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2.3.1
The Integrative Modeling Platform
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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
do_destroy
()
IMP::base::Object
protected
virtual
do_get_inputs
() const
IMP::kernel::Optimizer
protected
virtual
do_get_interactions
() const
IMP::kernel::ModelObject
protected
virtual
do_get_outputs
() const
IMP::kernel::Optimizer
protected
virtual
do_optimize
(unsigned int max_steps)
IMP::atom::Simulator
protected
virtual
do_step
(const kernel::ParticleIndexes &sc, double dt)=0
IMP::atom::Simulator
protected
pure virtual
get_check_level
() const (defined in
IMP::base::Object
)
IMP::base::Object
get_current_time
() const
IMP::atom::Simulator
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_simulation_particle
(kernel::ParticleIndex p) const =0
IMP::atom::Simulator
protected
pure 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_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_scoring_function
() const
IMP::kernel::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::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_version_info
() const
IMP::base::Object
virtual
handle_set_has_required_score_states
(bool)
IMP::kernel::ModelObject
protected
virtual
ModelObject
(kernel::Model *m, std::string name) (defined in
IMP::kernel::ModelObject
)
IMP::kernel::ModelObject
NonCopyable
() (defined in
IMP::base::NonCopyable
)
IMP::base::NonCopyable
protected
Object
(std::string name)
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
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_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_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_was_used
(bool tf) const
IMP::base::Object
setup
(const kernel::ParticleIndexes &)
IMP::atom::Simulator
protected
virtual
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
~ModelObject
() (defined in
IMP::kernel::ModelObject
)
IMP::kernel::ModelObject
~Object
() (defined in
IMP::base::Object
)
IMP::base::Object
virtual