core::optimization::MinimizerMap Class Reference

#include <MinimizerMap.hh>

Inheritance diagram for core::optimization::MinimizerMap:

Public Types
typedef std::list< DOF_NodeOP >	DOF_Nodes
typedef DOF_Nodes::iterator	iterator
typedef DOF_Nodes::const_iterator	const_iterator
typedef id::AtomID	AtomID
typedef id::DOF_ID	DOF_ID
typedef id::DOF_Type	DOF_Type
typedef kinematics::MinimizerMapBase	parent
typedef scoring::DerivVectorPair	DerivVectorPair
Public Types inherited from core::kinematics::MinimizerMapBase
typedef id::AtomID	AtomID
typedef id::DOF_ID	DOF_ID
typedef id::DOF_Type	DOF_Type

Public Member Functions
	MinimizerMap ()
	~MinimizerMap () override
void	setup (pose::Pose &pose, kinematics::MoveMap const &move_map)
void	add_torsion (DOF_ID const &new_torsion, DOF_ID const &parent) override
	Allow the AtomTree to communicate to this class that a particular torsion (or angle or distance – a particular DOF) belongs in the minimization task to inform this class the parent DOF for that torsion. More...
void	add_atom (AtomID const &atom_id, DOF_ID const &dof_id) override
	Allow the AtomTree to inform this class that a particular atom belongs in the derivative calculation for a certain DOF. That certain DOF must have already been included in the minimization process through a prior invocation of the add_torsion method. More...
const_iterator	begin () const
const_iterator	end () const
iterator	begin ()
iterator	end ()
DOF_Nodes const &	dof_nodes () const
DOF_Nodes &	dof_nodes ()
void	link_torsion_vectors ()
	this will only work if DOF_nodes are sorted! More...
void	zero_torsion_vectors ()
void	reset (pose::Pose const &pose)
	clears old data+dimensions dof_node_pointer using size data from the pose More...
void	copy_dofs_from_pose (pose::Pose const &pose, Multivec &dofs) const
void	copy_dofs_to_pose (pose::Pose &pose, Multivec const &dofs) const
int	nangles () const
void	reset_jump_rb_deltas (pose::Pose &pose, Multivec &dofs) const
Real	torsion_scale_factor (DOF_Node const &tor) const
kinematics::DomainMap const &	domain_map () const override
DOF_NodeOP	dof_node_from_id (DOF_ID const &id)
	get a dof_node by its dof_id More...
utility::vector1< DerivVectorPair > &	atom_derivatives (Size resid)
Public Member Functions inherited from core::kinematics::MinimizerMapBase
	MinimizerMapBase ()
	default ctor; noop More...
	~MinimizerMapBase () override
	dstor More...

Private Member Functions
void	clear_dof_nodes ()
	deletes and clears dof_nodes_ More...
void	assign_rosetta_torsions (pose::Pose const &pose)

Private Attributes
DOF_Nodes	dof_nodes_
	list of all the moving degrees of freedom More...
id::DOF_ID_Map< DOF_NodeOP >	dof_node_pointer_
	pointer from DOF_ID to the corresponding DOF_NodeOP More...
kinematics::DomainMap	domain_map_
utility::vector1< utility::vector1< DerivVectorPair > >	atom_derivatives_

Member Typedef Documentation

AtomID

typedef id::AtomID core::optimization::MinimizerMap::AtomID

const_iterator

typedef DOF_Nodes::const_iterator core::optimization::MinimizerMap::const_iterator

DerivVectorPair

typedef scoring::DerivVectorPair core::optimization::MinimizerMap::DerivVectorPair

DOF_ID

typedef id::DOF_ID core::optimization::MinimizerMap::DOF_ID

DOF_Nodes

typedef std::list< DOF_NodeOP > core::optimization::MinimizerMap::DOF_Nodes

DOF_Type

typedef id::DOF_Type core::optimization::MinimizerMap::DOF_Type

iterator

typedef DOF_Nodes::iterator core::optimization::MinimizerMap::iterator

parent

typedef kinematics::MinimizerMapBase core::optimization::MinimizerMap::parent

Constructor & Destructor Documentation

MinimizerMap()

core::optimization::MinimizerMap::MinimizerMap ( )

inline

~MinimizerMap()

core::optimization::MinimizerMap::~MinimizerMap ( )

override

References clear_dof_nodes().

Member Function Documentation

add_atom()

void core::optimization::MinimizerMap::add_atom ( AtomID const &  atom_id, DOF_ID const &  dof_id  )

overridevirtual

Allow the AtomTree to inform this class that a particular atom belongs in the derivative calculation for a certain DOF. That certain DOF must have already been included in the minimization process through a prior invocation of the add_torsion method.

Implements core::kinematics::MinimizerMapBase.

References dof_node_pointer_, and core::id::DOF_ID::valid().

add_torsion()

void core::optimization::MinimizerMap::add_torsion ( DOF_ID const &  new_torsion, DOF_ID const &  parent  )

overridevirtual

Allow the AtomTree to communicate to this class that a particular torsion (or angle or distance – a particular DOF) belongs in the minimization task to inform this class the parent DOF for that torsion.

Implements core::kinematics::MinimizerMapBase.

References dof_node_pointer_, dof_nodes_, and core::id::DOF_ID::valid().

assign_rosetta_torsions()

void core::optimization::MinimizerMap::assign_rosetta_torsions ( pose::Pose const &  pose )

private

References core::id::TorsionID::BOGUS_TORSION_ID(), core::optimization::DOF_Node::dof_id(), dof_nodes_, core::id::PHI, core::pose::setup_dof_to_torsion_map(), core::optimization::DOF_Node::torsion_id(), and core::optimization::DOF_Node::type().

Referenced by setup().

atom_derivatives()

utility::vector1< DerivVectorPair >& core::optimization::MinimizerMap::atom_derivatives ( Size  resid )

inline

References atom_derivatives_.

Referenced by core::optimization::atom_tree_get_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative().

begin() [1/2]

iterator core::optimization::MinimizerMap::begin ( )

inline

References dof_nodes_.

begin() [2/2]

const_iterator core::optimization::MinimizerMap::begin ( ) const

inline

References dof_nodes_.

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::atom_tree_get_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), and core::optimization::numerical_derivative_check().

clear_dof_nodes()

void core::optimization::MinimizerMap::clear_dof_nodes ( )

private

deletes and clears dof_nodes_

References core::id::DOF_ID_Map< T >::clear(), dof_node_pointer_, and dof_nodes_.

Referenced by reset(), and ~MinimizerMap().

copy_dofs_from_pose()

void core::optimization::MinimizerMap::copy_dofs_from_pose	(	pose::Pose const &	pose,
		Multivec &	dofs
	)		const

References core::pose::Pose::dof(), core::optimization::DOF_Node::dof_id(), dof_nodes_, and torsion_scale_factor().

Referenced by protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply(), protocols::normalmode::NormalModeMinimizer::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ncbb::SecStructMinimizeMultiFunc::get_dofs_for_pose0(), protocols::normalmode::NormalModeMultifunc::get_dofs_for_pose0(), core::util::getMLweight(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), and core::optimization::AtomTreeMinimizer::run().

copy_dofs_to_pose()

void core::optimization::MinimizerMap::copy_dofs_to_pose	(	pose::Pose &	pose,
		Multivec const &	dofs
	)		const

References core::optimization::DOF_Node::dof_id(), dof_nodes_, core::pose::Pose::set_dof(), and torsion_scale_factor().

Referenced by protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), core::optimization::atom_tree_dfunc(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::operator()(), protocols::ncbb::SecStructMinimizeMultiFunc::operator()(), protocols::normalmode::NormalModeMultifunc::operator()(), core::optimization::AtomTreeMultifunc::operator()(), and core::optimization::SingleResidueMultifunc::operator()().

dof_node_from_id()

DOF_NodeOP core::optimization::MinimizerMap::dof_node_from_id ( DOF_ID const &  id )

inline

get a dof_node by its dof_id

References dof_node_pointer_.

dof_nodes() [1/2]

DOF_Nodes& core::optimization::MinimizerMap::dof_nodes ( )

inline

References dof_nodes_.

dof_nodes() [2/2]

DOF_Nodes const& core::optimization::MinimizerMap::dof_nodes ( ) const

inline

References dof_nodes_.

Referenced by protocols::ncbb::SecStructMinimizeMultiFunc::get_dofs_for_pose0(), protocols::normalmode::NormalModeMultifunc::get_dofs_for_pose0(), protocols::ncbb::SecStructMinimizeMultiFunc::get_dofs_map(), protocols::normalmode::NormalModeMultifunc::get_dofs_map(), and protocols::normalmode::NormalModeMultifunc::vars_to_dofs().

domain_map()

kinematics::DomainMap const& core::optimization::MinimizerMap::domain_map ( ) const

inlineoverridevirtual

Implements core::kinematics::MinimizerMapBase.

References domain_map_.

Referenced by protocols::ncbb::SecStructMinimizeMover::apply(), protocols::normalmode::NormalModeMinimizer::apply(), core::optimization::atom_tree_get_atompairE_deriv(), protocols::cartesian::MolecularDynamics::createCartesianDerivatives(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), protocols::cartesian::MolecularDynamics::MolecularDynamics(), and core::optimization::AtomTreeMinimizer::run().

end() [1/2]

iterator core::optimization::MinimizerMap::end ( )

inline

References dof_nodes_.

end() [2/2]

const_iterator core::optimization::MinimizerMap::end ( ) const

inline

References dof_nodes_.

Referenced by core::optimization::atom_tree_dfunc(), core::optimization::atom_tree_get_atompairE_deriv(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), protocols::cartesian::MolecularDynamics::getCartesianDerivatives(), and core::optimization::numerical_derivative_check().

link_torsion_vectors()

void core::optimization::MinimizerMap::link_torsion_vectors

(

)

this will only work if DOF_nodes are sorted!

References core::optimization::DOF_Node::depth(), dof_nodes_, and core::optimization::DOF_Node::link_vectors().

Referenced by core::optimization::atom_tree_dfunc(), and protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc().

nangles()

int core::optimization::MinimizerMap::nangles ( ) const

inline

References dof_nodes_.

Referenced by protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply(), protocols::normalmode::NormalModeMinimizer::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), core::optimization::atom_tree_dfunc(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::util::getMLweight(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), core::optimization::numerical_derivative_check(), and core::optimization::AtomTreeMinimizer::run().

reset()

void core::optimization::MinimizerMap::reset

(

pose::Pose const &

pose

)

clears old data+dimensions dof_node_pointer using size data from the pose

References atom_derivatives_, clear_dof_nodes(), dof_node_pointer_, core::pose::initialize_dof_id_map(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by setup().

reset_jump_rb_deltas()

void core::optimization::MinimizerMap::reset_jump_rb_deltas	(	pose::Pose &	pose,
		Multivec &	dofs
	)		const

References core::optimization::DOF_Node::atom_id(), dof_nodes_, core::id::DOF_type_is_rb(), core::kinematics::Jump::fold_in_rb_deltas(), core::pose::Pose::jump(), core::pose::Pose::set_jump(), and core::optimization::DOF_Node::type().

Referenced by protocols::normalmode::NormalModeMinimizer::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), and core::optimization::AtomTreeMinimizer::run().

setup()

void core::optimization::MinimizerMap::setup	(	pose::Pose &	pose,
		kinematics::MoveMap const &	move_map
	)

References assign_rosetta_torsions(), core::conformation::Conformation::atom_tree(), core::pose::Pose::atom_tree(), core::id::DOF_ID::BOGUS_DOF_ID(), core::pose::Pose::conformation(), core::optimization::DOF_Node_sorter(), dof_nodes_, domain_map_, core::pose::initialize_atomid_map(), reset(), core::kinematics::AtomTree::root(), core::pose::setup_dof_mask_from_move_map(), core::pose::Pose::size(), and core::kinematics::AtomTree::update_domain_map().

Referenced by protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::normalmode::NormalModeMinimizer::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), core::util::getMLweight(), protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(), protocols::cartesian::MolecularDynamics::MolecularDynamics(), and core::optimization::AtomTreeMinimizer::run().

torsion_scale_factor()

Real core::optimization::MinimizerMap::torsion_scale_factor

(

DOF_Node const &

tor

)

const

References core::id::D, core::id::PHI, core::id::RB1, core::id::RB2, core::id::RB3, core::id::RB4, core::id::RB5, core::id::RB6, core::id::THETA, and core::optimization::DOF_Node::type().

Referenced by core::optimization::atom_tree_dfunc(), copy_dofs_from_pose(), copy_dofs_to_pose(), and protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc().

zero_torsion_vectors()

void core::optimization::MinimizerMap::zero_torsion_vectors

(

)

References atom_derivatives_, and dof_nodes_.

Referenced by core::optimization::atom_tree_dfunc(), and protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc().

Member Data Documentation

atom_derivatives_

utility::vector1< utility::vector1< DerivVectorPair > > core::optimization::MinimizerMap::atom_derivatives_

private

Referenced by atom_derivatives(), reset(), and zero_torsion_vectors().

dof_node_pointer_

id::DOF_ID_Map< DOF_NodeOP > core::optimization::MinimizerMap::dof_node_pointer_

private

pointer from DOF_ID to the corresponding DOF_NodeOP

Referenced by add_atom(), add_torsion(), clear_dof_nodes(), dof_node_from_id(), and reset().

dof_nodes_

DOF_Nodes core::optimization::MinimizerMap::dof_nodes_

private

list of all the moving degrees of freedom

Referenced by add_torsion(), assign_rosetta_torsions(), begin(), clear_dof_nodes(), copy_dofs_from_pose(), copy_dofs_to_pose(), dof_nodes(), end(), link_torsion_vectors(), nangles(), reset_jump_rb_deltas(), setup(), and zero_torsion_vectors().

domain_map_

kinematics::DomainMap core::optimization::MinimizerMap::domain_map_

private

Referenced by domain_map(), and setup().

---

The documentation for this class was generated from the following files:

• src/core/optimization/MinimizerMap.hh
• src/core/optimization/MinimizerMap.cc