IMP::atom::Simulator Member List

This is the complete list of members for IMP::atom::Simulator, including all inherited members.

add_optimizer_state(OptimizerState *obj) (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
add_optimizer_states(const OptimizerStates &objs) (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
add_particle(kernel::Particle *obj) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
add_particles(const kernel::Particles &objs) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
clear_caches()	IMP::base::Object	virtual
clear_optimizer_states() (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
clear_particles() (defined in IMP::atom::Simulator)	IMP::atom::Simulator
clear_range_cache()	IMP::kernel::Optimizer
do_destroy()	IMP::base::Object	virtual
do_get_inputs() const	IMP::kernel::Optimizer	protectedvirtual
do_get_interactions() const	IMP::kernel::ModelObject	protectedvirtual
do_get_outputs() const	IMP::kernel::Optimizer	protectedvirtual
do_optimize(unsigned int max_steps)	IMP::atom::Simulator	protectedvirtual
do_step(const kernel::ParticleIndexes &sc, double dt)=0	IMP::atom::Simulator	protectedpure virtual
get_check_level() const (defined in IMP::base::Object)	IMP::base::Object
get_current_time() const	IMP::atom::Simulator
get_derivative(FloatIndex fi) const	IMP::kernel::Optimizer
get_has_dependencies() const	IMP::kernel::ModelObject
get_has_optimizer_states() (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
get_has_particles() (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_has_required_score_states() const	IMP::kernel::ModelObject
get_inputs() const	IMP::kernel::ModelObject
get_interactions() const	IMP::kernel::ModelObject
get_is_part_of_model() const	IMP::kernel::ModelObject
get_is_simulation_particle(kernel::ParticleIndex p) const =0	IMP::atom::Simulator	protectedpure virtual
get_kt() const (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_last_score() const	IMP::kernel::Optimizer
get_last_time_step() const (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_log_level() const (defined in IMP::base::Object)	IMP::base::Object
get_maximum_time_step() const (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_model() const (defined in IMP::kernel::ModelObject)	IMP::kernel::ModelObject
get_name() const (defined in IMP::base::Object)	IMP::base::Object
get_number_of_optimizer_states() const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
get_number_of_particles() const (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_optimized_attributes() const	IMP::kernel::Optimizer
get_optimizer_state(unsigned int i) const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
get_optimizer_state_inputs() const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected
get_optimizer_states() const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
get_outputs() const	IMP::kernel::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::kernel::ModelObject
get_restraints() const	IMP::kernel::Optimizer
get_scaled_derivative(FloatIndex fi) const	IMP::kernel::Optimizer
get_scaled_value(FloatIndex fi) const	IMP::kernel::Optimizer
get_score_threshold() const	IMP::kernel::Optimizer
get_scoring_function() const	IMP::kernel::Optimizer
get_simulation_particle_indexes() const (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_simulation_particles() const	IMP::atom::Simulator
get_stop_on_good_score() const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
get_temperature() const (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_type_name() const (defined in IMP::base::Object)	IMP::base::Object	virtual
get_value(FloatIndex fi) const	IMP::kernel::Optimizer
get_version_info() const	IMP::base::Object	virtual
get_width(FloatKey k) const	IMP::kernel::Optimizer
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
optimize(unsigned int max_steps)	IMP::kernel::Optimizer
Optimizer(kernel::Model *m, std::string name="Optimizer %1%") (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
Optimizer()	IMP::kernel::Optimizer
remove_optimizer_state(OptimizerState *d) (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
remove_optimizer_states(const OptimizerStates &d) (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
remove_particle(kernel::Particle *d) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
remove_particles(const kernel::Particles &d) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
reserve_optimizer_states(unsigned int sz) (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
reserve_particles(unsigned int sz) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
set_check_level(CheckLevel l)	IMP::base::Object
set_current_time(double ct)	IMP::atom::Simulator
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_time_step(double ts) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
set_model(kernel::Model *m)	IMP::kernel::ModelObject	virtual
set_name(std::string name) (defined in IMP::base::Object)	IMP::base::Object
set_optimizer_states(const OptimizerStates &ps) (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
set_optimizer_states_order(const OptimizerStates &objs) (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
set_particles(const kernel::Particles &ps) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
set_particles_order(const kernel::Particles &objs) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
set_restraints(const RestraintsTemp &rs)	IMP::kernel::Optimizer
set_scaled_value(FloatIndex fi, Float v) const	IMP::kernel::Optimizer
set_score_threshold(double s)	IMP::kernel::Optimizer
set_scoring_function(ScoringFunctionAdaptor sf)	IMP::kernel::Optimizer	virtual
set_stop_on_good_score(bool tf)	IMP::kernel::Optimizer
set_temperature(double d) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
set_value(FloatIndex fi, double v) const	IMP::kernel::Optimizer
set_was_used(bool tf) const	IMP::base::Object
setup(const kernel::ParticleIndexes &)	IMP::atom::Simulator	protectedvirtual
show(std::ostream &out=std::cout) const (defined in IMP::base::Object)	IMP::base::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(kernel::Model *m, std::string name="Simulator %1%", double wave_factor=1.0)	IMP::atom::Simulator
update_states() const	IMP::kernel::Optimizer	protected
width(FloatKey k) const	IMP::kernel::Optimizer
~ModelObject() (defined in IMP::kernel::ModelObject)	IMP::kernel::ModelObject