 |
|
IMP Reference Guide
2.21.0
The Integrative Modeling Platform
|
Sample best solutions using Domino. More...
#include <IMP/domino/DominoSampler.h>
Inheritance diagram for IMP::domino::DominoSampler:Sample best solutions using Domino.
Note that if there are many solutions, the ConfigurationSet returned by get_sample() might be huge (in terms of memory usage) and slow to generate. The Assignments returned by get_sample_assignments() can be a lot smaller and faster.
Definition at line 32 of file DominoSampler.h.
Public Member Functions | |
| DominoSampler (Model *m, std::string name="DominoSampler %1%") | |
| DominoSampler (Model *m, ParticleStatesTable *pst, std::string name="DominoSampler %1%") | |
| Assignments | do_get_sample_assignments (const IMP::domino::Subset &known) const override |
| virtual std::string | get_type_name () const override |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| Get information about the module and version of the object. More... | |
| void | set_use_cross_subset_filtering (bool tf) |
| Public Member Functions inherited from IMP::domino::DiscreteSampler | |
| DiscreteSampler (Model *m, ParticleStatesTable *pst, std::string name) | |
| unsigned int | get_maximum_number_of_assignments () const |
| Assignments | get_sample_assignments (const Subset &s) const |
| void | set_maximum_number_of_assignments (unsigned int mx) |
| void | set_particle_states (Particle *p, ParticleStates *se) |
| void | set_restraints (RestraintsAdaptor rs) |
| Set the Restraints to use in the RestraintScoreSubsetFilterTable. More... | |
| void | set_particle_states_table (ParticleStatesTable *cse) |
| void | set_assignments_table (AssignmentsTable *sst) |
| ParticleStatesTable * | get_particle_states_table () const |
| void | remove_subset_filter_table (SubsetFilterTable *d) |
| void | remove_subset_filter_tables (const SubsetFilterTables &d) |
| void | set_subset_filter_tables (const SubsetFilterTables &ps) |
| void | set_subset_filter_tables_order (const SubsetFilterTables &objs) |
| unsigned int | add_subset_filter_table (SubsetFilterTable *obj) |
| void | add_subset_filter_tables (const SubsetFilterTables &objs) |
| void | clear_subset_filter_tables () |
| unsigned int | get_number_of_subset_filter_tables () const |
| bool | get_has_subset_filter_tables () |
| SubsetFilterTable * | get_subset_filter_table (unsigned int i) const |
| SubsetFilterTables | get_subset_filter_tables () const |
| void | erase_subset_filter_table (unsigned int i) |
| void | reserve_subset_filter_tables (unsigned int sz) |
| Public Member Functions inherited from IMP::Sampler | |
| Sampler (Model *m, std::string name="Sampler %1%") | |
| ConfigurationSet * | create_sample () const |
| Model * | get_model () const |
| ScoringFunction * | get_scoring_function () const |
| Return the scoring function that is being used. More... | |
| void | set_scoring_function (ScoringFunctionAdaptor sf) |
| Public Member Functions inherited from IMP::Object | |
| virtual void | clear_caches () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Advanced | |
Default values are provided, you only need to replace these if you want to do something special. See the overview of the module for a general description. | |
| void | set_merge_tree (const MergeTree &mt) |
| Specify the merge tree directly. More... | |
Statistics | |
If you specify the merge tree explicitly, you can query for statistics about particular nodes in the merge tree. | |
| unsigned int | get_number_of_assignments_for_vertex (unsigned int tree_vertex) const |
| Get the number of states found for the merge at that vertex of the tree. More... | |
| Assignments | get_sample_assignments_for_vertex (unsigned int tree_vertex) const |
| Return a few subset states from that merge. More... | |
Interactive mode | |
Once a merge tree is specified, one can interactively perform the sampling by requesting that domino fill in the Assignments for a given node of the merge tree from the assignments for the children. This can be useful for debugging Domino as well as for providing a distributed implementation. For each method, you can pass max_states to limit how many states are generated. You might want to just use load_leaf_assignments() and load_merged_assignments() instead. | |
| Assignments | get_vertex_assignments (unsigned int node_index, unsigned int max_states=std::numeric_limits< int >::max()) const |
| Fill in assignments for a leaf. More... | |
| Assignments | get_vertex_assignments (unsigned int node_index, const Assignments &first, const Assignments &second, unsigned int max_states=std::numeric_limits< int >::max()) const |
| Fill in assignments for an internal node. More... | |
| void | load_vertex_assignments (unsigned int node_index, AssignmentContainer *ac, unsigned int max_states=std::numeric_limits< int >::max()) const |
| Fill in assignments for a leaf. More... | |
| void | load_vertex_assignments (unsigned int node_index, AssignmentContainer *first, AssignmentContainer *second, AssignmentContainer *ac, unsigned int max_states=std::numeric_limits< int >::max()) const |
| Fill in assignments for an internal node. More... | |
Additional Inherited Members | |
| Public Attributes inherited from IMP::domino::DiscreteSampler | |
| list | subset_filter_tables |
| A Python list of SubsetFilterTables More... | |
| Protected Member Functions inherited from IMP::domino::DiscreteSampler | |
| virtual ConfigurationSet * | do_sample () const override |
| AssignmentsTable * | get_assignments_table_to_use (const SubsetFilterTables &sfts, unsigned int max=std::numeric_limits< int >::max()) const |
| RestraintsTemp | get_restraints () const |
| SubsetFilterTables | get_subset_filter_tables_to_use (const RestraintsTemp &rs, ParticleStatesTable *pst) const |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| unsigned int IMP::domino::DominoSampler::get_number_of_assignments_for_vertex | ( | unsigned int | tree_vertex | ) | const |
Get the number of states found for the merge at that vertex of the tree.
| Assignments IMP::domino::DominoSampler::get_sample_assignments_for_vertex | ( | unsigned int | tree_vertex | ) | const |
Return a few subset states from that merge.
|
overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 46 of file DominoSampler.h.
| Assignments IMP::domino::DominoSampler::get_vertex_assignments | ( | unsigned int | node_index, |
| unsigned int | max_states = std::numeric_limits< int >::max() |
||
| ) | const |
Fill in assignments for a leaf.
| Assignments IMP::domino::DominoSampler::get_vertex_assignments | ( | unsigned int | node_index, |
| const Assignments & | first, | ||
| const Assignments & | second, | ||
| unsigned int | max_states = std::numeric_limits< int >::max() |
||
| ) | const |
Fill in assignments for an internal node.
The passed assignments, the ordering for the children is the node index for the children.
| void IMP::domino::DominoSampler::load_vertex_assignments | ( | unsigned int | node_index, |
| AssignmentContainer * | ac, | ||
| unsigned int | max_states = std::numeric_limits< int >::max() |
||
| ) | const |
Fill in assignments for a leaf.
| void IMP::domino::DominoSampler::load_vertex_assignments | ( | unsigned int | node_index, |
| AssignmentContainer * | first, | ||
| AssignmentContainer * | second, | ||
| AssignmentContainer * | ac, | ||
| unsigned int | max_states = std::numeric_limits< int >::max() |
||
| ) | const |
Fill in assignments for an internal node.
The passed assignments, the ordering for the children is that of the node indexes for the children.
| void IMP::domino::DominoSampler::set_merge_tree | ( | const MergeTree & | mt | ) |
Specify the merge tree directly.
| void IMP::domino::DominoSampler::set_use_cross_subset_filtering | ( | bool | tf | ) |
perform filtering between subsets based by eliminating states that cannot be realized in a subset.
Definition at line 62 of file DominoSampler.h.