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Rosetta 3.5
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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Rosetta 3.5
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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 |
| 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 | 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 | 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 |
| class | SymmLinearMemNode |
| class | SymmLinearMemEdge |
| class | SymmLinearMemoryInteractionGraph |
| class | SymmMinimalistNode |
| class | SymmMinimalistEdge |
| class | SymmMinimalistInteractionGraph |
| class | SymmOnTheFlyNode |
| class | SymmOnTheFlyEdge |
| class | SymmOnTheFlyInteractionGraph |
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. 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) |
| 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 ¢er, 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 ¢er, 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 ¢er, 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) |
Variables | |
| bool const | debug = { false } |
| For testing the LinMemIG, you'll want to set this to true. More... | |
| typedef utility::pointer::owning_ptr< DensePDInteractionGraph const > core::pack::interaction_graph::DensePDInteractionGraphCOP |
Definition at line 26 of file DensePDInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< DensePDInteractionGraph > core::pack::interaction_graph::DensePDInteractionGraphOP |
Definition at line 24 of file DensePDInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< DoubleDensePDInteractionGraph const > core::pack::interaction_graph::DoubleDensePDInteractionGraphCOP |
Definition at line 26 of file DoubleDensePDInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< DoubleDensePDInteractionGraph > core::pack::interaction_graph::DoubleDensePDInteractionGraphOP |
Definition at line 24 of file DoubleDensePDInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< DoubleLazyInteractionGraph const > core::pack::interaction_graph::DoubleLazyInteractionGraphCOP |
Definition at line 29 of file DoubleLazyInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< DoubleLazyInteractionGraph > core::pack::interaction_graph::DoubleLazyInteractionGraphOP |
Definition at line 26 of file DoubleLazyInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< FASTERInteractionGraph const > core::pack::interaction_graph::FASTERInteractionGraphCOP |
Definition at line 26 of file FASTERInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< FASTERInteractionGraph > core::pack::interaction_graph::FASTERInteractionGraphOP |
Definition at line 24 of file FASTERInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< FixedBBInteractionGraph const > core::pack::interaction_graph::FixedBBInteractionGraphCOP |
Definition at line 30 of file FixedBBInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< FixedBBInteractionGraph > core::pack::interaction_graph::FixedBBInteractionGraphOP |
Definition at line 27 of file FixedBBInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< InteractionGraphBase const > core::pack::interaction_graph::InteractionGraphBaseCOP |
Definition at line 30 of file InteractionGraphBase.fwd.hh.
| typedef utility::pointer::owning_ptr< InteractionGraphBase > core::pack::interaction_graph::InteractionGraphBaseOP |
Definition at line 27 of file InteractionGraphBase.fwd.hh.
| typedef utility::pointer::owning_ptr< InvRotamerDots const > core::pack::interaction_graph::InvRotamerDotsCOP |
Definition at line 32 of file RotamerDots.fwd.hh.
| typedef utility::pointer::owning_ptr< InvRotamerDots > core::pack::interaction_graph::InvRotamerDotsOP |
Definition at line 31 of file RotamerDots.fwd.hh.
| typedef utility::pointer::owning_ptr< LazyInteractionGraph const > core::pack::interaction_graph::LazyInteractionGraphCOP |
Definition at line 29 of file LazyInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< LazyInteractionGraph > core::pack::interaction_graph::LazyInteractionGraphOP |
Definition at line 26 of file LazyInteractionGraph.fwd.hh.
| typedef HPatchInteractionGraph< LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph > core::pack::interaction_graph::LinearMemoryHPatchInteractionGraph |
Definition at line 32 of file HPatchInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< LinearMemoryHPatchInteractionGraph > core::pack::interaction_graph::LinearMemoryHPatchInteractionGraphOP |
Definition at line 35 of file HPatchInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< LinearMemoryInteractionGraph const > core::pack::interaction_graph::LinearMemoryInteractionGraphCOP |
Definition at line 29 of file LinearMemoryInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< LinearMemoryInteractionGraph > core::pack::interaction_graph::LinearMemoryInteractionGraphOP |
Definition at line 26 of file LinearMemoryInteractionGraph.fwd.hh.
| typedef SurfaceInteractionGraph< LinearMemNode, LinearMemEdge, LinearMemoryInteractionGraph > core::pack::interaction_graph::LinearMemorySurfaceInteractionGraph |
Definition at line 32 of file SurfaceInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< LinearMemorySurfaceInteractionGraph > core::pack::interaction_graph::LinearMemorySurfaceInteractionGraphOP |
Definition at line 35 of file SurfaceInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< OnTheFlyInteractionGraph const > core::pack::interaction_graph::OnTheFlyInteractionGraphCOP |
Definition at line 28 of file OnTheFlyInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< OnTheFlyInteractionGraph > core::pack::interaction_graph::OnTheFlyInteractionGraphOP |
Definition at line 25 of file OnTheFlyInteractionGraph.fwd.hh.
| typedef HPatchInteractionGraph< PDNode, PDEdge, PDInteractionGraph > core::pack::interaction_graph::PDHPatchInteractionGraph |
Definition at line 29 of file HPatchInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< PDHPatchInteractionGraph > core::pack::interaction_graph::PDHPatchInteractionGraphOP |
Definition at line 34 of file HPatchInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< PDInteractionGraph > core::pack::interaction_graph::PDInteractionGraphOP |
Definition at line 27 of file PDInteractionGraph.fwd.hh.
| typedef SurfaceInteractionGraph< PDNode, PDEdge, PDInteractionGraph > core::pack::interaction_graph::PDSurfaceInteractionGraph |
Definition at line 29 of file SurfaceInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< PDSurfaceInteractionGraph > core::pack::interaction_graph::PDSurfaceInteractionGraphOP |
Definition at line 34 of file SurfaceInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< PrecomputedPairEnergiesInteractionGraph const > core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphCOP |
Definition at line 27 of file PrecomputedPairEnergiesInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< PrecomputedPairEnergiesInteractionGraph > core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraphOP |
Definition at line 24 of file PrecomputedPairEnergiesInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< RotamerDots const > core::pack::interaction_graph::RotamerDotsCOP |
Definition at line 29 of file RotamerDots.fwd.hh.
Definition at line 26 of file RotamerDots.fwd.hh.
| typedef utility::pointer::owning_ptr< SimpleInteractionGraph const > core::pack::interaction_graph::SimpleInteractionGraphCOP |
Definition at line 29 of file SimpleInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< SimpleInteractionGraph > core::pack::interaction_graph::SimpleInteractionGraphOP |
Definition at line 26 of file SimpleInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< SymmLinearMemoryInteractionGraph const > core::pack::interaction_graph::SymmLinearMemoryInteractionGraphCOP |
Definition at line 29 of file SymmLinMemInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< SymmLinearMemoryInteractionGraph > core::pack::interaction_graph::SymmLinearMemoryInteractionGraphOP |
Definition at line 26 of file SymmLinMemInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< SymmMinimalistInteractionGraph const > core::pack::interaction_graph::SymmMinimalistInteractionGraphCOP |
Definition at line 29 of file SymmMinimalistInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< SymmMinimalistInteractionGraph > core::pack::interaction_graph::SymmMinimalistInteractionGraphOP |
Definition at line 26 of file SymmMinimalistInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< SymmOnTheFlyInteractionGraph const > core::pack::interaction_graph::SymmOnTheFlyInteractionGraphCOP |
Definition at line 28 of file SymmOnTheFlyInteractionGraph.fwd.hh.
| typedef utility::pointer::owning_ptr< SymmOnTheFlyInteractionGraph > core::pack::interaction_graph::SymmOnTheFlyInteractionGraphOP |
Definition at line 25 of file SymmOnTheFlyInteractionGraph.fwd.hh.
| Enumerator | |
|---|---|
| whole_whole | |
| whole_sc | |
| sc_whole | |
| sc_sc | |
Definition at line 60 of file OnTheFlyInteractionGraph.hh.
| std::ostream & core::pack::interaction_graph::operator<< | ( | std::ostream & | os, |
| DotSphere const & | ds | ||
| ) |
invokes print on the input DotSphere object
operator<< ( ostream, DotSphere)
Definition at line 492 of file RotamerDots.cc.
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 )
Definition at line 1427 of file RotamerDots.cc.
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().
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| 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::RigidBodyDofSeqTransMover::apply(), protocols::rigid::RigidBodyDofRandomTransMover::apply(), protocols::rigid::RigidBodyDofSeqPerturbMover::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_chisamples_for_rotamer_chi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_chisamples_for_rotamer_chi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbind_nrchi_score(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::best_rotamer_energy(), protocols::unfolded_state_energy_calculator::calc_vector_boltzmann(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::chisamples_for_rotamer_and_chi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< 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(), core::graph::ArrayPool< Real >::create_new_block(), protocols::wum::DatabaseQueryWorkUnitManager< T >::create_work_units_from_query(), core::io::pdb::PDB_DReader::createRecords(), core::scoring::etable::EtableOptions::EtableOptions(), 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::scoring::dna::get_base_pair_params_old(), core::scoring::dna::get_base_pair_stub(), core::scoring::dna::get_base_step_params(), core::scoring::dna::get_base_stub(), core::io::raw_data::RawStruct::get_debug_rmsd(), core::pack::interaction_graph::SymmLinearMemEdge::get_energy_for_alt_state(), core::pack::interaction_graph::LinearMemEdge::get_energy_for_alt_state(), core::scoring::dna::get_midstep_stub(), 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::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static(), protocols::features::get_something_from_database(), core::scoring::dna::get_stub_stub_params(), 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::RotamericSingleResidueDunbrackLibrary< T >::nchi(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< 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::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(), protocols::analysis::InterfaceAnalyzerMover::print_pymol_selection_of_hbond_unsat(), 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::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_bbdep_continuous_minimization_data(), core::io::serialization::read_bytes(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_binary(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotamer_definitions(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::read_rotameric_data(), core::fragment::MapCacheUnit< T >::remap_value(), core::fragment::VectorCacheUnit< T >::remap_value(), protocols::analysis::InterfaceAnalyzerMover::report_data(), core::fragment::CacheWrapper< protocols::simple_moves::GunnTuple, MapCacheUnit< protocols::simple_moves::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< protocols::simple_moves::GunnTuple, MapCacheUnit< protocols::simple_moves::GunnTuple > >::scored_frag_ids(), core::grid::CartGrid< core::Real >::serialize(), 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().
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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().
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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().
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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().
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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().
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| bool core::pack::interaction_graph::unpack_ubyte | ( | ObjexxFCL::ubyte const & | value, |
| core::Size | which_bit | ||
| ) |
Definition at line 67 of file RotamerDots.cc.
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 | ||
| ) |
Definition at line 102 of file RotamerDots.cc.
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 | ||
| ) |
Definition at line 140 of file RotamerDots.cc.
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 |
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| ) |
Definition at line 93 of file RotamerDots.cc.
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 | ||
| ) |
Definition at line 109 of file RotamerDots.cc.
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().
| bool const core::pack::interaction_graph::debug = { false } |
For testing the LinMemIG, you'll want to set this to true.
For testing the symminIG, you'll want to set this to true.
For testing the symmlinmemIG, you'll want to set this to true.
Definition at line 44 of file LinearMemoryInteractionGraph.cc.
Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::relax::FastRelax::apply(), protocols::abinitio::MembraneAbinitio::apply(), protocols::abinitio::ClassicAbinitio::apply(), core::pack::interaction_graph::SymmLinearMemNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), protocols::relax::FastRelax::batch_apply(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::abinitio::ClassicAbinitio::ClassicAbinitio(), protocols::abinitio::AbrelaxApplication::close_loops(), core::pack::interaction_graph::SymmLinearMemNode::commit_considered_substitution(), 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::scoring::electron_density::ElectronDensity::expandToUnitCell(), core::import_pose::pose_stream::LazySilentFilePoseInputStream::fill_pose(), core::import_pose::pose_stream::SilentFilePoseInputStream::fill_pose(), protocols::abinitio::AbrelaxApplication::fold(), core::scoring::constraints::SoedingFunc::func(), 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(), protocols::loops::loop_mover::refine::LoopRefineInnerCycle::init_options(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), 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::SymmLinearMemNode::project_deltaE_for_substitution(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::read_options(), protocols::anchored_design::AnchoredPerturbMover::read_options(), protocols::anchored_design::AnchoredRefineMover::read_options(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::abinitio::AbrelaxApplication::register_options(), protocols::abinitio::FragmentSampler::register_options(), protocols::abinitio::ClassicAbinitio::register_options(), protocols::abinitio::MembraneAbinitio::register_options(), protocols::abinitio::register_options_broker(), core::scoring::electron_density::ElectronDensity::rotAlign2DPose(), protocols::abinitio::run_boinc_debug(), protocols::anchored_design::AnchoredPerturbMover::set_debug(), protocols::anchored_design::AnchoredRefineMover::set_debug(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), protocols::abinitio::AbrelaxApplication::setup_fold(), core::scoring::electron_density::ElectronDensity::setup_patterson_first_time(), and core::kinematics::AtomTree::torsion_angle_dof_id().
1.8.4