A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver. More...

#include <SimpleInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SimpleInteractionGraph:

[legend]

Public Member Functions
	SimpleInteractionGraph ()

	~SimpleInteractionGraph () override

virtual void	set_scorefunction (scoring::ScoreFunction const &sfxn)

scoring::ScoreFunction const &	scorefunction () const

std::list< scoring::methods::EnergyMethodCOP > const &	setup_for_scoring_for_residue_energy_methods ()

pose::Pose const &	pose () const

pose::PoseCOP	pose_cop () const

virtual void	initialize (pose::Pose const &pose)
	Initialization where the graph adds its own edges; use set_pose_no_initialize if the edges should be added externally. Assumes that the pose does not change its sequence. More...

virtual void	initialize (pose::Pose const &pose, task::PackerTaskCOP task)
	Initialization where the graph creates a packer-neighbor graph from the input packer task so that edges between residues that might become larger than they are in the input Pose (e.g., GLY --> ARG mutation) can be added to the graph. More...

virtual void	set_pose_no_initialize (pose::Pose const &pose)
	Initialize the graph so that all nodes take their current state from the input Pose – this does not add any edges to the graph. More...

virtual void	setup_after_edge_addition ()
	If set_pose_no_initialize was called, then after edges have been added. This function will also do any bookkeeping necessary before the start of simulated annealing. More...

virtual void	commit_change (Size node_id)

virtual void	reject_change (Size node_id, conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache)

virtual Real	consider_substitution (Size node_id, conformation::ResidueCOP new_state, basic::datacache::BasicDataCache &residue_data_cache)

virtual Real	total_energy ()

Size	count_static_memory () const override

Size	count_dynamic_memory () const override

void	delete_edge (utility::graph::Edge *) override

SimpleNode *	get_simple_node (Size ind)

SimpleNode const *	get_simple_node (Size ind) const

conformation::ResidueCOP	get_current_for_node (Size id) const

conformation::ResidueCOP	get_alternate_for_node (Size id) const

Protected Member Functions
utility::graph::Node *	create_new_node (Size node_index) override

utility::graph::Edge *	create_new_edge (Size index1, platform::Size index2) override

Private Attributes
scoring::ScoreFunctionOP	sfxn_

std::list< scoring::methods::EnergyMethodCOP >	sfs_energy_methods_

pose::PoseCOP	pose_

Detailed Description

A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver.

Constructor & Destructor Documentation

◆ SimpleInteractionGraph()

core::pack::interaction_graph::SimpleInteractionGraph::SimpleInteractionGraph ( )

◆ ~SimpleInteractionGraph()

core::pack::interaction_graph::SimpleInteractionGraph::~SimpleInteractionGraph ( )

overridedefault

Member Function Documentation

◆ commit_change()

void core::pack::interaction_graph::SimpleInteractionGraph::commit_change ( Size node_id )

virtual

Reimplemented in core::pack::interaction_graph::NPDHBSimpleInteractionGraph.

Referenced by core::pack::off_rotamer_pack_optimize().

◆ consider_substitution()

Real core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution	(	Size	node_id,
		conformation::ResidueCOP	new_state,
		basic::datacache::BasicDataCache &	residue_data_cache
	)

virtual

Note, this function returns (currE - altE) which represents the negative of the change in energy for the substition

Reimplemented in core::pack::interaction_graph::NPDHBSimpleInteractionGraph.

Referenced by core::pack::interaction_graph::NPDHBSimpleInteractionGraph::consider_substitution(), and core::pack::off_rotamer_pack_optimize().

◆ count_dynamic_memory()

Size core::pack::interaction_graph::SimpleInteractionGraph::count_dynamic_memory ( ) const

inlineoverride

◆ count_static_memory()

Size core::pack::interaction_graph::SimpleInteractionGraph::count_static_memory ( ) const

inlineoverride

◆ create_new_edge()

Edge * core::pack::interaction_graph::SimpleInteractionGraph::create_new_edge	(	platform::Size	index1,
		platform::Size	index2
	)

overrideprotected

◆ create_new_node()

Node * core::pack::interaction_graph::SimpleInteractionGraph::create_new_node ( platform::Size node_index )

overrideprotected

◆ delete_edge()

void core::pack::interaction_graph::SimpleInteractionGraph::delete_edge ( utility::graph::Edge * edge )

override

◆ get_alternate_for_node()

conformation::ResidueCOP core::pack::interaction_graph::SimpleInteractionGraph::get_alternate_for_node ( Size id ) const

inline

References core::pack::interaction_graph::SimpleNode::get_alternate(), and get_simple_node().

◆ get_current_for_node()

conformation::ResidueCOP core::pack::interaction_graph::SimpleInteractionGraph::get_current_for_node ( Size id ) const

inline

References core::pack::interaction_graph::SimpleNode::get_current(), and get_simple_node().

◆ get_simple_node() [1/2]

SimpleNode* core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node ( Size ind )

inline

Referenced by core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), get_alternate_for_node(), and get_current_for_node().

◆ get_simple_node() [2/2]

SimpleNode const* core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node ( Size ind ) const

inline

◆ initialize() [1/2]

void core::pack::interaction_graph::SimpleInteractionGraph::initialize ( pose::Pose const & pose )

virtual

Initialization where the graph adds its own edges; use set_pose_no_initialize if the edges should be added externally. Assumes that the pose does not change its sequence.

Reimplemented in core::pack::interaction_graph::NPDHBSimpleInteractionGraph.

References core::pack::task::TaskFactory::create_packer_task(), pose(), and core::pose::Pose::total_residue().

Referenced by core::pack::interaction_graph::NPDHBSimpleInteractionGraph::initialize().

◆ initialize() [2/2]

void core::pack::interaction_graph::SimpleInteractionGraph::initialize	(	pose::Pose const &	pose,
		task::PackerTaskCOP	task
	)

virtual

Initialization where the graph creates a packer-neighbor graph from the input packer task so that edges between residues that might become larger than they are in the input Pose (e.g., GLY --> ARG mutation) can be added to the graph.

References core::pack::interaction_graph::SimpleEdge::calc_long_range(), core::pack::interaction_graph::SimpleEdge::calc_short_range(), core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::create_packer_graph(), core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), pose(), pose_, set_pose_no_initialize(), sfxn_, and core::pack::interaction_graph::TR().

◆ pose()

pose::Pose const& core::pack::interaction_graph::SimpleInteractionGraph::pose ( ) const

inline

References pose_.

Referenced by initialize(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::initialize(), set_pose_no_initialize(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_pose_no_initialize(), and core::pack::interaction_graph::NPDHBSimpleInteractionGraph::total_energy().

◆ pose_cop()

pose::PoseCOP core::pack::interaction_graph::SimpleInteractionGraph::pose_cop ( ) const

References pose_.

◆ reject_change()

void core::pack::interaction_graph::SimpleInteractionGraph::reject_change	(	Size	node_id,
		conformation::ResidueCOP	res,
		basic::datacache::BasicDataCache &	residue_data_cache
	)

virtual

Reimplemented in core::pack::interaction_graph::NPDHBSimpleInteractionGraph.

Referenced by core::pack::off_rotamer_pack_optimize().

◆ scorefunction()

scoring::ScoreFunction const& core::pack::interaction_graph::SimpleInteractionGraph::scorefunction ( ) const

inline

References sfxn_.

Referenced by core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hb_weight().

◆ set_pose_no_initialize()

void core::pack::interaction_graph::SimpleInteractionGraph::set_pose_no_initialize ( pose::Pose const & pose )

virtual

Initialize the graph so that all nodes take their current state from the input Pose – this does not add any edges to the graph.

Reimplemented in core::pack::interaction_graph::NPDHBSimpleInteractionGraph.

References pose(), pose_, sfs_energy_methods_, sfxn_, and core::pose::Pose::size().

Referenced by initialize(), and core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_pose_no_initialize().

◆ set_scorefunction()

void core::pack::interaction_graph::SimpleInteractionGraph::set_scorefunction ( scoring::ScoreFunction const & sfxn )

virtual

Reimplemented in core::pack::interaction_graph::NPDHBSimpleInteractionGraph.

References core::scoring::ScoreFunction::clone(), pose_, sfs_energy_methods_, and sfxn_.

Referenced by core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_scorefunction().

◆ setup_after_edge_addition()

void core::pack::interaction_graph::SimpleInteractionGraph::setup_after_edge_addition ( )

virtual

If set_pose_no_initialize was called, then after edges have been added. This function will also do any bookkeeping necessary before the start of simulated annealing.

Reimplemented in core::pack::interaction_graph::NPDHBSimpleInteractionGraph.

References pose_.

◆ setup_for_scoring_for_residue_energy_methods()

std::list< scoring::methods::EnergyMethodCOP > const& core::pack::interaction_graph::SimpleInteractionGraph::setup_for_scoring_for_residue_energy_methods ( )

inline

References sfs_energy_methods_.

◆ total_energy()

Real core::pack::interaction_graph::SimpleInteractionGraph::total_energy ( )

virtual

Reimplemented in core::pack::interaction_graph::NPDHBSimpleInteractionGraph.

References core::pack::interaction_graph::SimpleNode::one_body_energy(), and pose_.

Referenced by core::pack::off_rotamer_pack_optimize(), and core::pack::interaction_graph::NPDHBSimpleInteractionGraph::total_energy().

Member Data Documentation

◆ pose_

pose::PoseCOP core::pack::interaction_graph::SimpleInteractionGraph::pose_

private

Referenced by initialize(), pose(), pose_cop(), set_pose_no_initialize(), set_scorefunction(), setup_after_edge_addition(), and total_energy().

◆ sfs_energy_methods_

std::list< scoring::methods::EnergyMethodCOP > core::pack::interaction_graph::SimpleInteractionGraph::sfs_energy_methods_

private

Referenced by set_pose_no_initialize(), set_scorefunction(), and setup_for_scoring_for_residue_energy_methods().

◆ sfxn_

scoring::ScoreFunctionOP core::pack::interaction_graph::SimpleInteractionGraph::sfxn_

private

Referenced by initialize(), scorefunction(), set_pose_no_initialize(), and set_scorefunction().

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

src/core/pack/interaction_graph/SimpleInteractionGraph.hh
src/core/pack/interaction_graph/SimpleInteractionGraph.cc

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SimpleInteractionGraph()

◆ ~SimpleInteractionGraph()

Member Function Documentation

◆ commit_change()

◆ consider_substitution()

◆ count_dynamic_memory()

◆ count_static_memory()

◆ create_new_edge()

◆ create_new_node()

◆ delete_edge()

◆ get_alternate_for_node()

◆ get_current_for_node()

◆ get_simple_node() [1/2]

◆ get_simple_node() [2/2]

◆ initialize() [1/2]

◆ initialize() [2/2]

◆ pose()

◆ pose_cop()

◆ reject_change()

◆ scorefunction()

◆ set_pose_no_initialize()

◆ set_scorefunction()

◆ setup_after_edge_addition()

◆ setup_for_scoring_for_residue_energy_methods()

◆ total_energy()

Member Data Documentation

◆ pose_

◆ sfs_energy_methods_

◆ sfxn_