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 override | IMP::Optimizer | protectedvirtual |
do_get_interactions() const | IMP::ModelObject | protectedvirtual |
do_get_outputs() const override | IMP::Optimizer | protectedvirtual |
do_optimize(unsigned int max_steps) override | 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) override | IMP::atom::MolecularDynamics | virtual |
erase_optimizer_state(unsigned int i) (defined in IMP::Optimizer) | IMP::Optimizer | |
erase_particle(unsigned int i) (defined in IMP::atom::Simulator) | IMP::atom::Simulator | |
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 override | 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 | IMP::atom::Simulator | |
get_log_level() const (defined in IMP::Object) | IMP::Object | |
get_maximum_time_step() const | 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 | IMP::atom::Simulator | |
get_type_name() const override (defined in IMP::atom::MolecularDynamics) | IMP::atom::MolecularDynamics | virtual |
get_version_info() const override | 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 | |
ModelObject() (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 | |
Optimizer() (defined in IMP::Optimizer) | IMP::Optimizer | |
optimizer_states | IMP::Optimizer | |
particles | IMP::atom::Simulator | |
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) | IMP::atom::Simulator | |
set_velocity_cap(Float velocity_cap) | IMP::atom::MolecularDynamics | |
set_was_used(bool tf) const | IMP::Object | |
setup(const ParticleIndexes &ps) override | 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 | virtual |
~Object() (defined in IMP::Object) | IMP::Object | virtual |