Public Member Functions | |
| void | add_restraint (Restraint *r, Particles ps, float weight=1.) |
| Add a restraint that should be used in the optimization procedure. | |
| void | add_restraint (Restraint *r) |
| Add a restraint that should be used in the optimization procedure. | |
| DominoOptimizer (const JunctionTree &jt, Model *m, RestraintEvaluatorI *r_eval) | |
| Constructor. | |
| void | exhaustive_enumeration (CombStates &states, bool calc_score=false, bool use_rsr_eval=false) |
| RestraintGraph * | get_graph () const |
| unsigned int | get_number_of_solutions () const |
| DiscreteSampler * | get_sampling_space () const |
| virtual std::string | get_type_name () const |
| virtual ::IMP::VersionInfo | get_version_info () const |
| void | move_to_opt_comb (unsigned int i) const |
| virtual Float | optimize (unsigned int max_steps) |
| void | score_combinations (const CombStates &states, std::vector< Floats > &scores) |
| void | set_number_of_solutions (unsigned int n) |
| void | set_restraint_evaluator (RestraintEvaluatorI *rstr_eval) |
| void | set_sampling_space (DiscreteSampler *ds) |
| void | show_optimum_configuration (unsigned int conf_ind, std::ostream &out=std::cout) const |
| void | show_restraint_graph (std::ostream &out=std::cout) const |
Protected Member Functions | |
| void | add_jt_edge (int node1_ind, int node2_ind) |
| Adds an undirected edge between a pair of nodes. | |
| void | add_jt_node (int node_index, std::vector< Int > &particles_ind, Model &m) |
| void | add_restraint_recursive (Restraint *rs, Float weight) |
| Recursivly add restraints. | |
| void | clear () |
| void | initialize_jt_graph (int number_of_nodes) |
Protected Attributes | |
| DiscreteSampler * | ds_ |
| RestraintGraph * | g_ |
| unsigned int | num_of_solutions_ |
| std::vector< OptTuple > | rs_ |
| RestraintEvaluatorI * | rstr_eval_ |
Friends | |
| template<class T > | |
| void | IMP::internal::unref (T *) |
| IMP::domino::DominoOptimizer::DominoOptimizer | ( | const JunctionTree & | jt, | |
| Model * | m, | |||
| RestraintEvaluatorI * | r_eval | |||
| ) |
Constructor.
| [in] | jt | A special type of tree decomposition that holds the graph on which inference will be run |
| [in] | m | The model to be optimized |
| [in] | r_eval | evaluator used to evaluate the restraints |
| void IMP::domino::DominoOptimizer::add_jt_edge | ( | int | node1_ind, | |
| int | node2_ind | |||
| ) | [protected] |
Adds an undirected edge between a pair of nodes.
| [in] | node1_ind | the index of the first node |
| [in] | node2_ind | the index of the second node |
| void IMP::domino::DominoOptimizer::add_jt_node | ( | int | node_index, | |
| std::vector< Int > & | particles_ind, | |||
| Model & | m | |||
| ) | [protected] |
Creates a new node and add it to the graphs that take part in the optimization
Add a restraint that should be used in the optimization procedure.
To support hierarchy, some time the particles of the restraint are a refined set of the particles represented in the restraint graph. In this function the user set the particles of the restraint (as interpert by the restraint graph). It is up to the user to make sure that ps represents a coarser set of particles than the ones actually used in the restraint.
| void IMP::domino::DominoOptimizer::add_restraint | ( | Restraint * | r | ) |
Add a restraint that should be used in the optimization procedure.
/param[in] r the restraint /note The input restraint can also be a RestraintSet, a recursive addition of restraints is performed in these cases.
| void IMP::domino::DominoOptimizer::exhaustive_enumeration | ( | CombStates & | states, | |
| bool | calc_score = false, |
|||
| bool | use_rsr_eval = false | |||
| ) |
A function used mostly for debugging and learning purposes. Should NOT be used for real optimization protocol.
| [in] | states | to be filled with all of the combinations encoded in the restraint graph |
| [in] | calc_score | should scores be calculated for each combination |
| [in] | use_rsr_eval | if True use RestraintEvaluator else use model.evaluate() |
| void IMP::domino::DominoOptimizer::score_combinations | ( | const CombStates & | states, | |
| std::vector< Floats > & | scores | |||
| ) |
A function used mostly for debugging and learning purposes. Should NOT be used for real optimization protocol.
| [in] | states | states to score |
| [out] | scores | the i'th entry will contain the values of all restraint for states[i] |
