IMP::atom::MolecularDynamics Member List

This is the complete list of members for IMP::atom::MolecularDynamics, 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(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::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	protected
degrees_of_freedom_	IMP::atom::MolecularDynamics	protected
do_optimize(unsigned int ns)=0	IMP::kernel::Optimizer	protectedpure virtual
get_current_time() const	IMP::atom::Simulator
get_derivative(FloatIndex fi) const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected
get_has_optimizer_states() (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
get_has_particles() (defined in IMP::atom::Simulator)	IMP::atom::Simulator
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::kernel::Optimizer
get_last_time_step() const (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_maximum_time_step() const (defined in IMP::atom::Simulator)	IMP::atom::Simulator
get_model() const	IMP::kernel::Optimizer
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 (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected
get_optimizer_state(unsigned int i) const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
get_optimizer_states() const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
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_scaled_derivative(FloatIndex fi) const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected
get_scaled_value(FloatIndex fi) const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected
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_value(FloatIndex fi) const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected
get_version_info() const =0	IMP::base::Object	pure virtual
IMP_OPTIMIZER(Simulator) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
initialize() (defined in IMP::atom::MolecularDynamics)	IMP::atom::MolecularDynamics	protected
MolecularDynamics(Model *m=nullptr)	IMP::atom::MolecularDynamics
NonCopyable() (defined in IMP::base::NonCopyable)	IMP::base::NonCopyable	protected
Object(std::string name)	IMP::base::Object	protected
ObjectsTemp typedef	IMP::base::Object	related
optimize(unsigned int max_steps)	IMP::kernel::Optimizer
Optimizer() (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
Optimizer(Model *m, std::string name="Optimizer %1%") (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer
OptimizersTemp typedef	IMP::kernel::Optimizer	related
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::kernel::Optimizer)	IMP::kernel::Optimizer
remove_optimizer_states(const OptimizerStates &d) (defined in IMP::kernel::Optimizer)	IMP::kernel::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::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	related
set_log_level(LogLevel l)	IMP::base::Object
set_maximum_time_step(double ts) (defined in IMP::atom::Simulator)	IMP::atom::Simulator
set_model(Model *m)	IMP::kernel::Optimizer
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 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_scaled_value(FloatIndex fi, Float v) const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected
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 (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected
set_velocity_cap(Float velocity_cap)	IMP::atom::MolecularDynamics
set_was_used(bool tf) const	IMP::base::Object
setup_degrees_of_freedom(const ParticleIndexes &ps) (defined in IMP::atom::MolecularDynamics)	IMP::atom::MolecularDynamics	protectedvirtual
show(std::ostream &out=std::cout) const	IMP::kernel::Optimizer	virtual
simulate(double time_in_fs)	IMP::atom::Simulator
Simulator(Model *m, std::string name="Simulator %1%")	IMP::atom::Simulator
SimulatorsTemp typedef	IMP::atom::Simulator	related
update_states() const	IMP::kernel::Optimizer	protected
velocity_cap_	IMP::atom::MolecularDynamics	protected
vs_	IMP::atom::MolecularDynamics	protected
width(FloatKey k) const (defined in IMP::kernel::Optimizer)	IMP::kernel::Optimizer	protected