core::scoring::MinimizationNode Class Reference

#include <MinimizationGraph.hh>

Inheritance diagram for core::scoring::MinimizationNode:

Collaboration diagram for core::scoring::MinimizationNode:

List of all members.

Public Types
typedef graph::Node	parent
typedef utility::vector1 < OneBodyEnergyCOP >	OneBodyEnergies
typedef OneBodyEnergies::const_iterator	OneBodyEnergiesIterator
typedef utility::vector1 < TwoBodyEnergyCOP >	TwoBodyEnergies
typedef TwoBodyEnergies::const_iterator	TwoBodyEnergiesIterator
typedef conformation::Residue	Residue
typedef pose::Pose	Pose
Public Member Functions
	MinimizationNode (graph::Graph *owner, Size index)
virtual	~MinimizationNode ()
virtual void	copy_from (parent const *source)
	copy mmember data from source node
virtual void	print ()
virtual Size	count_static_memory () const
	memory accounting scheme
virtual Size	count_dynamic_memory () const
	memory accounting scheme
ResSingleMinimizationData const &	res_min_data () const
ResSingleMinimizationData &	res_min_data ()
bool	add_onebody_enmeth (OneBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, int domain_map_color)
bool	add_twobody_enmeth (TwoBodyEnergyCOP enmeth, Residue const &rsd, Pose const &pose, EnergyMap const &weights, int domain_map_color)
void	setup_for_minimizing (Residue const &rsd, Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map)
void	setup_for_scoring (Residue const &rsd, Pose const &pose, ScoreFunction const &sfxn)
void	setup_for_derivatives (Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn)
void	update_active_enmeths_for_residue (Residue const &rsd, pose::Pose const &pose, EnergyMap const &weights, int domain_map_color)
Real	weight () const
void	weight (Real setting)
OneBodyEnergiesIterator	active_1benmeths_begin () const
OneBodyEnergiesIterator	active_1benmeths_end () const
OneBodyEnergiesIterator	active_1benmeths_std_begin () const
OneBodyEnergiesIterator	active_1benmeths_std_end () const
OneBodyEnergiesIterator	active_1benmeths_ext_begin () const
OneBodyEnergiesIterator	active_1benmeths_ext_end () const
OneBodyEnergiesIterator	dof_deriv_1benmeths_begin () const
OneBodyEnergiesIterator	dof_deriv_1benmeths_end () const
OneBodyEnergiesIterator	sfs_req_1benmeths_begin () const
OneBodyEnergiesIterator	sfs_req_1benmeths_end () const
OneBodyEnergiesIterator	sfd_req_1benmeths_begin () const
OneBodyEnergiesIterator	sfd_req_1benmeths_end () const
TwoBodyEnergiesIterator	active_intrares2benmeths_begin () const
TwoBodyEnergiesIterator	active_intrares2benmeths_end () const
TwoBodyEnergiesIterator	active_intrares2benmeths_std_begin () const
TwoBodyEnergiesIterator	active_intrares2benmeths_std_end () const
TwoBodyEnergiesIterator	active_intrares2benmeths_ext_begin () const
TwoBodyEnergiesIterator	active_intrares2benmeths_ext_end () const
TwoBodyEnergiesIterator	dof_deriv_2benmeths_begin () const
TwoBodyEnergiesIterator	dof_deriv_2benmeths_end () const
TwoBodyEnergiesIterator	sfs_req_2benmeths_begin () const
TwoBodyEnergiesIterator	sfs_req_2benmeths_end () const
TwoBodyEnergiesIterator	sfd_req_2benmeths_begin () const
TwoBodyEnergiesIterator	sfd_req_2benmeths_end () const
Public Attributes
	__pad0__:OneBodyEnergyCOP OneBodyEnergyCOP
	__pad1__:TwoBodyEnergyCOP TwoBodyEnergyCOP

---

Detailed Description

Class MinimizationNode holds the ResSingleMinimizationData information for a single residue in a Pose which is being minimized. The data held in this node will be used in both scoring the residue one-body energies and evaluating atom derivatives during minimization.

---

Member Typedef Documentation

typedef utility::vector1< OneBodyEnergyCOP > core::scoring::MinimizationNode::OneBodyEnergies

typedef OneBodyEnergies::const_iterator core::scoring::MinimizationNode::OneBodyEnergiesIterator

typedef graph::Node core::scoring::MinimizationNode::parent

typedef pose::Pose core::scoring::MinimizationNode::Pose

typedef conformation::Residue core::scoring::MinimizationNode::Residue

typedef utility::vector1< TwoBodyEnergyCOP > core::scoring::MinimizationNode::TwoBodyEnergies

typedef TwoBodyEnergies::const_iterator core::scoring::MinimizationNode::TwoBodyEnergiesIterator

---

Constructor & Destructor Documentation

core::scoring::MinimizationNode::MinimizationNode	(	graph::Graph *	owner,
		Size	index
	)

Referenced by count_static_memory().

core::scoring::MinimizationNode::~MinimizationNode

(

)

[virtual]

---

Member Function Documentation

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_begin

(

)

const

Referenced by core::scoring::eval_atom_derivatives_for_minnode(), and setup_for_minimizing().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_end

(

)

const

Referenced by core::scoring::eval_atom_derivatives_for_minnode(), and setup_for_minimizing().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_ext_begin

(

)

const

Referenced by core::scoring::eval_res_onebody_energies_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_ext_end

(

)

const

Referenced by core::scoring::eval_res_onebody_energies_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_std_begin

(

)

const

Referenced by core::scoring::eval_res_onebody_energies_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::active_1benmeths_std_end

(

)

const

Referenced by core::scoring::eval_res_onebody_energies_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_begin

(

)

const

Referenced by core::scoring::eval_atom_derivatives_for_minnode().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_end

(

)

const

Referenced by core::scoring::eval_atom_derivatives_for_minnode().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_ext_begin

(

)

const

Referenced by core::scoring::eval_res_onebody_energies_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_ext_end

(

)

const

Referenced by core::scoring::eval_res_onebody_energies_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_std_begin

(

)

const

Referenced by core::scoring::eval_res_onebody_energies_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::active_intrares2benmeths_std_end

(

)

const

Referenced by core::scoring::eval_res_onebody_energies_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

bool core::scoring::MinimizationNode::add_onebody_enmeth	(	OneBodyEnergyCOP	enmeth,
		Residue const &	rsd,
		Pose const &	pose,
		int	domain_map_color
	)

Referenced by core::scoring::ScoreFunction::setup_for_minimizing_for_node().

bool core::scoring::MinimizationNode::add_twobody_enmeth	(	TwoBodyEnergyCOP	enmeth,
		Residue const &	rsd,
		Pose const &	pose,
		EnergyMap const &	weights,
		int	domain_map_color
	)

Note that the minimization graph is used both to evaluate the scores for both the "modern" EnergyMethods and the "old" energy methods (those which still define eval_atom_derivative instead of the pairwise-decomposable derivative evaluation methods) so when these older energy methods are added to the minimization graph, they should not simply be rejected.

Referenced by core::scoring::ScoreFunction::setup_for_minimizing_for_node().

void core::scoring::MinimizationNode::copy_from

(

parent const *

source

)

[virtual]

copy mmember data from source node

invoked by copy ctor and operator= methods from Graph base class

Reimplemented from core::graph::Node.

Size core::scoring::MinimizationNode::count_dynamic_memory

(

)

const [virtual]

memory accounting scheme

recursively descend through heirarchy accounting for heap memory usage. Each derived class in the heirarchy should recursively add the amount of dynamic memory its parent allocates by calling parent::count_dynamic_memory

Reimplemented from core::graph::Node.

References core::graph::Node::count_dynamic_memory().

Size core::scoring::MinimizationNode::count_static_memory

(

)

const [virtual]

memory accounting scheme

called on most-derived class. The most-derived class should NOT recursively call this method on its parent class. The sizeof function will handle the whole Node (or DerivedNode).

Reimplemented from core::graph::Node.

References MinimizationNode().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_1benmeths_begin

(

)

const

Referenced by core::scoring::eval_dof_deriv_for_minnode(), and core::scoring::eval_weighted_dof_deriv_for_minnode().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_1benmeths_end

(

)

const

Referenced by core::scoring::eval_dof_deriv_for_minnode(), and core::scoring::eval_weighted_dof_deriv_for_minnode().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_2benmeths_begin

(

)

const

Referenced by core::scoring::eval_dof_deriv_for_minnode(), and core::scoring::eval_weighted_dof_deriv_for_minnode().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::dof_deriv_2benmeths_end

(

)

const

Referenced by core::scoring::eval_dof_deriv_for_minnode(), and core::scoring::eval_weighted_dof_deriv_for_minnode().

void core::scoring::MinimizationNode::print

(

)

[virtual]

References core::graph::Node::print().

ResSingleMinimizationData const& core::scoring::MinimizationNode::res_min_data

(

)

const [inline]

Referenced by core::scoring::eval_atom_derivatives_for_minnode(), core::scoring::eval_dof_deriv_for_minnode(), core::scoring::eval_res_onebody_energies_for_minnode(), core::scoring::eval_weighted_dof_deriv_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

ResSingleMinimizationData& core::scoring::MinimizationNode::res_min_data

(

)

[inline]

void core::scoring::MinimizationNode::setup_for_derivatives	(	Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)

References sfd_req_1benmeths_begin(), sfd_req_1benmeths_end(), sfd_req_2benmeths_begin(), and sfd_req_2benmeths_end().

Referenced by core::scoring::ScoreFunction::setup_for_derivatives().

void core::scoring::MinimizationNode::setup_for_minimizing	(	Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		kinematics::MinimizerMapBase const &	min_map
	)

References active_1benmeths_begin(), and active_1benmeths_end().

Referenced by core::scoring::ScoreFunction::reinitialize_minnode_for_residue(), and core::scoring::ScoreFunction::setup_for_minimizing_for_node().

void core::scoring::MinimizationNode::setup_for_scoring	(	Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn
	)

References sfs_req_1benmeths_begin(), sfs_req_1benmeths_end(), sfs_req_2benmeths_begin(), and sfs_req_2benmeths_end().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_1benmeths_begin

(

)

const

Referenced by setup_for_derivatives().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_1benmeths_end

(

)

const

Referenced by setup_for_derivatives().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_2benmeths_begin

(

)

const

Referenced by setup_for_derivatives().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfd_req_2benmeths_end

(

)

const

Referenced by setup_for_derivatives().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfs_req_1benmeths_begin

(

)

const

Referenced by setup_for_scoring().

MinimizationNode::OneBodyEnergiesIterator core::scoring::MinimizationNode::sfs_req_1benmeths_end

(

)

const

Referenced by setup_for_scoring().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfs_req_2benmeths_begin

(

)

const

Referenced by setup_for_scoring().

MinimizationNode::TwoBodyEnergiesIterator core::scoring::MinimizationNode::sfs_req_2benmeths_end

(

)

const

Referenced by setup_for_scoring().

void core::scoring::MinimizationNode::update_active_enmeths_for_residue	(	Residue const &	rsd,
		pose::Pose const &	pose,
		EnergyMap const &	weights,
		int	domain_map_color
	)

Referenced by core::scoring::ScoreFunction::reinitialize_minnode_for_residue().

Real core::scoring::MinimizationNode::weight

(

)

const [inline]

Referenced by core::scoring::eval_weighted_dof_deriv_for_minnode(), and core::scoring::eval_weighted_res_onebody_energies_for_minnode().

void core::scoring::MinimizationNode::weight

(

Real

setting

)

[inline]

---

Member Data Documentation

core::scoring::MinimizationNode::__pad0__

core::scoring::MinimizationNode::__pad1__

---

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

• src/core/scoring/MinimizationGraph.hh
• src/core/scoring/MinimizationGraph.cc