| add_contribution(kernel::Particle *p1, kernel::Particle *p2) (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| add_contribution(kernel::Particles p1, kernel::Particles p2) (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| add_score_and_derivatives(ScoreAccumulator sa) const | IMP::kernel::Restraint | |
| clear_caches() | IMP::base::Object | virtual |
| const | IMP::isd::CysteineCrossLinkRestraint | |
| create_current_decomposition() const | IMP::kernel::Restraint | |
| create_decomposition() const | IMP::kernel::Restraint | |
| create_scoring_function(double weight=1.0, double max=NO_MAX) const | IMP::kernel::Restraint | virtual |
| CysteineCrossLinkRestraint(kernel::Particle *beta, kernel::Particle *sigma, kernel::Particle *epsilon, kernel::Particle *weight, CrossLinkData *data, double fexp) | IMP::isd::CysteineCrossLinkRestraint | |
| CysteineCrossLinkRestraint(kernel::Particle *beta, kernel::Particle *sigma, kernel::Particle *epsilon, kernel::Particle *weight, CrossLinkData *data, CysteineCrossLinkData *ccldata) (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| do_add_score_and_derivatives(ScoreAccumulator sa) const | IMP::kernel::Restraint | protectedvirtual |
| do_create_current_decomposition() const | IMP::kernel::Restraint | protectedvirtual |
| do_create_decomposition() const | IMP::kernel::Restraint | protectedvirtual |
| do_destroy() | IMP::base::Object | virtual |
| do_get_inputs() const | IMP::isd::CysteineCrossLinkRestraint | virtual |
| do_get_interactions() const | IMP::kernel::ModelObject | protectedvirtual |
| do_get_outputs() const | IMP::kernel::Restraint | protectedvirtual |
| do_set_model(kernel::Model *) | IMP::kernel::ModelObject | virtual |
| get_CB_coordinates(const kernel::Particles &ps) const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_check_level() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_distances() const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_frequencies() const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_has_dependencies() const | IMP::kernel::ModelObject | |
| get_has_required_score_states() const | IMP::kernel::ModelObject | |
| get_input_containers() const | IMP::kernel::Restraint | |
| get_input_particles() const | IMP::kernel::Restraint | |
| get_inputs() const | IMP::kernel::ModelObject | |
| get_interactions() const | IMP::kernel::ModelObject | |
| get_is_part_of_model() const | IMP::kernel::ModelObject | |
| get_last_score() const | IMP::kernel::Restraint | virtual |
| get_log_level() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_maximum_score() const (defined in IMP::kernel::Restraint) | IMP::kernel::Restraint | |
| get_model() const (defined in IMP::kernel::ModelObject) | IMP::kernel::ModelObject | |
| get_model_frequency() const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_name() const (defined in IMP::base::Object) | IMP::base::Object | |
| get_normal_pdf(double mean, double sigma, double x) const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_number_of_contributions() const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_outputs() const | IMP::kernel::ModelObject | |
| get_probability() const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_required_score_states() const | IMP::kernel::ModelObject | |
| get_score() const | IMP::kernel::Restraint | |
| get_standard_error() const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_truncated_normalization(double mean, double sigma) const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | |
| get_type_name() const (defined in IMP::isd::CysteineCrossLinkRestraint) | IMP::isd::CysteineCrossLinkRestraint | virtual |
| get_version_info() const | IMP::isd::CysteineCrossLinkRestraint | virtual |
| get_was_good() const | IMP::kernel::Restraint | |
| get_weight() const (defined in IMP::kernel::Restraint) | IMP::kernel::Restraint | |
| handle_set_has_required_score_states(bool) | IMP::kernel::ModelObject | protectedvirtual |
| ModelObject(kernel::Model *m, std::string name) (defined in IMP::kernel::ModelObject) | IMP::kernel::ModelObject | |
| ModelObject(std::string name) | IMP::kernel::ModelObject | |
| NonCopyable() (defined in IMP::base::NonCopyable) | IMP::base::NonCopyable | protected |
| Object(std::string name) | IMP::base::Object | protected |
| Object() | IMP::base::Object | protected |
| Restraint(kernel::Model *m, std::string name) | IMP::kernel::Restraint | |
| Restraint(std::string name="Restraint %1%") | IMP::kernel::Restraint | |
| set_check_level(CheckLevel l) | IMP::base::Object | |
| set_has_dependencies(bool tf) | IMP::kernel::ModelObject | |
| set_has_required_score_states(bool tf) | IMP::kernel::ModelObject | |
| set_log_level(LogLevel l) | IMP::base::Object | |
| set_maximum_score(double s) (defined in IMP::kernel::Restraint) | IMP::kernel::Restraint | |
| set_model(kernel::Model *m) | IMP::kernel::ModelObject | virtual |
| set_name(std::string name) (defined in IMP::base::Object) | IMP::base::Object | |
| set_was_used(bool tf) const | IMP::base::Object | |
| set_weight(Float weight) (defined in IMP::kernel::Restraint) | IMP::kernel::Restraint | |
| show(std::ostream &out=std::cout) const (defined in IMP::base::Object) | IMP::base::Object | |
| ~ModelObject() (defined in IMP::kernel::ModelObject) | IMP::kernel::ModelObject | |
