core::pack::interaction_graph Namespace Reference

Classes
class	AdditionalBackgroundNodesInteractionGraph
	Function declarations for the AdditionalBackgroundNodesInteractionGraph. More...
class	AminoAcidNeighborSparseMatrix
class	BackgroundNode
	A node which is not changing type or rotamer throughout a simulation. More...
class	BackgroundToFirstClassEdge
	An edge between a background node and a first class node. More...
class	DensePDEdge
class	DensePDInteractionGraph
class	DensePDNode
class	DotSphere
	Represents the sphere of dots on the vdW surface of an atom, for use in the LeGrand and Merz method of calculating SASA. More...
class	DoubleDensePDEdge
class	DoubleDensePDInteractionGraph
class	DoubleDensePDNode
class	DoubleLazyEdge
class	DoubleLazyInteractionGraph
	The double lazy interaction graph is primarily useful for multistate design where one is interested in knowing at particular edge, all of the rotamer pair energies for a particular amino acid assignment. The double lazy interaction graph is lazy in two ways: first, in delaying the computation of rotamer pair energies until they are needed, and second, in delaying the allocation of memory for rotamer pair energies until that memory is needed. The DLIG will do one of two things once it allocates space for a block of rotamer pairs: 1) In its standard operating behavior, it will leave that space allocated until the graph is destroyed, which means that the energies it stores in that block will never be computed more than once; or 2) In its alternate operating behavior, the LMIG will deallocate some of those blocks to make sure that it never uses more than some maximum amount of memory on RPEs. More...
class	DoubleLazyNode
class	EdgeBase
struct	exposed_hydrophobic_data
class	FASTEREdge
class	FASTERInteractionGraph
class	FASTERNode
class	FirstClassEdge
class	FirstClassNode
class	FixedBBEdge
class	FixedBBInteractionGraph
class	FixedBBNode
struct	history_queue_struct
	for storing three peices of associated data describing the recent history structure on a LinearMemNode. More...
class	HPatchBackgroundEdge
	Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode) More...
class	HPatchBackgroundNode
	Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable. More...
class	HPatchEdge
	Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...
class	HPatchEnergy
	Defines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms. The difference from this energy method from the plain SurfaceEnergy method is that it calculates the patch area using methods in sasa.cc instead of using average values. This new method also uses a new approach for finding which residues to include in a patch, not just all residues within 10A. More...
class	HPatchEnergyCreator
class	HPatchInteractionGraph
	Defines the interaction graph that will keep track of changes to the hpatch score. More...
class	HPatchNode
	Defines a FirstClass node which will keep track of changes in the SASA and hpatch score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
class	InteractionGraphBase
class	InteractionGraphFactory
class	InvRotamerDots
	Used to determine whether the overlap between two atoms is buried or exposed. More...
class	LazyEdge
class	LazyInteractionGraph
class	LazyNode
class	LinearMemEdge
class	LinearMemNode
class	LinearMemoryInteractionGraph
class	NodeBase
class	OnTheFlyEdge
class	OnTheFlyInteractionGraph
class	OnTheFlyNode
class	PDEdge
class	PDInteractionGraph
class	PDNode
class	PrecomputedPairEnergiesEdge
class	PrecomputedPairEnergiesInteractionGraph
class	PrecomputedPairEnergiesNode
class	RotamerDots
	Handles sphere-sphere overlap calculations for the HPatchInteractionGraph. More...
class	RotamerDotsCache
	A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes. More...
class	RotamerDotsRadiusData
	A singleton class which reads in database SASA radii files and provides accessors for those values to the RotamerDots class. More...
class	SimpleEdge
class	SimpleInteractionGraph
	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...
class	SimpleNode
class	SparseMatrixIndex
class	SurfaceBackgroundEdge
	Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode) More...
class	SurfaceBackgroundNode
	Defines a BackgroundResidue node which will contribute to changes in surface energy due to state changes on neighboring nodes, and not because of state changes to it. More...
class	SurfaceEdge
	Defines a Surface edge which will be used in determining surface energy. More...
class	SurfaceEnergy
	Defines a (pseudo) context-dependent one-body surface energy. Really, this class is only being used as a hack for the optE protocol so that the non-PD surface energy can be optimized together with the other PD-terms. More...
class	SurfaceEnergyCreator
class	SurfaceInteractionGraph
	Defines the interaction graph that will keep track of changes to the surface score. More...
class	SurfaceNode
	Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
class	SurfacePotential
class	SymmLinearMemEdge
class	SymmLinearMemNode
class	SymmLinearMemoryInteractionGraph
class	SymmMinimalistEdge
class	SymmMinimalistInteractionGraph
class	SymmMinimalistNode
class	SymmOnTheFlyEdge
class	SymmOnTheFlyInteractionGraph
class	SymmOnTheFlyNode

Typedefs
typedef utility::pointer::owning_ptr < DensePDInteractionGraph >	DensePDInteractionGraphOP
typedef utility::pointer::owning_ptr < DensePDInteractionGraph const >	DensePDInteractionGraphCOP
typedef utility::pointer::owning_ptr < DoubleDensePDInteractionGraph >	DoubleDensePDInteractionGraphOP
typedef utility::pointer::owning_ptr < DoubleDensePDInteractionGraph const >	DoubleDensePDInteractionGraphCOP
typedef utility::pointer::owning_ptr < DoubleLazyInteractionGraph >	DoubleLazyInteractionGraphOP
typedef utility::pointer::owning_ptr < DoubleLazyInteractionGraph const >	DoubleLazyInteractionGraphCOP
typedef utility::pointer::owning_ptr < FASTERInteractionGraph >	FASTERInteractionGraphOP
typedef utility::pointer::owning_ptr < FASTERInteractionGraph const >	FASTERInteractionGraphCOP
typedef utility::pointer::owning_ptr < FixedBBInteractionGraph >	FixedBBInteractionGraphOP
typedef utility::pointer::owning_ptr < FixedBBInteractionGraph const >	FixedBBInteractionGraphCOP
typedef HPatchInteractionGraph < PDNode, PDEdge, PDInteractionGraph >	PDHPatchInteractionGraph
typedef HPatchInteractionGraph < LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph >	LinearMemoryHPatchInteractionGraph
typedef utility::pointer::owning_ptr < PDHPatchInteractionGraph >	PDHPatchInteractionGraphOP
typedef utility::pointer::owning_ptr < LinearMemoryHPatchInteractionGraph >	LinearMemoryHPatchInteractionGraphOP
typedef utility::pointer::owning_ptr < InteractionGraphBase >	InteractionGraphBaseOP
typedef utility::pointer::owning_ptr < InteractionGraphBase const >	InteractionGraphBaseCOP
typedef utility::pointer::owning_ptr < LazyInteractionGraph >	LazyInteractionGraphOP
typedef utility::pointer::owning_ptr < LazyInteractionGraph const >	LazyInteractionGraphCOP
typedef utility::pointer::owning_ptr < LinearMemoryInteractionGraph >	LinearMemoryInteractionGraphOP
typedef utility::pointer::owning_ptr < LinearMemoryInteractionGraph const >	LinearMemoryInteractionGraphCOP
typedef utility::pointer::owning_ptr < OnTheFlyInteractionGraph >	OnTheFlyInteractionGraphOP
typedef utility::pointer::owning_ptr < OnTheFlyInteractionGraph const >	OnTheFlyInteractionGraphCOP
typedef utility::pointer::owning_ptr < PDInteractionGraph >	PDInteractionGraphOP
typedef utility::pointer::owning_ptr < PrecomputedPairEnergiesInteractionGraph >	PrecomputedPairEnergiesInteractionGraphOP
typedef utility::pointer::owning_ptr < PrecomputedPairEnergiesInteractionGraph const >	PrecomputedPairEnergiesInteractionGraphCOP
typedef utility::pointer::owning_ptr < RotamerDots >	RotamerDotsOP
typedef utility::pointer::owning_ptr < RotamerDots const >	RotamerDotsCOP
typedef utility::pointer::owning_ptr < InvRotamerDots >	InvRotamerDotsOP
typedef utility::pointer::owning_ptr < InvRotamerDots const >	InvRotamerDotsCOP
typedef utility::pointer::owning_ptr < SimpleInteractionGraph >	SimpleInteractionGraphOP
typedef utility::pointer::owning_ptr < SimpleInteractionGraph const >	SimpleInteractionGraphCOP
typedef SurfaceInteractionGraph < PDNode, PDEdge, PDInteractionGraph >	PDSurfaceInteractionGraph
typedef SurfaceInteractionGraph < LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph >	LinearMemorySurfaceInteractionGraph
typedef utility::pointer::owning_ptr < PDSurfaceInteractionGraph >	PDSurfaceInteractionGraphOP
typedef utility::pointer::owning_ptr < LinearMemorySurfaceInteractionGraph >	LinearMemorySurfaceInteractionGraphOP
typedef utility::pointer::owning_ptr < SymmLinearMemoryInteractionGraph >	SymmLinearMemoryInteractionGraphOP
typedef utility::pointer::owning_ptr < SymmLinearMemoryInteractionGraph const >	SymmLinearMemoryInteractionGraphCOP
typedef utility::pointer::owning_ptr < SymmMinimalistInteractionGraph >	SymmMinimalistInteractionGraphOP
typedef utility::pointer::owning_ptr < SymmMinimalistInteractionGraph const >	SymmMinimalistInteractionGraphCOP
typedef utility::pointer::owning_ptr < SymmOnTheFlyInteractionGraph >	SymmOnTheFlyInteractionGraphOP
typedef utility::pointer::owning_ptr < SymmOnTheFlyInteractionGraph const >	SymmOnTheFlyInteractionGraphCOP

Enumerations
enum	ResiduePairEvalType { whole_whole = 0, whole_sc, sc_whole, sc_sc }

Functions
static basic::Tracer	T ("core.pack.interaction_graph.linmem_ig", basic::t_error)
static basic::Tracer	T ("core.pack.interaction_graph.otf_ig", basic::t_error)
bool	unpack_ubyte (ObjexxFCL::ubyte const &value, core::Size which_bit)
void	write_sphere_list_header (std::ostream &ostr, std::string const &color, bool off=false)
void	write_dot (std::ostream &ostr, core::Vector const &center, core::Real radius, Size const dot_index, std::string const &dot_name)
void	write_sphere_list_uv1 (std::ostream &ostr, std::string const &label, std::string const &color, core::Vector const &center, core::Real radius, utility::vector1< ObjexxFCL::ubyte > const &dot_masks)
void	write_sphere_list_farray (std::ostream &ostr, std::string const &label, std::string const &color, core::Vector const &center, core::Real radius, ObjexxFCL::FArray1< ObjexxFCL::ubyte > const &dot_masks)
std::ostream &	operator<< (std::ostream &os, DotSphere const &ds)
	invokes print on the input DotSphere object More...
std::ostream &	operator<< (std::ostream &os, RotamerDots const &rd)
	invokes print on the input RotamerDots object More...
static basic::Tracer	T ("core.pack.interaction_graph.symmlinmem_ig", basic::t_error)
static basic::Tracer	T ("core.pack.interaction_graph.symm_symmin_ig", basic::t_error)
static basic::Tracer	T ("core.pack.interaction_graph.otf_ig", basic::t_error)

Variables
static numeric::random::RandomGenerator	RG (6425)
static basic::Tracer	TR_NODE ("core.pack.hpatchig.node")
	Tracer instance for this file. More...
static basic::Tracer	TR_EDGE ("core.pack.hpatchig.edge")
static basic::Tracer	TR_BGNODE ("core.pack.hpatchig.bgnode")
static basic::Tracer	TR_BGEDGE ("core.pack.hpatchig.bgedge")
static basic::Tracer	TR_HIG ("core.pack.hpatchig.ig")
static basic::Tracer	TR_STATS ("core.pack.hpatchig.stats")
basic::Tracer	T ("core.pack.interaction_graph.interaction_graph_factory", basic::t_info)
bool const	debug = { false }
	For testing the LinMemIG, you'll want to set this to true. More...
static basic::Tracer	TR ("core.pack.interaction_graph.SimpleInteractionGraph")
static basic::Tracer	TR ("core.pack.interaction_graph.SurfacePotential")

Typedef Documentation

typedef utility::pointer::owning_ptr< DensePDInteractionGraph const > core::pack::interaction_graph::DensePDInteractionGraphCOP

typedef utility::pointer::owning_ptr< DensePDInteractionGraph > core::pack::interaction_graph::DensePDInteractionGraphOP

typedef utility::pointer::owning_ptr< DoubleDensePDInteractionGraph const > core::pack::interaction_graph::DoubleDensePDInteractionGraphCOP

typedef utility::pointer::owning_ptr< DoubleDensePDInteractionGraph > core::pack::interaction_graph::DoubleDensePDInteractionGraphOP

typedef utility::pointer::owning_ptr< DoubleLazyInteractionGraph const > core::pack::interaction_graph::DoubleLazyInteractionGraphCOP

typedef utility::pointer::owning_ptr< DoubleLazyInteractionGraph > core::pack::interaction_graph::DoubleLazyInteractionGraphOP

typedef utility::pointer::owning_ptr< FASTERInteractionGraph const > core::pack::interaction_graph::FASTERInteractionGraphCOP

typedef utility::pointer::owning_ptr< FASTERInteractionGraph > core::pack::interaction_graph::FASTERInteractionGraphOP

typedef utility::pointer::owning_ptr< FixedBBInteractionGraph const > core::pack::interaction_graph::FixedBBInteractionGraphCOP

typedef utility::pointer::owning_ptr< FixedBBInteractionGraph > core::pack::interaction_graph::FixedBBInteractionGraphOP

typedef utility::pointer::owning_ptr< InteractionGraphBase const > core::pack::interaction_graph::InteractionGraphBaseCOP

typedef utility::pointer::owning_ptr< InteractionGraphBase > core::pack::interaction_graph::InteractionGraphBaseOP

typedef utility::pointer::owning_ptr< InvRotamerDots const > core::pack::interaction_graph::InvRotamerDotsCOP

typedef utility::pointer::owning_ptr< InvRotamerDots > core::pack::interaction_graph::InvRotamerDotsOP

typedef utility::pointer::owning_ptr< LazyInteractionGraph const > core::pack::interaction_graph::LazyInteractionGraphCOP

typedef utility::pointer::owning_ptr< LazyInteractionGraph > core::pack::interaction_graph::LazyInteractionGraphOP

typedef HPatchInteractionGraph< LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph > core::pack::interaction_graph::LinearMemoryHPatchInteractionGraph

typedef utility::pointer::owning_ptr< LinearMemoryHPatchInteractionGraph > core::pack::interaction_graph::LinearMemoryHPatchInteractionGraphOP

typedef utility::pointer::owning_ptr< LinearMemoryInteractionGraph const > core::pack::interaction_graph::LinearMemoryInteractionGraphCOP

typedef utility::pointer::owning_ptr< LinearMemoryInteractionGraph > core::pack::interaction_graph::LinearMemoryInteractionGraphOP

typedef SurfaceInteractionGraph< LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph > core::pack::interaction_graph::LinearMemorySurfaceInteractionGraph

typedef utility::pointer::owning_ptr< LinearMemorySurfaceInteractionGraph > core::pack::interaction_graph::LinearMemorySurfaceInteractionGraphOP

typedef utility::pointer::owning_ptr< OnTheFlyInteractionGraph const > core::pack::interaction_graph::OnTheFlyInteractionGraphCOP

typedef utility::pointer::owning_ptr< OnTheFlyInteractionGraph > core::pack::interaction_graph::OnTheFlyInteractionGraphOP

typedef HPatchInteractionGraph< PDNode, PDEdge, PDInteractionGraph > core::pack::interaction_graph::PDHPatchInteractionGraph

typedef utility::pointer::owning_ptr< PDHPatchInteractionGraph > core::pack::interaction_graph::PDHPatchInteractionGraphOP

typedef utility::pointer::owning_ptr< PDInteractionGraph > core::pack::interaction_graph::PDInteractionGraphOP

typedef SurfaceInteractionGraph< PDNode, PDEdge, PDInteractionGraph > core::pack::interaction_graph::PDSurfaceInteractionGraph

typedef utility::pointer::owning_ptr< PDSurfaceInteractionGraph > core::pack::interaction_graph::PDSurfaceInteractionGraphOP

typedef utility::pointer::owning_ptr< PrecomputedPairEnergiesInteractionGraph const > core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphCOP

typedef utility::pointer::owning_ptr< PrecomputedPairEnergiesInteractionGraph > core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphOP

typedef utility::pointer::owning_ptr< RotamerDots const > core::pack::interaction_graph::RotamerDotsCOP

typedef utility::pointer::owning_ptr< RotamerDots > core::pack::interaction_graph::RotamerDotsOP

typedef utility::pointer::owning_ptr< SimpleInteractionGraph const > core::pack::interaction_graph::SimpleInteractionGraphCOP

typedef utility::pointer::owning_ptr< SimpleInteractionGraph > core::pack::interaction_graph::SimpleInteractionGraphOP

typedef utility::pointer::owning_ptr< SymmLinearMemoryInteractionGraph const > core::pack::interaction_graph::SymmLinearMemoryInteractionGraphCOP

typedef utility::pointer::owning_ptr< SymmLinearMemoryInteractionGraph > core::pack::interaction_graph::SymmLinearMemoryInteractionGraphOP

typedef utility::pointer::owning_ptr< SymmMinimalistInteractionGraph const > core::pack::interaction_graph::SymmMinimalistInteractionGraphCOP

typedef utility::pointer::owning_ptr< SymmMinimalistInteractionGraph > core::pack::interaction_graph::SymmMinimalistInteractionGraphOP

typedef utility::pointer::owning_ptr< SymmOnTheFlyInteractionGraph const > core::pack::interaction_graph::SymmOnTheFlyInteractionGraphCOP

typedef utility::pointer::owning_ptr< SymmOnTheFlyInteractionGraph > core::pack::interaction_graph::SymmOnTheFlyInteractionGraphOP

Enumeration Type Documentation

enum core::pack::interaction_graph::ResiduePairEvalType

Enumerator
whole_whole
whole_sc
sc_whole
sc_sc

Function Documentation

std::ostream & core::pack::interaction_graph::operator<<	(	std::ostream &	os,
		DotSphere const &	ds
	)

invokes print on the input DotSphere object

operator<< ( ostream, DotSphere)

References core::pack::interaction_graph::DotSphere::print().

std::ostream & core::pack::interaction_graph::operator<<	(	std::ostream &	os,
		RotamerDots const &	rd
	)

invokes print on the input RotamerDots object

operator<< ( ostream, RotamerDots )

References core::pack::interaction_graph::RotamerDots::get_sasa(), core::pack::interaction_graph::RotamerDots::name3(), core::pack::interaction_graph::RotamerDots::seqpos(), and core::pack::interaction_graph::RotamerDots::state_unassigned().

static basic::Tracer core::pack::interaction_graph::T ( "core.pack.interaction_graph.otf_ig"  , basic::t_error    )

static

static basic::Tracer core::pack::interaction_graph::T ( "core.pack.interaction_graph.symm_symmin_ig"  , basic::t_error    )

static

static basic::Tracer core::pack::interaction_graph::T ( "core.pack.interaction_graph.linmem_ig"  , basic::t_error    )

static

static basic::Tracer core::pack::interaction_graph::T ( "core.pack.interaction_graph.symmlinmem_ig"  , basic::t_error    )

static

static basic::Tracer core::pack::interaction_graph::T ( "core.pack.interaction_graph.otf_ig"  , basic::t_error    )

static

bool core::pack::interaction_graph::unpack_ubyte	(	ObjexxFCL::ubyte const &	value,
		core::Size	which_bit
	)

References utility_exit.

Referenced by core::pack::interaction_graph::InvRotamerDots::dot_exposed(), write_sphere_list_farray(), and write_sphere_list_uv1().

void core::pack::interaction_graph::write_dot	(	std::ostream &	ostr,
		core::Vector const &	center,
		core::Real	radius,
		Size const	dot_index,
		std::string const &	dot_name
	)

References numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by write_sphere_list_farray(), and write_sphere_list_uv1().

void core::pack::interaction_graph::write_sphere_list_farray	(	std::ostream &	ostr,
		std::string const &	label,
		std::string const &	color,
		core::Vector const &	center,
		core::Real	radius,
		ObjexxFCL::FArray1< ObjexxFCL::ubyte > const &	dot_masks
	)

References unpack_ubyte(), write_dot(), and write_sphere_list_header().

void core::pack::interaction_graph::write_sphere_list_header	(	std::ostream &	ostr,
		std::string const &	color,
		bool	off = false
	)

Referenced by write_sphere_list_farray(), and write_sphere_list_uv1().

void core::pack::interaction_graph::write_sphere_list_uv1	(	std::ostream &	ostr,
		std::string const &	label,
		std::string const &	color,
		core::Vector const &	center,
		core::Real	radius,
		utility::vector1< ObjexxFCL::ubyte > const &	dot_masks
	)

References unpack_ubyte(), write_dot(), and write_sphere_list_header().

Referenced by core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage(), and core::pack::interaction_graph::InvRotamerDots::write_exposed_dots_to_kinemage().

Variable Documentation

bool const core::pack::interaction_graph::debug = { false }

For testing the LinMemIG, you'll want to set this to true.

For testing the symmlinmemIG, you'll want to set this to true.

Referenced by core::pack::interaction_graph::SymmLinearMemNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::SymmLinearMemNode::commit_considered_substitution(), core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), core::scoring::packing::compute_holes_surfs(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), core::pack::interaction_graph::SymmLinearMemEdge::get_energy_for_alt_state(), core::pack::interaction_graph::LinearMemEdge::get_energy_for_alt_state(), core::scoring::methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::scoring::membrane::FaMPSolvEnergy::get_residue_pair_energy(), core::pack::interaction_graph::SymmLinearMemNode::project_deltaE_for_substitution(), and core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution().

numeric::random::RandomGenerator core::pack::interaction_graph::RG(6425)

static

Referenced by core::pack::interaction_graph::FASTERNode::get_random_neighbor(), and core::pack::interaction_graph::FASTERNode::partial_assign_relaxed_state().

basic::Tracer core::pack::interaction_graph::T("core.pack.interaction_graph.otf_ig", basic::t_error)	(	"core.pack.interaction_graph.interaction_graph_factory"	,
		basic::t_info
	)

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::pack::interaction_graph::SymmLinearMemEdge::get_energy_for_alt_state(), core::pack::interaction_graph::LinearMemEdge::get_energy_for_alt_state(), core::pack::interaction_graph::SymmMinimalistNode::print(), core::pack::interaction_graph::SymmLinearMemNode::print(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::SymmMinimalistEdge::print_current_energy(), core::pack::interaction_graph::SymmLinearMemEdge::print_current_energy(), core::pack::interaction_graph::LinearMemEdge::print_current_energy(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::LinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::SymmMinimalistNode::print_internal_energies(), core::pack::interaction_graph::SymmLinearMemNode::print_internal_energies(), core::pack::interaction_graph::LinearMemNode::print_internal_energies(), and core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution().

basic::Tracer core::pack::interaction_graph::TR("core.pack.interaction_graph.SimpleInteractionGraph")

static

Referenced by core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), core::pack::interaction_graph::SimpleInteractionGraph::initialize(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), core::pack::interaction_graph::SurfacePotential::read_hASA_score_database_file(), core::pack::interaction_graph::SurfacePotential::read_hpatch_score_database_file(), and core::pack::interaction_graph::SimpleNode::set_alternate().

basic::Tracer core::pack::interaction_graph::TR("core.pack.interaction_graph.SurfacePotential")

static

basic::Tracer core::pack::interaction_graph::TR_BGEDGE("core.pack.hpatchig.bgedge")

static

basic::Tracer core::pack::interaction_graph::TR_BGNODE("core.pack.hpatchig.bgnode")

static

Referenced by core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::calculate_amount_total_hydrophobic_ASA(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::initialize_num_neighbors_counting_self(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::print(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::reset_alt_state_dots(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::reset_alt_state_total_hASA(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::SurfaceBackgroundNode(), and core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::update_state_for_substitution().

basic::Tracer core::pack::interaction_graph::TR_EDGE("core.pack.hpatchig.edge")

static

Referenced by core::pack::interaction_graph::HPatchEdge< V, E, G >::prepare_for_simulated_annealing().

basic::Tracer core::pack::interaction_graph::TR_HIG("core.pack.hpatchig.ig")

static

Referenced by core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::blanket_assign_state_0(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_hpatch_deltaE(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::commit_considered_substitution(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::consider_substitution(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::create_background_edge(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::create_background_node(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::create_new_edge(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::create_new_node(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::decide_procrastinate_hpatch_computations(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::detect_background_residue_and_first_class_residue_overlap(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::initialize(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::prepare_for_simulated_annealing(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::print_internal_energies_for_current_state_assignment(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::reset_from_previous_deltaHpatch_comp(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_errorfull_deltaE_threshold(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_network_state(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_num_background_residues(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_pose(), and core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_residue_as_background_residue().

basic::Tracer core::pack::interaction_graph::TR_NODE("core.pack.hpatchig.node")

static

Tracer instance for this file.

Referenced by core::pack::interaction_graph::SurfaceNode< V, E, G >::assign_state_surface(), core::pack::interaction_graph::HPatchNode< V, E, G >::assign_zero_state(), core::pack::interaction_graph::SurfaceNode< V, E, G >::calculate_amount_total_hydrophobic_ASA(), core::pack::interaction_graph::HPatchNode< V, E, G >::commit_considered_substitution(), core::pack::interaction_graph::SurfaceNode< V, E, G >::commit_considered_substitution_surface(), core::pack::interaction_graph::HPatchNode< V, E, G >::consider_alternate_state(), core::pack::interaction_graph::SurfaceNode< V, E, G >::decide_procrastinate_surface_computations(), core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution(), core::pack::interaction_graph::SurfaceNode< V, E, G >::initialize_num_neighbors_counting_self(), core::pack::interaction_graph::HPatchNode< V, E, G >::prepare_for_simulated_annealing(), core::pack::interaction_graph::HPatchNode< V, E, G >::print(), core::pack::interaction_graph::SurfaceNode< V, E, G >::project_deltaE_for_substitution_surface(), core::pack::interaction_graph::SurfaceNode< V, E, G >::project_surface_deltaE(), core::pack::interaction_graph::HPatchNode< V, E, G >::reset_alt_state_dots(), core::pack::interaction_graph::SurfaceNode< V, E, G >::reset_alt_state_total_hASA(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_rotamer_dots_for_node_state(), core::pack::interaction_graph::SurfaceNode< V, E, G >::set_rotamers(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), core::pack::interaction_graph::SurfaceNode< V, E, G >::SurfaceNode(), core::pack::interaction_graph::HPatchNode< V, E, G >::update_state_for_neighbors_substitution(), and core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct().

basic::Tracer core::pack::interaction_graph::TR_STATS("core.pack.hpatchig.stats")

static

Referenced by core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::print_hpatch_avoidance_stats(), and core::pack::interaction_graph::SurfaceNode< V, E, G >::print_surface_avoidance_stats().