kernel::PairPredicate
Abstract predicate function.
Definition: kernel/PairPredicate.h:32
IMP::kernel::Particle
Class to handle individual model particles.
Definition: kernel/Particle.h:37
IMP::TripletScore
IMP::kernel::TripletScore TripletScore
Definition: kernel/doxygen.h:248
IMP::DependencyGraph
IMP::kernel::DependencyGraph DependencyGraph
Definition: kernel/doxygen.h:37
IMP::OptionParser
IMP::kernel::OptionParser OptionParser
Definition: kernel/doxygen.h:85
IMP::kernel::Configuration
A class to store a configuration of a model.
Definition: kernel/Configuration.h:21
IMP::kernel::Optimizer
Base class for all optimizers.
Definition: kernel/Optimizer.h:44
IMP::kernel::SingletonPredicate
Abstract predicate function.
Definition: kernel/SingletonPredicate.h:32
IMP::Sampler
IMP::kernel::Sampler Sampler
Definition: kernel/doxygen.h:184
IMP::ParticleIndexKeys
IMP::kernel::ParticleIndexKeys ParticleIndexKeys
Definition: kernel/doxygen.h:109
IMP::ParticleIndexesKeys
IMP::kernel::ParticleIndexesKeys ParticleIndexesKeys
Definition: kernel/doxygen.h:127
IMP::kernel.CommandDispatcher
Allow applications to easily implement commmands.
Definition: kernel/__init__.py:7094
IMP::RestraintStatistics
IMP::kernel::RestraintStatistics RestraintStatistics
Definition: kernel/doxygen.h:178
IMP::Particle
IMP::kernel::Particle Particle
Definition: kernel/doxygen.h:100
IMP::PairPredicate
IMP::kernel::PairPredicate PairPredicate
Definition: kernel/doxygen.h:94
IMP::ParticleIndexesKey
IMP::kernel::ParticleIndexesKey ParticleIndexesKey
Definition: kernel/doxygen.h:124
IMP::kernel::SingletonScore
Abstract class for scoring object(s) of type Particle.
Definition: kernel/SingletonScore.h:38
IMP::kernel::Sampler
Base class for all samplers.
Definition: kernel/Sampler.h:31
IMP::ParticleQuad
IMP::kernel::ParticleQuad ParticleQuad
Definition: kernel/doxygen.h:136
IMP::ConfigurationSet
IMP::kernel::ConfigurationSet ConfigurationSet
Definition: kernel/doxygen.h:25
IMP::PairContainer
IMP::kernel::PairContainer PairContainer
Definition: kernel/doxygen.h:88
IMP::ParticleTripletsTemp
IMP::kernel::ParticleTripletsTemp ParticleTripletsTemp
Definition: kernel/doxygen.h:145
IMP::OptimizerState
IMP::kernel::OptimizerState OptimizerState
Definition: kernel/doxygen.h:82
IMP::kernel::Constraint
Implement a constraint on the Model.
Definition: kernel/Constraint.h:49
IMP::TripletPredicate
IMP::kernel::TripletPredicate TripletPredicate
Definition: kernel/doxygen.h:245
IMP::ScopedRestraint
IMP::kernel::ScopedRestraint ScopedRestraint
Definition: kernel/doxygen.h:197
IMP::Decorator
IMP::kernel::Decorator Decorator
Definition: kernel/doxygen.h:34
IMP::SingletonScore
IMP::kernel::SingletonScore SingletonScore
Definition: kernel/doxygen.h:230
IMP::Restraint
IMP::kernel::Restraint Restraint
Definition: kernel/doxygen.h:169
IMP::ScoreAccumulators
IMP::kernel::ScoreAccumulators ScoreAccumulators
Definition: kernel/doxygen.h:209
IMP::kernel::Refiner
Abstract class to implement hierarchical methods.
Definition: kernel/Refiner.h:34
IMP::RestraintStatisticsList
IMP::kernel::RestraintStatisticsList RestraintStatisticsList
Definition: kernel/doxygen.h:181
IMP::RestraintSet
IMP::kernel::RestraintSet RestraintSet
Definition: kernel/doxygen.h:175
IMP::kernel::QuadModifier
A base class for modifiers of kernel::ParticleQuadsTemp.
Definition: kernel/QuadModifier.h:33
IMP::ParticleIndex
IMP::kernel::ParticleIndex ParticleIndex
Definition: kernel/doxygen.h:103
IMP::FloatIndex
IMP::kernel::FloatIndex FloatIndex
Definition: kernel/doxygen.h:49
IMP::kernel::TripletScore
Abstract class for scoring object(s) of type ParticleTriplet.
Definition: kernel/TripletScore.h:38
IMP::ScopedScoreState
IMP::kernel::ScopedScoreState ScopedScoreState
Definition: kernel/doxygen.h:200
IMP::kernel::get_required_score_states
ScoreStatesTemp get_required_score_states(ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
IMP::kernel::SingletonContainer
A shared container for Singletons.
Definition: kernel/SingletonContainer.h:37
IMP::Configuration
IMP::kernel::Configuration Configuration
Definition: kernel/doxygen.h:22
IMP::kernel::get_update_order
ScoreStatesTemp get_update_order(ScoreStatesTemp input)
IMP::kernel::PairModifier
A base class for modifiers of kernel::ParticlePairsTemp.
Definition: kernel/PairModifier.h:33
IMP::IntKey
IMP::kernel::IntKey IntKey
Definition: kernel/doxygen.h:61
IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73
IMP::RestraintBase
IMP::kernel::RestraintBase RestraintBase
Definition: kernel/doxygen.h:172
IMP::FloatIndexes
IMP::kernel::FloatIndexes FloatIndexes
Definition: kernel/doxygen.h:52