core::optimization Namespace Reference

Namespaces
	symmetry

Classes
class	ArmijoLineMinimization
class	AtomTreeMinimizer
	High-level atom tree minimizer class. More...
class	AtomTreeMultifunc
	Atom tree multifunction class. More...
class	BrentLineMinimization
class	CartesianMinimizer
	High-level atom tree minimizer class. More...
class	CartesianMinimizerMap
class	CartesianMultifunc
	Atom tree multifunction class. More...
class	ConvergenceTest
class	DerivCheckDataPoint
class	DescentDirectionAlgorithm
class	DFPMinConvergedAbsolute
class	DFPMinConvergedFractional
class	DOF_DataPoint
class	DOF_Node
class	EItem
	Inner class for Genetic Algorithm, hold one population with some additional info. More...
class	func_1d
class	GA_Minimizer
class	JJH_Minimizer
class	lbfgs_iteration_data
class	LineMinimizationAlgorithm
class	Minimizer
	Simple low-level minimizer class. More...
class	MinimizerMap
class	MinimizerOptions
class	Multifunc
	Multifunction interface class. More...
class	NelderMeadSimplex
class	NumDerivCheckData
class	NumericalDerivCheckResult
class	Particle
	Simple data container for PSO algorithm. More...
class	ParticleSwarmMinimizer
	Particle Swarm Optimization engine. More...
class	SimpleDerivCheckResult
class	SingleResidueMultifunc
	A streamlined AtomTreeMultifunc designed specifically for RTMIN. More...
struct	sort_pred
class	StrongWolfeLineMinimization

Typedefs
typedef utility::pointer::shared_ptr < AtomTreeMinimizer >	AtomTreeMinimizerOP
typedef utility::pointer::shared_ptr < AtomTreeMinimizer const >	AtomTreeMinimizerCOP
typedef boost::tuple< Vector, Vector, Vector, Vector >	VectorQuad
typedef utility::pointer::shared_ptr < CartesianMinimizer >	CartesianMinimizerOP
typedef utility::pointer::shared_ptr < CartesianMinimizer const >	CartesianMinimizerCOP
typedef utility::pointer::shared_ptr < CartesianMinimizerMap >	CartesianMinimizerMapOP
typedef utility::pointer::shared_ptr < CartesianMinimizerMap const >	CartesianMinimizerMapCOP
typedef utility::pointer::shared_ptr < DOF_Node >	DOF_NodeOP
typedef utility::pointer::shared_ptr < DOF_Node const >	DOF_NodeCOP
typedef utility::pointer::shared_ptr < LineMinimizationAlgorithm >	LineMinimizationAlgorithmOP
typedef utility::pointer::shared_ptr < LineMinimizationAlgorithm const >	LineMinimizationAlgorithmCOP
typedef utility::pointer::shared_ptr < MinimizerMap >	MinimizerMapOP
typedef utility::pointer::shared_ptr < MinimizerMap const >	MinimizerMapCOP
typedef utility::pointer::shared_ptr < MinimizerOptions >	MinimizerOptionsOP
typedef utility::pointer::shared_ptr < MinimizerOptions const >	MinimizerOptionsCOP
typedef utility::pointer::shared_ptr < Multifunc >	MultifuncOP
typedef utility::pointer::shared_ptr < Multifunc const >	MultifuncCOP
typedef utility::pointer::shared_ptr < SimpleDerivCheckResult >	SimpleDerivCheckResultOP
typedef utility::pointer::shared_ptr < SimpleDerivCheckResult const >	SimpleDerivCheckResultCOP
typedef utility::pointer::shared_ptr < NumDerivCheckData >	NumDerivCheckDataOP
typedef utility::pointer::shared_ptr < NumDerivCheckData const >	NumDerivCheckDataCOP
typedef utility::pointer::shared_ptr < NumericalDerivCheckResult >	NumericalDerivCheckResultOP
typedef utility::pointer::shared_ptr < NumericalDerivCheckResult const >	NumericalDerivCheckResultCOP
typedef utility::pointer::shared_ptr < Particle >	ParticleOP
typedef utility::pointer::shared_ptr < Particle const >	ParticleCOP
typedef utility::vector1 < ParticleOP >	ParticleOPs
typedef utility::pointer::shared_ptr < ParticleSwarmMinimizer >	ParticleSwarmMinimizerOP
typedef utility::pointer::shared_ptr < ParticleSwarmMinimizer const >	ParticleSwarmMinimizerCOP
typedef utility::vector1< Real >	Multivec

Functions
static THREAD_LOCAL basic::Tracer	TR ("core.optimization")
void	atom_tree_dfunc (pose::Pose &pose, MinimizerMap &min_map, scoring::ScoreFunction const &scorefxn, Multivec const &vars, Multivec &dE_dvars)
Real	torsional_derivative_from_cartesian_derivatives (kinematics::tree::Atom const &atom, optimization::DOF_Node const &dof_node, Real dof_deriv, Real torsion_scale_factor)
void	atom_tree_get_atompairE_deriv (pose::Pose &pose, MinimizerMap &min_map, scoring::ScoreFunction const &scorefxn)
SimpleDerivCheckResult	simple_numeric_deriv_check (Multifunc const &func, Multivec const &start_vars, Multivec const &dE_dvars, bool send_to_stdout, bool verbose, Size nsteps=5)
	Numeric deriv check for Multifuncs other than the AtomTreeMultifunc. More...
void	numerical_derivative_check (MinimizerMap const &min_map, Multifunc const &func, Multivec const &start_vars, Multivec const &dE_dvars, NumericalDerivCheckResultOP deriv_check_result, bool const verbose)
static THREAD_LOCAL basic::Tracer	TR ("core.optimization.AtomTreeMinimizer")
static THREAD_LOCAL basic::Tracer	TR ("core.optimization")
void	cartesian_dfunc (pose::Pose &pose, CartesianMinimizerMap &min_map, scoring::ScoreFunction const &scorefxn, Multivec const &vars, Multivec &dE_dvars)
void	cartesian_collect_atompairE_deriv (pose::Pose &pose, CartesianMinimizerMap &min_map, scoring::ScoreFunction const &scorefxn, Multivec &dE_dvars, core::Real scale)
void	cartesian_collect_torsional_deriv (pose::Pose &pose, CartesianMinimizerMap &min_map, core::scoring::ScoreFunction const &scorefxn, Multivec &dE_dvars, core::Real scale)
void	cart_numerical_derivative_check (CartesianMinimizerMap const &min_map, CartesianMultifunc const &func, Multivec const &start_vars, Multivec const &dE_dvars, NumericalDerivCheckResultOP deriv_check_result, bool const verbose)
void	tors_deriv_to_cartesian (Real dE_dtor, VectorQuad const &coords, VectorQuad &dE_dxs)
static THREAD_LOCAL basic::Tracer	TR ("core.optimization.CartesianMinimizer")
static THREAD_LOCAL basic::Tracer	TR ("core.optimization.GA_Minimizer")
static bool	yes_no_random (Real probability)
	Return true with given probability. More...
static THREAD_LOCAL basic::Tracer	TR ("core.optimization.LineMinimizer")
static THREAD_LOCAL basic::Tracer	TR ("core.optimization.Minimizer")
bool	DOF_Node_sorter (DOF_NodeCOP a, DOF_NodeCOP b)
static THREAD_LOCAL basic::Tracer	TR ("core.optimization.NelderMeadSimplex")
std::ostream &	operator<< (std::ostream &os, Particle const &p)
	stream output operator for Particle types More...
bool	cmp_particles (ParticleOP a, ParticleOP b)

Typedef Documentation

typedef utility::pointer::shared_ptr< AtomTreeMinimizer const > core::optimization::AtomTreeMinimizerCOP

typedef utility::pointer::shared_ptr< AtomTreeMinimizer > core::optimization::AtomTreeMinimizerOP

typedef utility::pointer::shared_ptr< CartesianMinimizer const > core::optimization::CartesianMinimizerCOP

typedef utility::pointer::shared_ptr< CartesianMinimizerMap const > core::optimization::CartesianMinimizerMapCOP

typedef utility::pointer::shared_ptr< CartesianMinimizerMap > core::optimization::CartesianMinimizerMapOP

typedef utility::pointer::shared_ptr< CartesianMinimizer > core::optimization::CartesianMinimizerOP

typedef utility::pointer::shared_ptr< DOF_Node const > core::optimization::DOF_NodeCOP

typedef utility::pointer::shared_ptr< DOF_Node > core::optimization::DOF_NodeOP

typedef utility::pointer::shared_ptr< LineMinimizationAlgorithm const > core::optimization::LineMinimizationAlgorithmCOP

typedef utility::pointer::shared_ptr< LineMinimizationAlgorithm > core::optimization::LineMinimizationAlgorithmOP

typedef utility::pointer::shared_ptr< MinimizerMap const > core::optimization::MinimizerMapCOP

typedef utility::pointer::shared_ptr< MinimizerMap > core::optimization::MinimizerMapOP

typedef utility::pointer::shared_ptr< MinimizerOptions const > core::optimization::MinimizerOptionsCOP

typedef utility::pointer::shared_ptr< MinimizerOptions > core::optimization::MinimizerOptionsOP

typedef utility::pointer::shared_ptr< Multifunc const > core::optimization::MultifuncCOP

typedef utility::pointer::shared_ptr< Multifunc > core::optimization::MultifuncOP

typedef utility::vector1< Real > core::optimization::Multivec

typedef utility::pointer::shared_ptr< NumDerivCheckData const > core::optimization::NumDerivCheckDataCOP

typedef utility::pointer::shared_ptr< NumDerivCheckData > core::optimization::NumDerivCheckDataOP

typedef utility::pointer::shared_ptr< NumericalDerivCheckResult const > core::optimization::NumericalDerivCheckResultCOP

typedef utility::pointer::shared_ptr< NumericalDerivCheckResult > core::optimization::NumericalDerivCheckResultOP

typedef utility::pointer::shared_ptr< Particle const > core::optimization::ParticleCOP

typedef utility::pointer::shared_ptr< Particle > core::optimization::ParticleOP

typedef utility::vector1< ParticleOP > core::optimization::ParticleOPs

typedef utility::pointer::shared_ptr< ParticleSwarmMinimizer const > core::optimization::ParticleSwarmMinimizerCOP

typedef utility::pointer::shared_ptr< ParticleSwarmMinimizer > core::optimization::ParticleSwarmMinimizerOP

typedef utility::pointer::shared_ptr< SimpleDerivCheckResult const > core::optimization::SimpleDerivCheckResultCOP

typedef utility::pointer::shared_ptr< SimpleDerivCheckResult > core::optimization::SimpleDerivCheckResultOP

typedef boost::tuple< Vector,Vector,Vector,Vector > core::optimization::VectorQuad

Function Documentation

void core::optimization::atom_tree_dfunc	(	pose::Pose &	pose,
		MinimizerMap &	min_map,
		scoring::ScoreFunction const &	scorefxn,
		Multivec const &	vars,
		Multivec &	dE_dvars
	)

car note that this calculates the deriv for all torsion angles even car those that are fixed. Because of the way that the derivative is car calculated, I don't believe this is a significant slow down (ie car have to run over all the atom pairs twice, regardless of the number car of torsion angles)

car multiple neighborlists: car cendist centroid distances in current structure, cutoff for vdw car dis2_tether centroid distances in tether structure, cutoff for tether

db computes the derivative of E with respect to each db of the torsion angles. Using the chain rule, we have db db dE/d phi = dE/dr * dr/dphi db db dr/dphi = Eab x (V-Vb) . (V' - V)/|V-V'| db db (the first cross product is the displacement of V upon a rotation dphi db around the unit vector Eab, Vb is the coordinates of the second atom in db the bond) db car dE/dR = 2r (for vdw at least) db since | V-V'| = r, db db dE/ dphi = 2 Eab x (V-Vb) . (V' - V) db db note that Eab and Vb are different for each torsion angle, but V' db and V are the same. rearranging: db db = - 2 Eab X Vb . (V' - V) - 2 Eab . (V' x V). db db now we need the averages over all Vi of the difference and the db crossproduct of V and V'.

car below, Eab x Vb is 'vec' car Eab is 'unit' car (V'-V) is 'f2' car 'F2tot' = f2*dE_dR (cumulative) car (V' X V) is 'f1' ('F1_xxxE' is cumulative for potential xxx) car eval_dE_dR actually returns dE_dR/r

car if two atoms are fixed relatively in cartesian space, then dr/dphi = 0 car and there is no contribution to the derivative

References core::kinematics::AtomTree::atom(), core::optimization::DOF_Node::atom_id(), core::pose::Pose::atom_tree(), atom_tree_get_atompairE_deriv(), core::optimization::MinimizerMap::begin(), core::optimization::MinimizerMap::copy_dofs_to_pose(), core::optimization::DOF_Node::dof_id(), core::optimization::MinimizerMap::end(), core::scoring::ScoreFunction::eval_dof_derivative(), core::scoring::ScoreFunction::finalize_after_derivatives(), core::optimization::MinimizerMap::link_torsion_vectors(), core::optimization::MinimizerMap::nangles(), core::scoring::ScoreFunction::setup_for_derivatives(), core::optimization::DOF_Node::torsion_id(), core::optimization::MinimizerMap::torsion_scale_factor(), torsional_derivative_from_cartesian_derivatives(), and core::optimization::MinimizerMap::zero_torsion_vectors().

Referenced by core::optimization::AtomTreeMultifunc::dfunc(), protocols::ncbb::SecStructMinimizeMultiFunc::dfunc(), and protocols::normalmode::NormalModeMultifunc::dfunc().

void core::optimization::atom_tree_get_atompairE_deriv	(	pose::Pose &	pose,
		MinimizerMap &	min_map,
		scoring::ScoreFunction const &	scorefxn
	)

First evaluate all derivatives for the residue- and residue-pair decomposable terms, using the minimization graph as a guide. Then, evaluate any further derivatives for those terms that are not residue- or residue-pair decomposable

References core::optimization::MinimizerMap::atom_derivatives(), core::id::AtomID::atomno(), core::optimization::DOF_Node::atoms(), core::optimization::MinimizerMap::begin(), core::optimization::MinimizerMap::domain_map(), core::optimization::MinimizerMap::end(), core::pose::Pose::energies(), core::scoring::eval_atom_derivatives_for_minedge(), core::scoring::eval_atom_derivatives_for_minnode(), core::scoring::ScoreFunction::eval_npd_atom_derivative(), core::optimization::DOF_Node::F1(), core::optimization::DOF_Node::F2(), core::scoring::Energies::minimization_graph(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::pose::Pose::total_residue(), and core::scoring::ScoreFunction::weights().

Referenced by atom_tree_dfunc().

void core::optimization::cart_numerical_derivative_check	(	CartesianMinimizerMap const &	min_map,
		CartesianMultifunc const &	func,
		Multivec const &	start_vars,
		Multivec const &	dE_dvars,
		NumericalDerivCheckResultOP	deriv_check_result,
		bool const	verbose
	)

References protocols::comparative_modeling::features::A, core::chemical::element::F, core::optimization::CartesianMinimizerMap::get_atom(), core::chemical::element::I, core::optimization::CartesianMinimizerMap::natoms(), core::optimization::CartesianMinimizerMap::ndofs(), and TR().

Referenced by core::optimization::CartesianMultifunc::dfunc().

void core::optimization::cartesian_collect_atompairE_deriv	(	pose::Pose &	pose,
		CartesianMinimizerMap &	min_map,
		scoring::ScoreFunction const &	scorefxn,
		Multivec &	dE_dvars,
		core::Real	scale
	)

References core::optimization::CartesianMinimizerMap::atom_derivatives(), core::optimization::CartesianMinimizerMap::domain_map(), core::pose::Pose::energies(), core::scoring::eval_atom_derivatives_for_minnode(), core::scoring::ScoreFunction::eval_npd_atom_derivative(), core::scoring::eval_weighted_atom_derivatives_for_minedge(), core::optimization::CartesianMinimizerMap::get_atom(), core::conformation::symmetry::is_symmetric(), core::scoring::Energies::minimization_graph(), core::optimization::CartesianMinimizerMap::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::scoring::ScoreFunction::weights().

Referenced by cartesian_dfunc().

void core::optimization::cartesian_collect_torsional_deriv	(	pose::Pose &	pose,
		CartesianMinimizerMap &	min_map,
		core::scoring::ScoreFunction const &	scorefxn,
		Multivec &	dE_dvars,
		core::Real	scale
	)

References core::pose::Pose::conformation(), protocols::simple_filters::coords(), core::scoring::ScoreFunction::eval_dof_derivative(), core::optimization::CartesianMinimizerMap::get_atom_index(), core::optimization::CartesianMinimizerMap::get_dof_id(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::optimization::CartesianMinimizerMap::get_TorsionID(), core::optimization::CartesianMinimizerMap::ntorsions(), tors_deriv_to_cartesian(), and core::pose::Pose::xyz().

Referenced by cartesian_dfunc().

void core::optimization::cartesian_dfunc	(	pose::Pose &	pose,
		CartesianMinimizerMap &	min_map,
		scoring::ScoreFunction const &	scorefxn,
		Multivec const &	vars,
		Multivec &	dE_dvars
	)

References cartesian_collect_atompairE_deriv(), cartesian_collect_torsional_deriv(), core::pose::Pose::conformation(), core::optimization::CartesianMinimizerMap::copy_dofs_to_pose(), core::scoring::ScoreFunction::finalize_after_derivatives(), core::conformation::symmetry::is_symmetric(), core::optimization::CartesianMinimizerMap::ndofs(), core::scoring::ScoreFunction::setup_for_derivatives(), and core::optimization::CartesianMinimizerMap::zero_stored_derivs().

Referenced by core::optimization::CartesianMultifunc::dfunc().

bool core::optimization::cmp_particles	(	ParticleOP	a,
		ParticleOP	b
	)

Referenced by core::optimization::ParticleSwarmMinimizer::run().

bool core::optimization::DOF_Node_sorter	(	DOF_NodeCOP	a,
		DOF_NodeCOP	b
	)

References protocols::match::upstream::b.

Referenced by core::optimization::MinimizerMap::setup().

void core::optimization::numerical_derivative_check	(	MinimizerMap const &	min_map,
		Multifunc const &	func,
		Multivec const &	start_vars,
		Multivec const &	dE_dvars,
		NumericalDerivCheckResultOP	deriv_check_result,
		bool const	verbose
	)

References protocols::comparative_modeling::features::A, core::id::DOF_ID::atomno(), core::optimization::DOF_Node::atomno(), core::optimization::DOF_Node::atoms(), core::optimization::MinimizerMap::begin(), core::id::BOGUS_DOF_ID, core::optimization::DOF_Node::dependent(), core::optimization::DOF_Node::dof_id(), core::optimization::MinimizerMap::end(), core::chemical::element::F, core::chemical::element::I, core::optimization::MinimizerMap::nangles(), core::optimization::DOF_Node::parent(), core::id::DOF_ID::rsd(), core::optimization::DOF_Node::rsd(), core::id::DOF_ID::type(), and core::optimization::DOF_Node::type().

Referenced by core::optimization::AtomTreeMultifunc::dfunc().

std::ostream & core::optimization::operator<<	(	std::ostream &	os,
		Particle const &	p
	)

stream output operator for Particle types

References core::chemical::element::F, core::optimization::Particle::fitness_, core::optimization::Particle::fitness_pbest(), and core::optimization::Particle::p_.

SimpleDerivCheckResult core::optimization::simple_numeric_deriv_check	(	Multifunc const &	func,
		Multivec const &	start_vars,
		Multivec const &	dE_dvars,
		bool	send_to_stdout,
		bool	verbose,
		Size	nsteps
	)

Numeric deriv check for Multifuncs other than the AtomTreeMultifunc.

References protocols::comparative_modeling::features::A, core::optimization::SimpleDerivCheckResult::abs_deriv_dev(), core::optimization::SimpleDerivCheckResult::best_abs_log_norm_ratio(), core::optimization::SimpleDerivCheckResult::best_cos_theta(), core::optimization::SimpleDerivCheckResult::best_norm_analytic(), core::optimization::SimpleDerivCheckResult::best_norm_numeric(), core::chemical::element::F, core::chemical::element::I, core::optimization::SimpleDerivCheckResult::rel_deriv_dev(), and core::optimization::SimpleDerivCheckResult::step_data().

void core::optimization::tors_deriv_to_cartesian	(	Real	dE_dtor,
		VectorQuad const &	coords,
		VectorQuad &	dE_dxs
	)

Referenced by cartesian_collect_torsional_deriv(), and core::pack::scmin::CartSCMinMultifunc::dfunc().

Real core::optimization::torsional_derivative_from_cartesian_derivatives	(	kinematics::tree::Atom const &	atom,
		optimization::DOF_Node const &	dof_node,
		Real	dof_deriv,
		Real	torsion_scale_factor
	)

Refactored from atom_tree_dfunc above for use in alternate minimization contexts

References core::kinematics::tree::Atom::dof(), core::optimization::DOF_Node::F1(), core::optimization::DOF_Node::F2(), core::kinematics::tree::Atom::get_dof_axis_and_end_pos(), core::chemical::rings::PHI, core::id::RB4, core::id::RB5, core::id::RB6, core::chemical::rings::THETA, and core::optimization::DOF_Node::type().

Referenced by atom_tree_dfunc(), core::optimization::symmetry::atom_tree_dfunc(), and core::pack::scmin::SCMinMultifunc::dfunc().

static THREAD_LOCAL basic::Tracer core::optimization::TR ( "core.optimization.GA_Minimizer"  )

static

static THREAD_LOCAL basic::Tracer core::optimization::TR ( "core.optimization.NelderMeadSimplex"  )

static

static THREAD_LOCAL basic::Tracer core::optimization::TR ( "core.optimization.Minimizer"  )

static

static THREAD_LOCAL basic::Tracer core::optimization::TR ( "core.optimization.CartesianMinimizer"  )

static

Referenced by core::optimization::CartesianMinimizer::run().

static THREAD_LOCAL basic::Tracer core::optimization::TR ( "core.optimization.AtomTreeMinimizer"  )

static

Referenced by core::optimization::AtomTreeMinimizer::check_setup().

static THREAD_LOCAL basic::Tracer core::optimization::TR ( "core.optimization"  )

static

Referenced by cart_numerical_derivative_check().

static THREAD_LOCAL basic::Tracer core::optimization::TR ( "core.optimization.LineMinimizer"  )

static

static THREAD_LOCAL basic::Tracer core::optimization::TR ( "core.optimization"  )

static

Referenced by core::optimization::Minimizer::dfpmin(), core::optimization::Minimizer::dfpmin_armijo(), core::optimization::Minimizer::lbfgs(), core::optimization::Minimizer::linmin_iterated(), core::optimization::GA_Minimizer::loop(), core::optimization::GA_Minimizer::run(), core::optimization::JJH_Minimizer::run(), and core::optimization::GA_Minimizer::step().

static bool core::optimization::yes_no_random ( Real  probability )

static

Return true with given probability.

References core::scoring::rg.

Referenced by core::optimization::GA_Minimizer::cross_over(), core::optimization::GA_Minimizer::mutate(), and core::optimization::GA_Minimizer::step().