| add_optimizer_state(OptimizerState *obj) (defined in IMP::Optimizer) | IMP::Optimizer | |
| add_optimizer_states(const OptimizerStates &objs) (defined in IMP::Optimizer) | IMP::Optimizer | |
| add_particle(Particle *obj) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| add_particles(const Particles &objs) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| assign_velocities(Float temperature) | IMP::atom::MolecularDynamics | virtual |
| cap_velocity_component(Float &vel) | IMP::atom::MolecularDynamics | protected |
| clear_caches() | IMP::Object | virtual |
| clear_optimizer_states() (defined in IMP::Optimizer) | IMP::Optimizer | |
| clear_particles() (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| degrees_of_freedom_ | IMP::atom::MolecularDynamics | protected |
| do_destroy() | IMP::Object | protectedvirtual |
| do_get_inputs() const | IMP::Optimizer | protectedvirtual |
| do_get_interactions() const | IMP::ModelObject | protectedvirtual |
| do_get_outputs() const | IMP::Optimizer | protectedvirtual |
| do_optimize(unsigned int max_steps) | IMP::atom::Simulator | protectedvirtual |
| do_simulate(double time) | IMP::atom::Simulator | protectedvirtual |
| do_simulate_wave(double time_in_fs, double max_time_step_factor=10.0, double base=1.5) | IMP::atom::Simulator | protectedvirtual |
| do_step(const ParticleIndexes &sc, double dt) | IMP::atom::MolecularDynamics | virtual |
| get_check_level() const (defined in IMP::Object) | IMP::Object | |
| get_current_time() const | IMP::atom::Simulator | |
| get_has_dependencies() const | IMP::ModelObject | |
| get_has_optimizer_states() (defined in IMP::Optimizer) | IMP::Optimizer | |
| get_has_particles() (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| get_has_required_score_states() const | IMP::ModelObject | |
| get_inputs() const | IMP::ModelObject | |
| get_interactions() const | IMP::ModelObject | |
| get_is_simulation_particle(ParticleIndex p) const | IMP::atom::MolecularDynamics | virtual |
| get_kinetic_energy() const | IMP::atom::MolecularDynamics | virtual |
| get_kinetic_temperature(Float ekinetic) const | IMP::atom::MolecularDynamics | |
| get_kt() const (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| get_last_score() const | IMP::Optimizer | |
| get_last_time_step() const (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| get_log_level() const (defined in IMP::Object) | IMP::Object | |
| get_maximum_time_step() const (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| get_model() const (defined in IMP::ModelObject) | IMP::ModelObject | |
| get_name() const (defined in IMP::Object) | IMP::Object | |
| get_number_of_optimizer_states() const (defined in IMP::Optimizer) | IMP::Optimizer | |
| get_number_of_particles() const (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| get_optimizer_state(unsigned int i) const (defined in IMP::Optimizer) | IMP::Optimizer | |
| get_optimizer_state_inputs() const (defined in IMP::Optimizer) | IMP::Optimizer | protected |
| get_optimizer_states() const (defined in IMP::Optimizer) | IMP::Optimizer | |
| get_outputs() const | IMP::ModelObject | |
| get_particle(unsigned int i) const (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| get_particles() const (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| get_required_score_states() const | IMP::ModelObject | |
| get_scoring_function() const | IMP::Optimizer | |
| get_simulation_particle_indexes() const | IMP::atom::Simulator | |
| get_simulation_particles() const | IMP::atom::Simulator | |
| get_stop_on_good_score() const (defined in IMP::Optimizer) | IMP::Optimizer | |
| get_temperature() const (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| get_type_name() const (defined in IMP::atom::MolecularDynamics) | IMP::atom::MolecularDynamics | virtual |
| get_version_info() const | IMP::atom::MolecularDynamics | virtual |
| handle_set_has_required_score_states(bool) | IMP::ModelObject | protectedvirtual |
| initialize() (defined in IMP::atom::MolecularDynamics) | IMP::atom::MolecularDynamics | protected |
| ModelObject(Model *m, std::string name) (defined in IMP::ModelObject) | IMP::ModelObject | |
| MolecularDynamics(Model *m) | IMP::atom::MolecularDynamics | |
| NonCopyable() (defined in IMP::NonCopyable) | IMP::NonCopyable | protected |
| Object(std::string name) | IMP::Object | protected |
| optimize(unsigned int max_steps) | IMP::Optimizer | |
| Optimizer(Model *m, std::string name="Optimizer %1%") (defined in IMP::Optimizer) | IMP::Optimizer | |
| propagate_coordinates(const ParticleIndexes &ps, double step_size) | IMP::atom::MolecularDynamics | protectedvirtual |
| propagate_velocities(const ParticleIndexes &ps, double step_size) | IMP::atom::MolecularDynamics | protectedvirtual |
| remove_optimizer_state(OptimizerState *d) (defined in IMP::Optimizer) | IMP::Optimizer | |
| remove_optimizer_states(const OptimizerStates &d) (defined in IMP::Optimizer) | IMP::Optimizer | |
| remove_particle(Particle *d) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| remove_particles(const Particles &d) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| reserve_optimizer_states(unsigned int sz) (defined in IMP::Optimizer) | IMP::Optimizer | |
| reserve_particles(unsigned int sz) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| set_check_level(CheckLevel l) | IMP::Object | |
| set_current_time(double ct) | IMP::atom::Simulator | |
| set_has_dependencies(bool tf) | IMP::ModelObject | |
| set_has_required_score_states(bool tf) | IMP::ModelObject | |
| set_log_level(LogLevel l) | IMP::Object | |
| set_maximum_time_step(double ts) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| set_name(std::string name) (defined in IMP::Object) | IMP::Object | |
| set_optimizer_states(const OptimizerStates &ps) (defined in IMP::Optimizer) | IMP::Optimizer | |
| set_optimizer_states_order(const OptimizerStates &objs) (defined in IMP::Optimizer) | IMP::Optimizer | |
| set_particles(const Particles &ps) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| set_particles_order(const Particles &objs) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| set_scoring_function(ScoringFunctionAdaptor sf) | IMP::Optimizer | virtual |
| set_stop_on_good_score(bool tf) | IMP::Optimizer | |
| set_temperature(double d) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
| set_velocity_cap(Float velocity_cap) | IMP::atom::MolecularDynamics | |
| set_was_used(bool tf) const | IMP::Object | |
| setup(const ParticleIndexes &ps) | IMP::atom::MolecularDynamics | virtual |
| setup_degrees_of_freedom(const ParticleIndexes &ps) (defined in IMP::atom::MolecularDynamics) | IMP::atom::MolecularDynamics | protectedvirtual |
| show(std::ostream &out=std::cout) const (defined in IMP::Object) | IMP::Object | |
| simulate(double time_in_fs) | IMP::atom::Simulator | |
| simulate_wave(double time_in_fs, double max_time_step_factor=10.0, double base=1.5) | IMP::atom::Simulator | |
| Simulator(Model *m, std::string name="Simulator %1%", double wave_factor=1.0) | IMP::atom::Simulator | |
| update_states() const | IMP::Optimizer | protected |
| velocity_cap_ | IMP::atom::MolecularDynamics | protected |
| ~ModelObject() (defined in IMP::ModelObject) | IMP::ModelObject | |
| ~MolecularDynamics() (defined in IMP::atom::MolecularDynamics) | IMP::atom::MolecularDynamics | protectedvirtual |
| ~Object() (defined in IMP::Object) | IMP::Object | virtual |
