IMP  2.0.1
The Integrative Modeling Platform
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::MolecularDynamicsvirtual
cap_velocity_component(Float &vel)IMP::atom::MolecularDynamicsprotected
clear_caches()IMP::base::Objectvirtual
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::Optimizerprotected
degrees_of_freedom_IMP::atom::MolecularDynamicsprotected
do_optimize(unsigned int ns)=0IMP::kernel::Optimizerprotectedpure virtual
get_current_time() const IMP::atom::Simulator
get_derivative(FloatIndex fi) const (defined in IMP::kernel::Optimizer)IMP::kernel::Optimizerprotected
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::MolecularDynamicsvirtual
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::Optimizerprotected
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::Optimizerprotected
get_scaled_value(FloatIndex fi) const (defined in IMP::kernel::Optimizer)IMP::kernel::Optimizerprotected
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::Optimizerprotected
get_version_info() const =0IMP::base::Objectpure virtual
IMP_OPTIMIZER(Simulator) (defined in IMP::atom::Simulator)IMP::atom::Simulator
initialize() (defined in IMP::atom::MolecularDynamics)IMP::atom::MolecularDynamicsprotected
MolecularDynamics(Model *m=nullptr)IMP::atom::MolecularDynamics
NonCopyable() (defined in IMP::base::NonCopyable)IMP::base::NonCopyableprotected
Object(std::string name)IMP::base::Objectprotected
ObjectsTemp typedefIMP::base::Objectrelated
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 typedefIMP::kernel::Optimizerrelated
propagate_coordinates(const ParticleIndexes &ps, double step_size)IMP::atom::MolecularDynamicsprotectedvirtual
propagate_velocities(const ParticleIndexes &ps, double step_size)IMP::atom::MolecularDynamicsprotectedvirtual
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::Simulatorrelated
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::Optimizerprotected
set_scoring_function(ScoringFunctionAdaptor sf)IMP::kernel::Optimizervirtual
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::Optimizerprotected
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::MolecularDynamicsprotectedvirtual
show(std::ostream &out=std::cout) const IMP::kernel::Optimizervirtual
simulate(double time_in_fs)IMP::atom::Simulator
Simulator(Model *m, std::string name="Simulator %1%")IMP::atom::Simulator
SimulatorsTemp typedefIMP::atom::Simulatorrelated
update_states() const IMP::kernel::Optimizerprotected
velocity_cap_IMP::atom::MolecularDynamicsprotected
vs_IMP::atom::MolecularDynamicsprotected
width(FloatKey k) const (defined in IMP::kernel::Optimizer)IMP::kernel::Optimizerprotected