Rosetta 3.4
Classes | Typedefs | Enumerations | Functions | Variables
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  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
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  HPatchInteractionGraph
 Defines the interaction graph that will keep track of changes to the hpatch score. 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  OnTheFlyNode
class  OnTheFlyEdge
class  OnTheFlyInteractionGraph
class  PDNode
class  PDEdge
class  PDInteractionGraph
class  PrecomputedPairEnergiesNode
class  PrecomputedPairEnergiesEdge
class  PrecomputedPairEnergiesInteractionGraph
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  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  SurfaceInteractionGraph
 Defines the interaction graph that will keep track of changes to the surface score. More...
class  SurfacePotential

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

Enumerations

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

Functions

static
numeric::random::RandomGenerator 
RG (6425)
static basic::Tracer TR_NODE ("core.pack.hpatchig.node")
 Tracer instance for this file.
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)
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
std::ostream & operator<< (std::ostream &os, RotamerDots const &rd)
 invokes print on the input RotamerDots object
static basic::Tracer TR ("core.pack.interaction_graph.SimpleInteractionGraph")
static basic::Tracer TR ("core.pack.interaction_graph.SurfacePotential")

Variables

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

Typedef Documentation


Enumeration Type Documentation

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 
)
static numeric::random::RandomGenerator core::pack::interaction_graph::RG ( 6425  ) [static]
basic::Tracer core::pack::interaction_graph::T ( "core.pack.interaction_graph.interaction_graph_factory"  ,
basic::t_info   
)

Referenced by core::chemical::AtomTypeSet::add_parameters_from_file(), protocols::simple_filters::MinValueEvaluator< T >::apply(), protocols::rigid::RigidBodyDofSeqPerturbMover::apply(), protocols::rigid::RigidBodyDofRandomTransMover::apply(), protocols::rigid::RigidBodyDofSeqTransMover::apply(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::assign_chi_for_interpolated_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::assign_random_rotamer_with_bias_bbind(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_score(), protocols::unfolded_state_energy_calculator::calc_vector_boltzmann(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), protocols::forge::methods::closed_range(), core::conformation::symmetry::comma_strings_to_vector_map(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), protocols::wum::DatabaseQueryWorkUnitManager< T >::create_work_units_from_query(), core::io::pdb::PDB_DReader::createRecords(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::find_another_representative_for_unlikely_rotamer(), core::graph::ArrayPool< Real >::footprint(), protocols::rigid::gaussian_jump_move(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_all_rotamer_samples_bbind(), core::io::raw_data::RawStruct::get_debug_rmsd(), core::pack::interaction_graph::LinearMemEdge::get_energy_for_alt_state(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_bbind(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static(), protocols::features::get_something_from_database(), protocols::ligand_docking::grid_to_kin(), protocols::forge::methods::half_open_range(), protocols::forge::methods::insert_closed_range(), protocols::forge::methods::insert_half_open_range(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), protocols::toolbox::InteratomicVarianceMatrix::kurtosis(), core::io::pdb::PDB_DReader::mapStringToRecord(), core::io::silent::ProteinSilentStruct_Template< T >::mem_footprint(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::nchi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::nchi(), protocols::toolbox::InteratomicVarianceMatrix::optimize_kurtosis(), protocols::toolbox::InteratomicVarianceMatrix::order_parameter(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::packed_rotamer_2_regular_rotamer(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >::pop(), core::pack::interaction_graph::LinearMemNode::print(), core::pack::interaction_graph::LinearMemEdge::print_current_energy(), core::pack::interaction_graph::LinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::LinearMemNode::print_internal_energies(), core::coarse::CoarseEtable::print_residue_info(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), core::grid::CartGrid< core::Real >::read(), protocols::cluster::read1(), core::sequence::read_alignment_file(), core::io::serialization::read_bytes(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_binary(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), core::fragment::VectorCacheUnit< T >::remap_value(), core::fragment::MapCacheUnit< T >::remap_value(), protocols::analysis::InterfaceAnalyzerMover::report_data(), core::fragment::CacheWrapper< GunnTuple, MapCacheUnit< GunnTuple > >::retrieve(), protocols::rigid::RigidBodyDofPerturbMover::RigidBodyDofPerturbMover(), protocols::rigid::RigidBodyDofRandomTransMover::RigidBodyDofRandomTransMover(), protocols::rigid::RigidBodyDofSeqPerturbMover::RigidBodyDofSeqPerturbMover(), protocols::rigid::RigidBodyDofSeqTransMover::RigidBodyDofSeqTransMover(), protocols::rigid::RigidBodyDofTransMover::RigidBodyDofTransMover(), protocols::rigid::RigidBodyPerturbMover::RigidBodyPerturbMover(), protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover(), core::import_pose::atom_tree_diffs::rms_error_with_noise(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbind(), core::fragment::CacheWrapper< GunnTuple, MapCacheUnit< GunnTuple > >::scored_frag_ids(), core::grid::CartGrid< core::Real >::setupZones(), core::id::SequenceMapping::show(), core::grid::CartGrid< core::Real >::sum(), core::coarse::TranslatorSet::TranslatorSet(), protocols::cluster::write1(), core::io::serialization::write_bytes(), and core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::write_to_binary().

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.otf_ig"  ,
basic::t_error   
) [static]
static basic::Tracer core::pack::interaction_graph::TR ( "core.pack.interaction_graph.SurfacePotential"  ) [static]
static basic::Tracer core::pack::interaction_graph::TR ( "core.pack.interaction_graph.SimpleInteractionGraph"  ) [static]
static basic::Tracer core::pack::interaction_graph::TR_BGEDGE ( "core.pack.hpatchig.bgedge"  ) [static]
static basic::Tracer core::pack::interaction_graph::TR_BGNODE ( "core.pack.hpatchig.bgnode"  ) [static]
static basic::Tracer core::pack::interaction_graph::TR_EDGE ( "core.pack.hpatchig.edge"  ) [static]
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 >::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 >::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().

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 >::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::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().

static basic::Tracer core::pack::interaction_graph::TR_STATS ( "core.pack.hpatchig.stats"  ) [static]
bool core::pack::interaction_graph::unpack_ubyte ( ObjexxFCL::ubyte const &  value,
core::Size  which_bit 
)
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 
)
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 
)
void core::pack::interaction_graph::write_sphere_list_header ( std::ostream &  ostr,
std::string const &  color,
bool  off = false 
)
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 
)

Variable Documentation

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

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::relax::FastRelax::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::MembraneAbinitio::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::ClassicAbinitio::apply(), core::pack::interaction_graph::LinearMemNode::assign_state(), protocols::relax::FastRelax::batch_apply(), protocols::abinitio::ClassicAbinitio::ClassicAbinitio(), protocols::abinitio::AbrelaxApplication::close_loops(), core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::star::emit_intermediate(), protocols::nonlocal::emit_intermediate(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), protocols::abinitio::AbrelaxApplication::fold(), core::scoring::constraints::SoedingFunc::func(), core::pack::interaction_graph::LinearMemEdge::get_energy_for_alt_state(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), core::import_pose::pose_stream::PoseInputStream::preprocess_pose(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), protocols::anchored_design::AnchoredRefineMover::read_options(), protocols::anchored_design::AnchoredPerturbMover::read_options(), protocols::abinitio::MembraneAbinitio::register_options(), protocols::abinitio::FragmentSampler::register_options(), protocols::abinitio::ClassicAbinitio::register_options(), protocols::abinitio::AbrelaxApplication::register_options(), protocols::abinitio::register_options_broker(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), protocols::abinitio::run_boinc_debug(), protocols::anchored_design::AnchoredRefineMover::set_debug(), protocols::anchored_design::AnchoredPerturbMover::set_debug(), protocols::abinitio::AbrelaxApplication::setup_fold(), and core::kinematics::AtomTree::torsion_angle_dof_id().

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