core::pack::interaction_graph Namespace Reference

Classes
class	FirstClassNode
class	FirstClassEdge
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	AdditionalBackgroundNodesInteractionGraph
	Function declarations for the AdditionalBackgroundNodesInteractionGraph. More...
class	AminoAcidNeighborSparseMatrix
class	AnnealableGraphBase
class	DensePDNode
class	DensePDEdge
class	DensePDInteractionGraph
class	DoubleDensePDNode
class	DoubleDensePDEdge
class	DoubleDensePDInteractionGraph
class	DoubleLazyNode
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	FASTERNode
class	FASTEREdge
class	FASTERInteractionGraph
class	FixedBBNode
class	FixedBBEdge
class	FixedBBInteractionGraph
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...
struct	exposed_hydrophobic_data
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	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	HPatchBackgroundEdge
	Defines an edge between a FirstClass (HPatchNode) and a background node (HPatchBackgroundNode) More...
class	NodeBase
class	EdgeBase
class	InteractionGraphBase
class	InteractionGraphFactory
class	LazyNode
class	LazyEdge
class	LazyInteractionGraph
struct	history_queue_struct
	for storing three peices of associated data describing the recent history structure on a LinearMemNode. More...
class	LinearMemNode
class	LinearMemEdge
class	LinearMemoryInteractionGraph
class	MultiplexedAnnealableGraph
class	NPDHBondInteractionGraph
	Defines the interaction graph that will keep track of changes to the hpatch score. More...
class	NPDHBondNode
	Defines a FirstClass node which will keep track of the hydrogen bonds coming in to the residue and the hydrogen bond score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...
class	NPDHBondBackgroundNode
	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	NPDHBondEdge
	Defines a NPDHBond Edge which connects two first-class NPDHBond Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...
class	NPDHBondBackgroundEdge
	Defines an edge between a FirstClass (NPDHBondNode) and a background node (NPDHBondBackgroundNode) More...
struct	NPDHBond
class	NPDHBSimpleNode
class	NPDHBSimpleEdge
class	NPDHBSimpleInteractionGraph
	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	OnTheFlyNode
class	OnTheFlyEdge
class	OnTheFlyInteractionGraph
class	PDNode
class	PDEdge
class	PDInteractionGraph
class	PrecomputedPairEnergiesNode
class	PrecomputedPairEnergiesEdge
class	PrecomputedPairEnergiesInteractionGraph
class	ResidueArrayAnnealingEvaluator
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	RotamerDots
	Handles sphere-sphere overlap calculations for the HPatchInteractionGraph. 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	RotamerDotsCache
	A lightweight version of the RotamerDots class. Used to cache overlap between interaction graph Nodes and BGNodes. More...
class	InvRotamerDots
	Used to determine whether the overlap between two atoms is buried or exposed. More...
class	SimpleNode
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	SparseMatrixIndex
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	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	SurfaceBackgroundEdge
	Defines an edge between a FirstClass (SurfaceNode) and a background node (SurfaceBackgroundNode) More...
class	SurfacePotential
	With the traditional scoring hierarchy, classes like this one are created and accessed via the ScoringManager, which is itself a Singleton class. These "potential" classes are only created and initialized when the use of the EnergyMethod these classes correspond is encountered. No point in reading database files for a term if that term is not being used in some score function. However, the surface energy is used when users specify they want to use it on the command line - NOT via a score function. The score/energy is done within an interaction graph. One might ask why I just don't put the logic for reading in the database file to the interaction graph init methods. However, there will be cases where I will want to just score a protein (and not do any design) where I will want the database file to be read in. Scoring doesn't use interaction graphs, so if the code for that was located there, these values would not be read in. Instead, I've decided to implement this as its own separate class. It uses the Singleton design pattern so the database will only get read in once during a run. More...
class	SymmLinearMemNode
class	SymmLinearMemEdge
class	SymmLinearMemoryInteractionGraph
class	SymmMinimalistNode
class	SymmMinimalistEdge
class	SymmMinimalistInteractionGraph
class	SymmOnTheFlyNode
class	SymmOnTheFlyEdge
class	SymmOnTheFlyInteractionGraph

Typedefs
typedef utility::pointer::shared_ptr< AnnealableGraphBase >	AnnealableGraphBaseOP
typedef utility::pointer::shared_ptr< AnnealableGraphBase const >	AnnealableGraphBaseCOP
typedef utility::pointer::shared_ptr< DensePDInteractionGraph >	DensePDInteractionGraphOP
typedef utility::pointer::shared_ptr< DensePDInteractionGraph const >	DensePDInteractionGraphCOP
typedef utility::pointer::shared_ptr< DoubleDensePDInteractionGraph >	DoubleDensePDInteractionGraphOP
typedef utility::pointer::shared_ptr< DoubleDensePDInteractionGraph const >	DoubleDensePDInteractionGraphCOP
typedef utility::pointer::shared_ptr< DoubleLazyInteractionGraph >	DoubleLazyInteractionGraphOP
typedef utility::pointer::shared_ptr< DoubleLazyInteractionGraph const >	DoubleLazyInteractionGraphCOP
typedef utility::pointer::shared_ptr< FASTERInteractionGraph >	FASTERInteractionGraphOP
typedef utility::pointer::shared_ptr< FASTERInteractionGraph const >	FASTERInteractionGraphCOP
typedef utility::pointer::shared_ptr< FixedBBInteractionGraph >	FixedBBInteractionGraphOP
typedef utility::pointer::shared_ptr< FixedBBInteractionGraph const >	FixedBBInteractionGraphCOP
typedef HPatchInteractionGraph< PDNode, PDEdge, PDInteractionGraph >	PDHPatchInteractionGraph
typedef HPatchInteractionGraph< LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph >	LinearMemoryHPatchInteractionGraph
typedef utility::pointer::shared_ptr< PDHPatchInteractionGraph >	PDHPatchInteractionGraphOP
typedef utility::pointer::shared_ptr< LinearMemoryHPatchInteractionGraph >	LinearMemoryHPatchInteractionGraphOP
typedef utility::pointer::shared_ptr< InteractionGraphBase >	InteractionGraphBaseOP
typedef utility::pointer::shared_ptr< InteractionGraphBase const >	InteractionGraphBaseCOP
typedef utility::pointer::shared_ptr< LazyInteractionGraph >	LazyInteractionGraphOP
typedef utility::pointer::shared_ptr< LazyInteractionGraph const >	LazyInteractionGraphCOP
typedef utility::pointer::shared_ptr< LinearMemoryInteractionGraph >	LinearMemoryInteractionGraphOP
typedef utility::pointer::shared_ptr< LinearMemoryInteractionGraph const >	LinearMemoryInteractionGraphCOP
typedef utility::pointer::shared_ptr< MultiplexedAnnealableGraph >	MultiplexedAnnealableGraphOP
typedef utility::pointer::shared_ptr< MultiplexedAnnealableGraph const >	MultiplexedAnnealableGraphCOP
typedef utility::pointer::shared_ptr< NPDHBond >	NPDHBondOP
typedef NPDHBondInteractionGraph< PDNode, PDEdge, PDInteractionGraph >	StandardNPDHBondInteractionGraph
typedef NPDHBondInteractionGraph< DensePDNode, DensePDEdge, DensePDInteractionGraph >	DenseNPDHBondInteractionGraph
typedef NPDHBondInteractionGraph< LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph >	LinearMemoryNPDHBondInteractionGraph
typedef utility::pointer::shared_ptr< StandardNPDHBondInteractionGraph >	StandardNPDHBondInteractionGraphOP
typedef utility::pointer::shared_ptr< DenseNPDHBondInteractionGraph >	DenseNPDHBondInteractionGraphOP
typedef utility::pointer::shared_ptr< LinearMemoryNPDHBondInteractionGraph >	LinearMemoryNPDHBondInteractionGraphOP
typedef utility::pointer::shared_ptr< NPDHBSimpleInteractionGraph >	NPDHBSimpleInteractionGraphOP
typedef utility::pointer::shared_ptr< NPDHBSimpleInteractionGraph const >	NPDHBSimpleInteractionGraphCOP
typedef utility::pointer::shared_ptr< OnTheFlyInteractionGraph >	OnTheFlyInteractionGraphOP
typedef utility::pointer::shared_ptr< OnTheFlyInteractionGraph const >	OnTheFlyInteractionGraphCOP
typedef utility::pointer::shared_ptr< PDInteractionGraph >	PDInteractionGraphOP
typedef utility::pointer::shared_ptr< PrecomputedPairEnergiesInteractionGraph >	PrecomputedPairEnergiesInteractionGraphOP
typedef utility::pointer::shared_ptr< PrecomputedPairEnergiesInteractionGraph const >	PrecomputedPairEnergiesInteractionGraphCOP
typedef utility::pointer::shared_ptr< ResidueArrayAnnealingEvaluator >	ResidueArrayAnnealingEvaluatorOP
typedef utility::pointer::shared_ptr< RotamerDots >	RotamerDotsOP
typedef utility::pointer::shared_ptr< RotamerDots const >	RotamerDotsCOP
typedef utility::pointer::shared_ptr< InvRotamerDots >	InvRotamerDotsOP
typedef utility::pointer::shared_ptr< InvRotamerDots const >	InvRotamerDotsCOP
typedef utility::pointer::shared_ptr< SimpleInteractionGraph >	SimpleInteractionGraphOP
typedef utility::pointer::shared_ptr< SimpleInteractionGraph const >	SimpleInteractionGraphCOP
typedef SurfaceInteractionGraph< PDNode, PDEdge, PDInteractionGraph >	PDSurfaceInteractionGraph
typedef SurfaceInteractionGraph< LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph >	LinearMemorySurfaceInteractionGraph
typedef utility::pointer::shared_ptr< PDSurfaceInteractionGraph >	PDSurfaceInteractionGraphOP
typedef utility::pointer::shared_ptr< LinearMemorySurfaceInteractionGraph >	LinearMemorySurfaceInteractionGraphOP
typedef utility::pointer::shared_ptr< SymmLinearMemoryInteractionGraph >	SymmLinearMemoryInteractionGraphOP
typedef utility::pointer::shared_ptr< SymmLinearMemoryInteractionGraph const >	SymmLinearMemoryInteractionGraphCOP
typedef utility::pointer::shared_ptr< SymmMinimalistInteractionGraph >	SymmMinimalistInteractionGraphOP
typedef utility::pointer::shared_ptr< SymmMinimalistInteractionGraph const >	SymmMinimalistInteractionGraphCOP
typedef utility::pointer::shared_ptr< SymmOnTheFlyInteractionGraph >	SymmOnTheFlyInteractionGraphOP
typedef utility::pointer::shared_ptr< SymmOnTheFlyInteractionGraph const >	SymmOnTheFlyInteractionGraphCOP

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

Functions
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")
static basic::Tracer	T ("core.pack.interaction_graph.interaction_graph_factory", basic::t_info)
Size	estimate_n_2body_calcs_for_precomputation (task::PackerTask const &the_task, rotamer_set::RotamerSets const &rotsets, utility::graph::Graph const &packer_neighbor_graph)
	estimate the amount of work require for precomputation More...
Size	estimate_n_2body_calcs_for_linmem_ig (rotamer_set::RotamerSets const &rotsets, utility::graph::Graph const &packer_neighbor_graph)
	estimate the amount of work require for on-the-fly calculations More...
bool	auto_use_linmem_ig (task::PackerTask const &the_task, rotamer_set::RotamerSets const &rotsets, utility::graph::Graph const &packer_neighbor_graph, core::Size const nloop)
	This function is called when the user does not specify an IG Type. More...
InteractionGraphBaseOP	make_linmem_ig (task::PackerTask const &the_task, rotamer_set::RotamerSets const &rotsets, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, utility::graph::Graph const &packer_neighbor_graph, core::Real const surface_weight, core::Real const hpatch_weight, core::Real const npd_hbond_weight)
static basic::Tracer	T ("core.pack.interaction_graph.linmem_ig", basic::t_error)
void	compute_alt_weights_for_npd_hbonds (conformation::Residue const &res, utility::vector1< utility::vector1< NPDHBondOP > > const &atom_hbonds, utility::vector1< Real > &tmp_energies, utility::vector1< Real > &temp_weights)
	Compute the don_wt_alt_s and the acc_wt_alt_s from the perspective of the input residue given the (complete) arrays of NPDHBondOPs for each atom. More...
static basic::Tracer	TR ("core.pack.npd_hbond_ig")
template<typename V , typename E , typename G >
void	create_hbonds_one_way (scoring::hbonds::HBondDatabase const &database, scoring::hbonds::HBondOptions const &hbondoptions, scoring::hbonds::HBondSet const &hbset, NPDHBondInteractionGraph< V, E, G > &ig, utility::vector1< char > &hbonding_to_res, conformation::Residue const &acc_res, utility::vector1< NPDHBondOP > &acc_hbonds, utility::vector1< utility::vector1< NPDHBondOP > > &acc_atom_hbonds, conformation::Residue const &don_res, utility::vector1< NPDHBondOP > &don_hbonds, utility::vector1< utility::vector1< NPDHBondOP > > &don_atom_hbonds)
void	create_hbonds_one_way (scoring::hbonds::HBondDatabase const &database, scoring::hbonds::HBondOptions const &hbondoptions, scoring::hbonds::HBondSet const &hbset, NPDHBSimpleInteractionGraph &ig, utility::vector1< char > &hbonding_to_res, conformation::Residue const &acc_res, utility::vector1< NPDHBondOP > &acc_hbonds, utility::vector1< utility::vector1< NPDHBondOP > > &acc_atom_hbonds, conformation::Residue const &don_res, utility::vector1< NPDHBondOP > &don_hbonds, utility::vector1< utility::vector1< NPDHBondOP > > &don_atom_hbonds)
static basic::Tracer	T ("core.pack.interaction_graph.otf_ig", basic::t_error)
static basic::Tracer	TR ("core.pack.interaction_graph.PDInteractionGraph")
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	TR ("core.pack.interaction_graph.SimpleInteractionGraph")
static basic::Tracer	TR ("core.pack.interaction_graph.SurfacePotential")
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)
void	get_annealable_graph_summary (std::ostream &igstream, core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rot_sets, AnnealableGraphBaseCOP const &anngraph, bool const short_version)
	Given an interaction graph, get a summary describing it fully. More...
void	set_externally_generated_packer_solution (core::pose::Pose &pose, std::string const &packer_problem_description, std::string const &packer_solution_description)
	Given a description of a packer problem, a description of the solution, and a pose to put a result in, generate a pose representing the solution. More...
void	generate_pose_from_packer_description (core::pose::Pose &pose, std::string const &packer_problem_description)
	Given the description of a packer problem as generated by get_annealable_graph_summary(), pull out and re-generate the pose. More...
void	generate_rotamers_from_packer_solution_description (utility::vector1< std::pair< core::Size, core::conformation::ResidueCOP > > &rotamers, std::string const &packer_problem_description, std::string const &packer_solution_description)
	Given a packer problem and its solution, generate rotamers from it. More...
void	add_rotamers_to_pose (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::conformation::ResidueCOP > > &rotamers)
	Given a vector of solution rotamers and a pose, put the rotamers on the pose. More...

Variables
bool const	debug = { false }
	For testing the symmlinmemIG, you'll want to set this to true. More...

Typedef Documentation

AnnealableGraphBaseCOP

typedef utility::pointer::shared_ptr< AnnealableGraphBase const > core::pack::interaction_graph::AnnealableGraphBaseCOP

AnnealableGraphBaseOP

typedef utility::pointer::shared_ptr< AnnealableGraphBase > core::pack::interaction_graph::AnnealableGraphBaseOP

DenseNPDHBondInteractionGraph

typedef NPDHBondInteractionGraph< DensePDNode, DensePDEdge, DensePDInteractionGraph > core::pack::interaction_graph::DenseNPDHBondInteractionGraph

DenseNPDHBondInteractionGraphOP

typedef utility::pointer::shared_ptr< DenseNPDHBondInteractionGraph > core::pack::interaction_graph::DenseNPDHBondInteractionGraphOP

DensePDInteractionGraphCOP

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

DensePDInteractionGraphOP

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

DoubleDensePDInteractionGraphCOP

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

DoubleDensePDInteractionGraphOP

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

DoubleLazyInteractionGraphCOP

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

DoubleLazyInteractionGraphOP

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

FASTERInteractionGraphCOP

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

FASTERInteractionGraphOP

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

FixedBBInteractionGraphCOP

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

FixedBBInteractionGraphOP

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

InteractionGraphBaseCOP

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

InteractionGraphBaseOP

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

InvRotamerDotsCOP

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

InvRotamerDotsOP

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

LazyInteractionGraphCOP

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

LazyInteractionGraphOP

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

LinearMemoryHPatchInteractionGraph

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

LinearMemoryHPatchInteractionGraphOP

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

LinearMemoryInteractionGraphCOP

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

LinearMemoryInteractionGraphOP

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

LinearMemoryNPDHBondInteractionGraph

typedef NPDHBondInteractionGraph< LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph > core::pack::interaction_graph::LinearMemoryNPDHBondInteractionGraph

LinearMemoryNPDHBondInteractionGraphOP

typedef utility::pointer::shared_ptr< LinearMemoryNPDHBondInteractionGraph > core::pack::interaction_graph::LinearMemoryNPDHBondInteractionGraphOP

LinearMemorySurfaceInteractionGraph

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

LinearMemorySurfaceInteractionGraphOP

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

MultiplexedAnnealableGraphCOP

typedef utility::pointer::shared_ptr< MultiplexedAnnealableGraph const > core::pack::interaction_graph::MultiplexedAnnealableGraphCOP

MultiplexedAnnealableGraphOP

typedef utility::pointer::shared_ptr< MultiplexedAnnealableGraph > core::pack::interaction_graph::MultiplexedAnnealableGraphOP

NPDHBondOP

typedef utility::pointer::shared_ptr< NPDHBond > core::pack::interaction_graph::NPDHBondOP

NPDHBSimpleInteractionGraphCOP

typedef utility::pointer::shared_ptr< NPDHBSimpleInteractionGraph const > core::pack::interaction_graph::NPDHBSimpleInteractionGraphCOP

NPDHBSimpleInteractionGraphOP

typedef utility::pointer::shared_ptr< NPDHBSimpleInteractionGraph > core::pack::interaction_graph::NPDHBSimpleInteractionGraphOP

OnTheFlyInteractionGraphCOP

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

OnTheFlyInteractionGraphOP

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

PDHPatchInteractionGraph

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

PDHPatchInteractionGraphOP

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

PDInteractionGraphOP

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

PDSurfaceInteractionGraph

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

PDSurfaceInteractionGraphOP

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

PrecomputedPairEnergiesInteractionGraphCOP

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

PrecomputedPairEnergiesInteractionGraphOP

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

ResidueArrayAnnealingEvaluatorOP

typedef utility::pointer::shared_ptr< ResidueArrayAnnealingEvaluator > core::pack::interaction_graph::ResidueArrayAnnealingEvaluatorOP

RotamerDotsCOP

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

RotamerDotsOP

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

SimpleInteractionGraphCOP

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

SimpleInteractionGraphOP

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

StandardNPDHBondInteractionGraph

typedef NPDHBondInteractionGraph< PDNode, PDEdge, PDInteractionGraph > core::pack::interaction_graph::StandardNPDHBondInteractionGraph

StandardNPDHBondInteractionGraphOP

typedef utility::pointer::shared_ptr< StandardNPDHBondInteractionGraph > core::pack::interaction_graph::StandardNPDHBondInteractionGraphOP

SymmLinearMemoryInteractionGraphCOP

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

SymmLinearMemoryInteractionGraphOP

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

SymmMinimalistInteractionGraphCOP

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

SymmMinimalistInteractionGraphOP

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

SymmOnTheFlyInteractionGraphCOP

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

SymmOnTheFlyInteractionGraphOP

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

Enumeration Type Documentation

ResiduePairEvalType

enum core::pack::interaction_graph::ResiduePairEvalType

Enumerator
whole_whole
whole_sc
sc_whole
sc_sc

Function Documentation

add_rotamers_to_pose()

void core::pack::interaction_graph::add_rotamers_to_pose	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::conformation::ResidueCOP > > &	rotamers
	)

Given a vector of solution rotamers and a pose, put the rotamers on the pose.

The vector is a vector of pairs of the form <seqpos, rotamerCOP>.

References core::pose::Pose::replace_residue(), core::id::to_string(), and core::pose::Pose::total_residue().

Referenced by set_externally_generated_packer_solution().

auto_use_linmem_ig()

bool core::pack::interaction_graph::auto_use_linmem_ig	(	task::PackerTask const &	the_task,
		rotamer_set::RotamerSets const &	rotsets,
		utility::graph::Graph const &	packer_neighbor_graph,
		core::Size const	nloop
	)

This function is called when the user does not specify an IG Type.

The goal is to use the most economical IG type based on the use case. This can get very complicated to predict, but the gist is that the O(N^2) precomputed IG should be used with a small number of rotamers and the O(N) linmem_ig should be used for a large number of rotamers.

Author

Jack Maguire

References estimate_n_2body_calcs_for_linmem_ig(), estimate_n_2body_calcs_for_precomputation(), core::pack::task::PackerTask::ig_threads_to_request(), and protocols::mean_field::min().

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph().

compute_alt_weights_for_npd_hbonds()

void core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds	(	conformation::Residue const &	res,
		utility::vector1< utility::vector1< NPDHBondOP > > const &	atom_hbonds,
		utility::vector1< Real > &	tmp_energies,
		utility::vector1< Real > &	temp_weights
	)

Compute the don_wt_alt_s and the acc_wt_alt_s from the perspective of the input residue given the (complete) arrays of NPDHBondOPs for each atom.

Remarks

Used by both the NPDHBondNode and the NPDHBondBackgroundNode, and so defined in the .cc file.

References core::conformation::Residue::atom_is_polar_hydrogen(), core::sequence::end, core::conformation::Residue::heavyatom_is_an_acceptor(), core::conformation::Residue::natoms(), and core::scoring::hbonds::weights_for_hbonds().

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::calc_curr_hbond_weights(), core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::compute_alt_weights_for_hbonds(), core::pack::interaction_graph::NPDHBondNode< V, E, G >::compute_alt_weights_for_hbonds(), and core::pack::interaction_graph::NPDHBSimpleNode::compute_alt_weights_for_hbonds().

create_hbonds_one_way() [1/2]

template<typename V , typename E , typename G >

void core::pack::interaction_graph::create_hbonds_one_way	(	scoring::hbonds::HBondDatabase const &	database,
		scoring::hbonds::HBondOptions const &	hbondoptions,
		scoring::hbonds::HBondSet const &	hbset,
		NPDHBondInteractionGraph< V, E, G > &	ig,
		utility::vector1< char > &	hbonding_to_res,
		conformation::Residue const &	acc_res,
		utility::vector1< NPDHBondOP > &	acc_hbonds,
		utility::vector1< utility::vector1< NPDHBondOP > > &	acc_atom_hbonds,
		conformation::Residue const &	don_res,
		utility::vector1< NPDHBondOP > &	don_hbonds,
		utility::vector1< utility::vector1< NPDHBondOP > > &	don_atom_hbonds
	)

References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_base(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::hbonds::hb_energy(), core::conformation::Residue::Hpos_polar(), core::scoring::hbonds::HBondOptions::max_hb_energy(), core::scoring::hbonds::MAX_R2, core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::npd_hb_weight(), core::conformation::Residue::seqpos(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::unused_hbond(), and core::conformation::Residue::xyz().

Referenced by core::pack::interaction_graph::NPDHBondEdge< V, E, G >::consider_alternate_state_step1(), core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1(), core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors(), core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step1(), and core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution().

create_hbonds_one_way() [2/2]

void core::pack::interaction_graph::create_hbonds_one_way	(	scoring::hbonds::HBondDatabase const &	database,
		scoring::hbonds::HBondOptions const &	hbondoptions,
		scoring::hbonds::HBondSet const &	hbset,
		NPDHBSimpleInteractionGraph &	ig,
		utility::vector1< char > &	hbonding_to_res,
		conformation::Residue const &	acc_res,
		utility::vector1< NPDHBondOP > &	acc_hbonds,
		utility::vector1< utility::vector1< NPDHBondOP > > &	acc_atom_hbonds,
		conformation::Residue const &	don_res,
		utility::vector1< NPDHBondOP > &	don_hbonds,
		utility::vector1< utility::vector1< NPDHBondOP > > &	don_atom_hbonds
	)

References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_base(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::hbonds::hb_energy(), core::conformation::Residue::Hpos_polar(), core::scoring::hbonds::HBondOptions::max_hb_energy(), core::scoring::hbonds::MAX_R2, core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hb_weight(), core::conformation::Residue::seqpos(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::unused_hbond(), and core::conformation::Residue::xyz().

estimate_n_2body_calcs_for_linmem_ig()

Size core::pack::interaction_graph::estimate_n_2body_calcs_for_linmem_ig	(	rotamer_set::RotamerSets const &	rotsets,
		utility::graph::Graph const &	packer_neighbor_graph
	)

estimate the amount of work require for on-the-fly calculations

This may be off by a constant factor, which will be measured using benchmarks

References core::pack::rotamer_set::RotamerSets::nrotamers(), core::pack::rotamer_set::RotamerSets::res_for_rotamer(), and rot().

Referenced by auto_use_linmem_ig().

estimate_n_2body_calcs_for_precomputation()

Size core::pack::interaction_graph::estimate_n_2body_calcs_for_precomputation	(	task::PackerTask const &	the_task,
		rotamer_set::RotamerSets const &	rotsets,
		utility::graph::Graph const &	packer_neighbor_graph
	)

estimate the amount of work require for precomputation

This may be off by a constant factor, which will be measured using benchmarks

References core::pack::task::PackerTask::being_packed(), core::sequence::end, core::pack::rotamer_set::RotamerSets::nrotamers_for_moltenres(), and core::pack::rotamer_set::RotamerSets::resid_2_moltenres().

Referenced by auto_use_linmem_ig().

generate_pose_from_packer_description()

void core::pack::interaction_graph::generate_pose_from_packer_description	(	core::pose::Pose &	pose,
		std::string const &	packer_problem_description
	)

Given the description of a packer problem as generated by get_annealable_graph_summary(), pull out and re-generate the pose.

The contents of the pose are destroyed and replaced by the pose from the description in this operation.

References core::pose::Pose::clear(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::init_from_lines(), and core::chemical::orbitals::strip_whitespace().

Referenced by set_externally_generated_packer_solution().

generate_rotamers_from_packer_solution_description()

void core::pack::interaction_graph::generate_rotamers_from_packer_solution_description	(	utility::vector1< std::pair< core::Size, core::conformation::ResidueCOP > > &	rotamers,
		std::string const &	packer_problem_description,
		std::string const &	packer_solution_description
	)

Given a packer problem and its solution, generate rotamers from it.

The rotamer vector (a vector of pairs of <seqpos, residueCOP>) is cleared and populated by this operation.

References core::pose::Pose::conformation(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::BinarySilentStruct::init_from_lines(), core::conformation::Conformation::residue_cop(), core::chemical::orbitals::strip_whitespace(), core::id::to_string(), and core::pose::Pose::total_residue().

Referenced by set_externally_generated_packer_solution().

get_annealable_graph_summary()

void core::pack::interaction_graph::get_annealable_graph_summary	(	std::ostream &	igstream,
		core::pose::Pose const &	pose,
		core::pack::rotamer_set::RotamerSets const &	rot_sets,
		AnnealableGraphBaseCOP const &	anngraph,
		bool const	short_version
	)

Given an interaction graph, get a summary describing it fully.

This is intended to be a machine-readable summary that facilitates a Rosetta interface to external annealers or optimizers.

Parameters

[out]	igstream	The output stream for the summary.
[in]	pose	The pose, for reference.
[in]	rot_sets	The RotamerSets object containing the set of sets of rotamers for each position.
[in]	anngraph	The pre-computed interaction graph.
[in]	short_version	If true, only the interaction graph summary is returned. If false, information needed to reconstruct the pose is also included. False by default.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

References core::pose::Pose::append_residue_by_jump(), core::pack::interaction_graph::NodeBase::get_num_states(), core::pack::interaction_graph::PrecomputedPairEnergiesNode::get_one_body_energy(), core::pack::interaction_graph::PrecomputedPairEnergiesEdge::get_two_body_energy(), core::pack::rotamer_set::RotamerSets::moltenres_2_resid(), core::pack::rotamer_set::RotamerSets::nmoltenres(), core::io::silent::BinarySilentStruct::print_conformation(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_moltenresidue(), core::id::to_string(), core::pose::Pose::total_residue(), and core::pack::rotamer_set::RotamerSets::total_residue().

Referenced by protocols::quantum_annealing::InteractionGraphSummaryMetric::calculate().

make_linmem_ig()

InteractionGraphBaseOP core::pack::interaction_graph::make_linmem_ig	(	task::PackerTask const &	the_task,
		rotamer_set::RotamerSets const &	rotsets,
		pose::Pose const &	pose,
		scoring::ScoreFunction const &	sfxn,
		utility::graph::Graph const &	packer_neighbor_graph,
		core::Real const	surface_weight,
		core::Real const	hpatch_weight,
		core::Real const	npd_hbond_weight
	)

References core::pack::task::PackerTask::ig_threads_to_request(), core::pose::symmetry::is_symmetric(), core::pack::task::PackerTask::linmem_ig_history_size(), core::pack::task::PackerTask::num_to_be_packed(), and T().

Referenced by core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph().

operator<<() [1/2]

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

invokes print on the input DotSphere object

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

operator<<() [2/2]

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

invokes print on the input RotamerDots object

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().

set_externally_generated_packer_solution()

void core::pack::interaction_graph::set_externally_generated_packer_solution	(	core::pose::Pose &	pose,
		std::string const &	packer_problem_description,
		std::string const &	packer_solution_description
	)

Given a description of a packer problem, a description of the solution, and a pose to put a result in, generate a pose representing the solution.

The contents of the pose are destroyed by this operation, and replaced by the pose described in the packer problem and the rotamers described in the solutions!

Parameters

[out]	pose	The pose, cleared and rebuilt by this operation.
[in]	packer_problem_description	A description of the packer problem, including blocks for the original pose, the rotamers, and the energies, as generated by get_annealable_graph_summary().
[out]	packer_solution_description	A solution to the packer problem, in the format of a series of lines, one for each packable position, consisting of <seqpos #> <rotamer #>.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

References add_rotamers_to_pose(), generate_pose_from_packer_description(), and generate_rotamers_from_packer_solution_description().

Referenced by protocols::quantum_annealing::ExternalPackerResultLoader::apply().

T() [1/6]

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

static

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

T() [2/6]

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

static

T() [3/6]

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

static

T() [4/6]

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

static

T() [5/6]

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

static

T() [6/6]

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

static

TR() [1/4]

static basic::Tracer core::pack::interaction_graph::TR ( "core.pack.interaction_graph.PDInteractionGraph"  )

static

TR() [2/4]

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

static

TR() [3/4]

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

static

TR() [4/4]

static basic::Tracer core::pack::interaction_graph::TR ( "core.pack.npd_hbond_ig"  )

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::ResidueArrayAnnealingEvaluator::initialize_symmetry_info(), core::pack::interaction_graph::NPDHBondNode< V, E, G >::print(), core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::print(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::print_internal_energies_for_current_state_assignment(), core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::print_npd_hbond_avoidance_stats(), 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(), core::pack::interaction_graph::SimpleNode::set_alternate(), and core::pack::interaction_graph::InteractionGraphBase::set_onebody_energies_multithreaded().

TR_BGEDGE()

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

static

TR_BGNODE()

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().

TR_EDGE()

static 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().

TR_HIG()

static 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_graph_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().

TR_NODE()

static 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::HPatchNode< V, E, G >::set_rotamers(), core::pack::interaction_graph::SurfaceNode< 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().

TR_STATS()

static 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().

unpack_ubyte()

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

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

write_dot()

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 core::conformation::membrane::center.

Referenced by protocols::vardist_solaccess::VarSolDRotamerDots::write_dot(), protocols::vardist_solaccess::VarSolDRotamerDots::write_dot_kinemage(), write_sphere_list_farray(), and write_sphere_list_uv1().

write_sphere_list_farray()

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 core::conformation::membrane::center, unpack_ubyte(), write_dot(), and write_sphere_list_header().

write_sphere_list_header()

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

References protocols::hybridization::off.

Referenced by write_sphere_list_farray(), and write_sphere_list_uv1().

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 core::conformation::membrane::center, 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

debug

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

constexpr

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

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

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::abinitio::ClassicAbinitio::apply(), protocols::abinitio::FragmentSampler::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::MembraneAbinitio::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::relax::FastRelax::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::SymmLinearMemNode::assign_state(), protocols::relax::FastRelax::batch_apply(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::abinitio::ClassicAbinitio::ClassicAbinitio(), protocols::abinitio::AbrelaxApplication::close_loops(), core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), core::pack::interaction_graph::SymmLinearMemNode::commit_considered_substitution(), core::scoring::packing::compute_holes_surfs(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::electron_density::density_grid_search(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::FragmentSampler::do_stage1_cycles(), protocols::nonlocal::emit_intermediate(), protocols::star::emit_intermediate(), protocols::abinitio::abscript::AbscriptMover::StageTracker::end_stage(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_lk(), core::scoring::electron_density::ElectronDensity::expandToUnitCell(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), protocols::abinitio::AbrelaxApplication::fold(), core::scoring::func::SoedingFunc::func(), core::pack::interaction_graph::LinearMemEdge::get_energy_for_alt_state(), core::energy_methods::Fa_MbsolvEnergy::get_residue_pair_energy(), core::energy_methods::FaMPSolvEnergy::get_residue_pair_energy(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::init_options(), protocols::relax::FastRelax::inner_loop_ramp_repack_min_command(), protocols::antibody::kink_dihedral(), protocols::floppy_tail::FloppyTailMover::low_res(), protocols::electron_density::DockFragmentsIntoDensityMover::map_from_spectrum(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::splice::min_seg(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), core::import_pose::pose_stream::PoseInputStream::preprocess_pose(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), core::pack::interaction_graph::SymmLinearMemNode::project_deltaE_for_substitution(), protocols::sic_dock::read_biounit(), protocols::anchored_design::AnchoredPerturbMover::read_options(), protocols::anchored_design::AnchoredRefineMover::read_options(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::read_options(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::abinitio::register_common_options(), protocols::abinitio::ClassicAbinitio::register_options(), protocols::abinitio::FragmentSampler::register_options(), protocols::abinitio::MembraneAbinitio::register_options(), protocols::electron_density::remove_occupied_density_from_density(), protocols::abinitio::run_boinc_debug(), protocols::pockets::PocketConstraint::score(), protocols::electron_density::select_density_points(), protocols::anchored_design::AnchoredPerturbMover::set_debug(), protocols::anchored_design::AnchoredRefineMover::set_debug(), protocols::denovo_design::movers::FoldArchitectMover::set_debug(), protocols::loop_grower::LoopGrower::set_debug(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), and protocols::abinitio::AbrelaxApplication::setup_fold().