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core::kinematics Namespace Reference

Namespaces

 tree
 

Classes

class  AtomTree
 The AtomTree class is a wrapper for a tree of kinematic Atoms. More...
 
class  AtomWithDOFChange
 simple class for use in output-sensitive refold subroutine. More...
 
class  Edge
 single edge of the fold_tree More...
 
class  EXCN_InvalidFoldTree
 
class  FoldTree
 The FoldTree is a residue-based tree-like representation of a molecule. More...
 
class  Jump
 an object which makes rigid-body transformation with translational and rotational perturbation More...
 
class  MinimizerMapBase
 
class  MoveMap
 A class specifying DOFs to be flexible or fixed. More...
 
struct  Node
 
class  ResidueCoordinateChangeList
 The AtomTree is responsible for informing the conformation of which residues have had either internal (DOF) or external (xyz) coordinate changes so that the Conformation may shuttle O(k) – output sensitive – data from the AtomTree to the Residue objects it manages. More...
 
class  RT
 Rotation + translation class. More...
 
class  ShortestPathInFoldTree
 
class  Stub
 Stub class – an object of orthogonal coordinate frame. More...
 
struct  TreeVizBuilder
 

Typedefs

typedef id::AtomID_Map
< tree::AtomOP
AtomPointer2D
 
typedef utility::vector1
< tree::AtomOP
AtomPointer1D
 
typedef
utility::pointer::weak_ptr
< AtomTree
AtomTreeAP
 
typedef
utility::pointer::weak_ptr
< AtomTree const > 
AtomTreeCAP
 
typedef
utility::pointer::shared_ptr
< AtomTree
AtomTreeOP
 
typedef
utility::pointer::shared_ptr
< AtomTree const > 
AtomTreeCOP
 
typedef utility::vector1
< AtomWithDOFChange
AtomDOFChangeSet
 
typedef ObjexxFCL::FArray1D_int DomainMap
 
typedef
utility::pointer::weak_ptr
< Edge
EdgeAP
 
typedef
utility::pointer::shared_ptr
< Edge
EdgeOP
 
typedef
utility::pointer::weak_ptr
< FoldTree
FoldTreeAP
 
typedef
utility::pointer::weak_ptr
< FoldTree const > 
FoldTreeCAP
 
typedef
utility::pointer::shared_ptr
< FoldTree
FoldTreeOP
 
typedef
utility::pointer::shared_ptr
< FoldTree const > 
FoldTreeCOP
 
typedef
utility::pointer::shared_ptr
< MinimizerMapBase
MinimizerMapBaseOP
 
typedef
utility::pointer::shared_ptr
< MinimizerMapBase const > 
MinimizerMapBaseCOP
 
typedef
utility::pointer::shared_ptr
< MoveMap
MoveMapOP
 
typedef
utility::pointer::shared_ptr
< MoveMap const > 
MoveMapCOP
 
typedef
utility::pointer::shared_ptr
< ResidueCoordinateChangeList
ResidueCoordinateChangeListOP
 
typedef utility::vector1< SizeResidueIndexList
 
typedef utility::vector1< Size >
::const_iterator 
ResidueListIterator
 
typedef
utility::pointer::weak_ptr< RT
RTAP
 
typedef
utility::pointer::shared_ptr
< RT
RTOP
 
typedef
utility::pointer::weak_ptr
< ShortestPathInFoldTree
ShortestPathInFoldTreeAP
 
typedef
utility::pointer::shared_ptr
< ShortestPathInFoldTree
ShortestPathInFoldTreeOP
 
typedef
utility::pointer::shared_ptr
< ShortestPathInFoldTree const > 
ShortestPathInFoldTreeCOP
 
using NodeOP = utility::pointer::shared_ptr< Node >
 
using NodeAP = utility::pointer::weak_ptr< Node >
 
typedef utility::vector1
< utility::vector1< Size > > 
Links
 

Functions

static basic::Tracer TR ("core.kinematics.AtomTree")
 
void find_stub_transform (Stub const &stub1, Stub const &stub2, RT const &rt, Stub::Matrix &A, Vector &b)
 
int const dir_jump (0)
 
static basic::Tracer tr ("core.kinematics")
 
std::ostream & operator<< (std::ostream &os, const Edge &e)
 
std::istream & operator>> (std::istream &is, Edge &e)
 
bool operator< (Edge const &a, Edge const &b)
 
bool operator== (Edge const &a, Edge const &b)
 
bool operator!= (Edge const &a, Edge const &b)
 
bool operator== (FoldTree const &a, FoldTree const &b)
 
bool operator!= (const FoldTree &a, const FoldTree &b)
 
std::ostream & operator<< (std::ostream &os, FoldTree const &t)
 
std::istream & operator>> (std::istream &is, FoldTree &t)
 
utility::vector1< Real > const & ZERO ()
 
std::istream & operator>> (std::istream &is, Jump &jump)
 
std::ostream & operator<< (std::ostream &os, const Jump &jump)
 
Real distance (Jump const &a_in, Jump const &b_in)
 RT root squared deviation. More...
 
void jump_distance (Jump const &a_in, Jump const &b_in, Real &dist, Real &theta)
 compare the difference of two jumps in term of the translation (dist) and rotational angle(theta) More...
 
std::ostream & operator<< (std::ostream &out, MoveMap const &mm)
 
std::ostream & operator<< (std::ostream &os, const RT &rt)
 
std::istream & operator>> (std::istream &is, RT &rt)
 
Real distance (RT const &a, RT const &b)
 root squared devitation of two RTs More...
 
static basic::Tracer tr ("core.kinematics.ShortestPathInFoldTree", basic::t_info)
 
std::ostream & operator<< (std::ostream &os, Stub const &a)
 output operator, 3x3 matrix followed by an xyzVector More...
 
Stub default_stub (Stub::Matrix::identity(), Stub::Vector(0.0))
 
double distance (Stub const &a, Stub const &b)
 root squared deviation between two stubs More...
 
static basic::Tracer TR ("core.kinematics.util")
 
tree::AtomOP add_atom (int const atomno, int const seqpos, Links const &links, AtomPointer1D &atom_ptr, bool const add_jump_atom)
 
int pick_loopy_cutpoint (Size const n_res, ObjexxFCL::FArray1D_float const &cut_bias_sum)
 pick a postion in n_res as the cutpoint More...
 
core::Size jump_which_partitions (FoldTree const &fold_tree, utility::vector1< bool > residues)
 Return the jump which separates the residues in the passed residue selection from all the ones which are not. If no such jump exists (e.g. there's a mixture of included/excluded residues on both sides of every jump) then return zero. Note that upstream/downstream is not specified - you can check this later. More...
 
FoldTree get_foldtree_which_partitions (FoldTree const &fold_tree, utility::vector1< bool > residues)
 Return a new FoldTree where a single jump separates the residues in the passed set from those not in the passed set. More...
 
utility::vector1< core::Sizeresidues_upstream_of_jump (FoldTree const &fold_tree, core::Size jump_id)
 Return a list of residue numbers which are on the upstream side of the jump. More...
 
utility::vector1< core::Sizeresidues_downstream_of_jump (FoldTree const &fold_tree, core::Size jump_id)
 Return a list of residue numbers which are on the downstream side of the jump. More...
 
void simple_visualize_fold_tree (FoldTree const &fold_tree, std::ostream &out)
 prints something like this ***1***C***1*********2***C********3****C****2********3***** More...
 
void simple_visualize_fold_tree_and_movemap (FoldTree const &fold_tree, MoveMap const &mm, std::ostream &out)
 prints something like this ***1***C***1*********2***C********3****C****2********3***** **********xxxxxxxxxxxxx************************************ More...
 
void simple_visualize_fold_tree_and_movemap_bb_chi (FoldTree const &fold_tree, MoveMap const &mm, std::ostream &out)
 prints something like this ***1***C***1*********2***C********3****C****2********3***** **********xxxxxxxxxxxxx************************************ More...
 
core::kinematics::FoldTree linearize_fold_tree (core::kinematics::FoldTree const &tree)
 linearizes (or defoliates, if you prefer) a FoldTree. "default" FoldTrees produced by the PDB reader have all chains (peptide edges) starting from jumps relative to residue 1. This code modifies the tree to instead have all the jumps be relative to the preceding edge. It is not tested with ligands and will not work with "functional" jumps. From A to B: A:FOLD_TREE EDGE 1 78 -1 EDGE 1 79 1 EDGE 79 454 -1 EDGE 1 455 2 EDGE 455 540 -1 EDGE 1 541 3 EDGE 541 697 -1 B:FOLD_TREE EDGE 1 78 -1 EDGE 78 79 1 EDGE 79 454 -1 EDGE 454 455 2 EDGE 455 540 -1 EDGE 540 541 3 EDGE 541 697 -1 More...
 
void replace_substr (std::string &str, const std::string &from, const std::string &to)
 
std::string operator* (std::string const &s, size_t n)
 
std::string pad_dash (Size npad, std::string s)
 
std::string pad_dash_left (Size npad, std::string s)
 
std::string pad_dash_right (Size npad, std::string s)
 
std::string visualize_fold_tree (FoldTree const &ft, std::map< Size, std::string > const &node_labels_partial_in, std::map< Size, char > const &mark_jump_to_res, std::map< Size, Size > const &jump_follows)
 
std::string visualize_fold_tree (FoldTree const &fold_tree)
 sheffler More...
 
std::string visualize_fold_tree (FoldTree const &ft, std::map< Size, std::string > const &node_labels_partial)
 
std::string visualize_fold_tree (FoldTree const &ft, std::map< Size, char > const &mark_jump_to_res)
 
core::kinematics::FoldTree remodel_fold_tree_to_account_for_insertion (core::kinematics::FoldTree const &input_tree, core::Size insert_after, core::Size insert_size)
 remodel a fold tree to account for a large insertion by adding the size of the insert to upstream positions More...
 
utility::vector1< core::Sizeget_residues_from_movemap_with_id (id::TorsionType query_torsion, MoveMap const &movemap)
 Get a vector of residues matching the id from a movemap. More...
 
utility::vector1< core::Sizeget_residues_from_movemap_bb_any_torsion (MoveMap const &movemap, Size total_resnum)
 Get a vector of residues that have any of their BB torsions on - either by way of the full bb or torsion ID setting in Movemap. More...
 
utility::vector1< core::Sizeget_residues_from_movemap_bb_or_chi (MoveMap const &movemap, Size total_resnum)
 Get residues that are on in the movemap, either for BB, Any Specific torsion (up to 4) or CHI. More...
 
tree::AtomOP add_atom (int const atomno, int const seqpos, utility::vector1< utility::vector1< Size > > const &links, AtomPointer1D &atom_ptr, bool const add_jump_atom)
 creat an atom and add it to the residue atom-tree based on information stored in links. More...
 

Variables

int const dir_jump
 
Stub default_stub
 Global default stub. More...
 

Typedef Documentation

typedef utility::vector1< tree::AtomOP > core::kinematics::AtomPointer1D
typedef utility::pointer::weak_ptr< AtomTree > core::kinematics::AtomTreeAP
typedef utility::pointer::weak_ptr< AtomTree const > core::kinematics::AtomTreeCAP
typedef utility::pointer::shared_ptr< AtomTree const > core::kinematics::AtomTreeCOP
typedef utility::pointer::shared_ptr< AtomTree > core::kinematics::AtomTreeOP
typedef ObjexxFCL::FArray1D_int core::kinematics::DomainMap
typedef utility::pointer::weak_ptr< Edge > core::kinematics::EdgeAP
typedef utility::pointer::shared_ptr< Edge > core::kinematics::EdgeOP
typedef utility::pointer::weak_ptr< FoldTree > core::kinematics::FoldTreeAP
typedef utility::pointer::weak_ptr< FoldTree const > core::kinematics::FoldTreeCAP
typedef utility::pointer::shared_ptr< FoldTree const > core::kinematics::FoldTreeCOP
typedef utility::pointer::shared_ptr< FoldTree > core::kinematics::FoldTreeOP
typedef utility::vector1< utility::vector1< Size > > core::kinematics::Links
typedef utility::pointer::shared_ptr< MinimizerMapBase const > core::kinematics::MinimizerMapBaseCOP
typedef utility::pointer::shared_ptr< MinimizerMapBase > core::kinematics::MinimizerMapBaseOP
typedef utility::pointer::shared_ptr< MoveMap const > core::kinematics::MoveMapCOP
typedef utility::pointer::shared_ptr< MoveMap > core::kinematics::MoveMapOP
using core::kinematics::NodeAP = typedef utility::pointer::weak_ptr<Node>
using core::kinematics::NodeOP = typedef utility::pointer::shared_ptr<Node>
typedef utility::vector1< Size > core::kinematics::ResidueIndexList
typedef utility::vector1< Size >::const_iterator core::kinematics::ResidueListIterator
typedef utility::pointer::weak_ptr< RT > core::kinematics::RTAP
typedef utility::pointer::shared_ptr< RT > core::kinematics::RTOP
typedef utility::pointer::shared_ptr< ShortestPathInFoldTree const > core::kinematics::ShortestPathInFoldTreeCOP
typedef utility::pointer::shared_ptr< ShortestPathInFoldTree > core::kinematics::ShortestPathInFoldTreeOP

Function Documentation

tree::AtomOP core::kinematics::add_atom ( int const  atomno,
int const  seqpos,
utility::vector1< utility::vector1< Size > > const &  links,
AtomPointer1D &  atom_ptr,
bool const  add_jump_atom 
)

creat an atom and add it to the residue atom-tree based on information stored in links.

tree::AtomOP core::kinematics::add_atom ( int const  atomno,
int const  seqpos,
Links const &  links,
AtomPointer1D &  atom_ptr,
bool const  add_jump_atom 
)

recursively called until all atoms in this residue are added.

Note
The Atoms that are allocated within this function are owned by the atom_ptr which is a container of AtomOP's (see AtomPointer.fwd.hh)
Returns a raw pointer for internal tree links but memory management is handled by atom_ptr

References protocols::sic_dock::scores::nbr.

Referenced by core::conformation::build_residue_tree().

Stub core::kinematics::default_stub ( Stub::Matrix::  identity(),
Stub::  Vector0.0 
)

a stub center at 0.0 with lab frame(identity matrix)

int const core::kinematics::dir_jump ( )
double core::kinematics::distance ( Stub const &  a,
Stub const &  b 
)
inline

root squared deviation between two stubs

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

Real core::kinematics::distance ( RT const &  a,
RT const &  b 
)
inline

root squared devitation of two RTs

References core::kinematics::RT::rotation, and core::kinematics::RT::translation.

Real core::kinematics::distance ( Jump const &  a_in,
Jump const &  b_in 
)

RT root squared deviation.

References core::pose::motif::a(), protocols::match::upstream::b, core::kinematics::Jump::fold_in_rb_deltas(), and core::kinematics::Jump::rt_.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::seeded_abinitio::add_dist_constraints(), protocols::indexed_structure_store::FragmentStore::add_threshold_distance_allFrag(), protocols::simple_filters::ResidueSelectionDistanceFilter::apply(), protocols::simple_filters::ResidueDistanceFilter::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::cyclic_peptide::PeptideCyclizeMover::apply(), protocols::simple_filters::StemFinder::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::task_operations::DesignAroundOperation::apply(), protocols::contact_map::ContactMap::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::ligand_docking::Transform::apply(), protocols::fldsgn::filters::StrandHelixGeometryFilter::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::task_operations::RestrictToMoveMapChiOperation::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), core::chemical::ResidueType::assign_neighbor_atom(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), protocols::loop_grower::LoopGrower::atomGDTha(), protocols::hotspot_hashing::HotspotStubSet::autofill(), protocols::rna::setup::RNA_CSA_JobDistributor::average_pairwise_distance(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), protocols::loop_grower::DensSkeleton::breadth_first_connect(), core::pack::rotamer_set::build_optimal_water_O_on_donor(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::build_optimal_water_Os_on_acceptor(), protocols::denovo_design::components::FoldGraph::build_seg2node(), protocols::features::strand_assembly::cal_min_avg_dis_between_two_sheets_by_cen_res(), core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor(), core::scoring::membrane::MPHelicalityEnergy::centroid_neighbors(), core::scoring::membrane::MPResidueLipophilicityEnergy::centroid_neighbors(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::splice::SpliceManager::chainbreak_check(), protocols::splice::Splice::chainbreak_check(), protocols::qsar::scoring_grid::ChargeGrid::charge_charge_electrostatic(), protocols::loop_grower::LoopGrower::check_coordinates(), protocols::splice::SpliceManager::check_sequence_profile(), protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms(), protocols::fold_from_loops::utils::Nub::closest_binder(), core::pose::rna::RNA_SuiteName::closest_by_dist4(), core::pose::rna::RNA_SuiteName::closest_suite(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::ResidueSelectionDistanceFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::ChainBreak::compute(), protocols::simple_filters::SequenceDistance::compute(), protocols::simple_filters::HelixHelixAngleFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), protocols::enzdes::LigBurialFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors(), core::pack::interaction_graph::SurfacePotential::compute_pose_surface_energy(), core::pack::interaction_graph::SurfacePotential::compute_residue_surface_energy(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::forge::build::BuildManager::create_directed_dependency(), protocols::toolbox::match_enzdes_util::GeomSampleInfo::create_sample_vector(), protocols::cryst::crystRMSfast(), protocols::relax::derive_sc_sc_restraints(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), protocols::features::strand_assembly::determine_heading_direction_by_vector(), protocols::toolbox::ResidueNetwork::dijkstras(), core::fragment::picking_old::concepts::Extent< PageIterator >::distance(), core::fragment::picking_old::vall::scores::VallFragmentScore::distance(), protocols::frag_picker::scores::DisulfideDistance::do_caching(), protocols::frag_picker::scores::PCS_FragDistance::do_caching(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::denovo_design::architects::BetaSheetArchitect::enumerate_permutations(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::scoring::atomic_depth::AtomicDepth::fastdistancemap(), protocols::hotspot_hashing::HotspotStubSet::fill(), core::scoring::constraints::RTConstraint::fill_f1_f2(), protocols::mpi_refinement::MultiObjective::filter_similar(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::loop_grower::DensSkeleton::find_closest_occupied_point(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), protocols::fold_from_loops::utils::find_cutpoint_from_secondary_structure(), protocols::splice::find_disulfs_in_range(), protocols::seeded_abinitio::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::scoring::func::GaussianChainGeneralFunc::func(), protocols::sewing::movers::LigandBindingAssemblyMover::generate_assembly(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), core::pack::interaction_graph::RotamerDots::get_atom_atom_coverage(), protocols::antibody::clusters::CDRClusterMatcher::get_cdr_cluster(), protocols::antibody::clusters::CDRClusterMatcher::get_closest_cluster(), protocols::seeded_abinitio::get_closest_residue_pair(), protocols::kinematic_closure::ClosureSolution::get_distance(), protocols::sewing::movers::LigandBindingAssemblyMover::get_min_distance(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::hotspot_hashing::HotspotStubSet::get_nearest_stub(), protocols::loops::loop_closure::ccd::get_overlap_pos(), protocols::qsar::scoring_grid::ShapeGrid::get_point_score(), protocols::relax::RangeRelaxMover::get_spherical_repack_residues(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::sewing::hashing::LigandBindingResPlacer::identify_possible_binders(), protocols::nonlocal::SheetTranslate::initialize(), protocols::hydrate::is_inside(), protocols::kinematic_closure::BalancedKicMover::is_solution_trivial(), protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts(), protocols::protein_interface_design::MinimizeInterface(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::NC_distance_filter(), core::scoring::nv::NVscore::neighbor_weight(), core::scoring::membrane::MPHelicalityEnergy::neighboring_atoms(), core::scoring::membrane::MPResidueLipophilicityEnergy::neighboring_atoms(), protocols::splice::neighbors_in_vector(), protocols::vardist_solaccess::VarSolDRotamerDots::overlap_atoms(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::loop_grower::DensSkeleton::path_length(), core::scoring::disulfides::FullatomDisulfidePotential::print_score_functions(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::SaltBridgeCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::simple_filters::ResidueSelectionDistanceFilter::report(), protocols::simple_filters::ResidueDistanceFilter::report(), protocols::features::SmotifFeatures::report_features(), protocols::simple_filters::ResidueSelectionDistanceFilter::report_sm(), protocols::simple_filters::ResidueDistanceFilter::report_sm(), core::scoring::methods::HRF_MSLabelingEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::scoring::methods::PointWaterEnergy::residue_pair_energy(), protocols::legacy_sewing::result_to_models(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::loop_grower::LoopGrower::RMStonative(), core::pack::RTMin::rtmin(), core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(), protocols::make_rot_lib::MakeRotLibMover::seed_centroids(), protocols::electron_density::DockIntoDensityMover::select_points(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D1D2(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D2D3(), core::select::residue_selector::NeighborhoodResidueSelector::set_distance(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::set_interface_distance(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::scoring::rna::RNP_LowResEnergy::setup_for_scoring(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), core::scoring::func::GaussianChainGeneralFunc::show_definition(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::sewing::scoring::IntraDesignTerminusMotifScorer::terminus_motif_score(), protocols::sewing::scoring::TerminusMotifScorer::terminus_motif_score(), protocols::sewing::requirements::KeepLigandContactsRequirement::test(), protocols::chemically_conjugated_docking::ubq_ras_distance(), protocols::mpi_refinement::MultiObjective::update_library_seeds(), core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct(), core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage(), core::chemical::ResidueDatabaseIO::write_residue_type_icoor_table_schema(), and protocols::features::SmotifFeatures::write_schema_to_db().

void core::kinematics::find_stub_transform ( Stub const &  stub1,
Stub const &  stub2,
RT const &  rt,
Stub::Matrix A,
Vector b 
)

This is a helper function to find a linear transform that when applied to the downstream stub has the effect that RT( instub, transformed-downstream-stub) == target_rt

References core::kinematics::RT::get_rotation(), core::kinematics::RT::get_translation(), core::kinematics::Stub::M, protocols::hybridization::t, and core::kinematics::Stub::v.

Referenced by core::kinematics::AtomTree::set_stub_transform().

FoldTree core::kinematics::get_foldtree_which_partitions ( FoldTree const &  fold_tree,
utility::vector1< bool residues 
)

Return a new FoldTree where a single jump separates the residues in the passed set from those not in the passed set.

The current root residue is preserved. If you want the passed residue set on a particular side of the jump, you can always call FoldTree::reorder() to re-root the FoldTree on the appropriate side.

References protocols::match::upstream::b, core::kinematics::Edge::CHEMICAL, core::kinematics::FoldTree::clear(), core::kinematics::FoldTree::jump_edge(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::root(), core::id::to_string(), and TR().

Referenced by protocols::ligand_docking::get_interface_deltas().

utility::vector1< core::Size > core::kinematics::get_residues_from_movemap_bb_any_torsion ( MoveMap const &  movemap,
Size  total_resnum 
)

Get a vector of residues that have any of their BB torsions on - either by way of the full bb or torsion ID setting in Movemap.

Author
Jared Adolf-Bryfogle

References core::kinematics::MoveMap::get_bb().

utility::vector1< core::Size > core::kinematics::get_residues_from_movemap_bb_or_chi ( MoveMap const &  movemap,
Size  total_resnum 
)

Get residues that are on in the movemap, either for BB, Any Specific torsion (up to 4) or CHI.

Author
Jared Adolf-Bryfogle

References core::kinematics::MoveMap::get_bb(), and core::kinematics::MoveMap::get_chi().

utility::vector1< core::Size > core::kinematics::get_residues_from_movemap_with_id ( id::TorsionType  query_torsion,
MoveMap const &  movemap 
)

Get a vector of residues matching the id from a movemap.

Author
Jared Adolf-Bryfogle

References core::kinematics::MoveMap::movemap_torsion_id_begin(), and core::kinematics::MoveMap::movemap_torsion_id_end().

void core::kinematics::jump_distance ( Jump const &  a_in,
Jump const &  b_in,
Real &  dist,
Real &  theta 
)
core::Size core::kinematics::jump_which_partitions ( FoldTree const &  fold_tree,
utility::vector1< bool residues 
)

Return the jump which separates the residues in the passed residue selection from all the ones which are not. If no such jump exists (e.g. there's a mixture of included/excluded residues on both sides of every jump) then return zero. Note that upstream/downstream is not specified - you can check this later.

References core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), and core::kinematics::FoldTree::partition_by_jump().

Referenced by protocols::ligand_docking::get_interface_deltas().

core::kinematics::FoldTree core::kinematics::linearize_fold_tree ( core::kinematics::FoldTree const &  tree)

linearizes (or defoliates, if you prefer) a FoldTree. "default" FoldTrees produced by the PDB reader have all chains (peptide edges) starting from jumps relative to residue 1. This code modifies the tree to instead have all the jumps be relative to the preceding edge. It is not tested with ligands and will not work with "functional" jumps. From A to B: A:FOLD_TREE EDGE 1 78 -1 EDGE 1 79 1 EDGE 79 454 -1 EDGE 1 455 2 EDGE 455 540 -1 EDGE 1 541 3 EDGE 541 697 -1 B:FOLD_TREE EDGE 1 78 -1 EDGE 78 79 1 EDGE 79 454 -1 EDGE 454 455 2 EDGE 455 540 -1 EDGE 540 541 3 EDGE 541 697 -1

References core::kinematics::FoldTree::add_edge().

Referenced by protocols::floppy_tail::FloppyTailMover::init_on_new_input().

bool core::kinematics::operator!= ( const FoldTree &  a,
const FoldTree &  b 
)
bool core::kinematics::operator!= ( Edge const &  a,
Edge const &  b 
)

when any of start residue number, stop residue number and label index number is not equal

References core::kinematics::Edge::label(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

std::string core::kinematics::operator* ( std::string const &  s,
size_t  n 
)
bool core::kinematics::operator< ( Edge const &  a,
Edge const &  b 
)

compare start residue number first, then stop residue number, then label index number, then start_atom, then stop_atom

References core::kinematics::Edge::label(), core::kinematics::Edge::start(), core::kinematics::Edge::start_atom(), core::kinematics::Edge::stop(), and core::kinematics::Edge::stop_atom().

std::ostream & core::kinematics::operator<< ( std::ostream &  os,
Stub const &  a 
)

output operator, 3x3 matrix followed by an xyzVector

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

std::ostream& core::kinematics::operator<< ( std::ostream &  os,
const Edge &  e 
)
std::ostream& core::kinematics::operator<< ( std::ostream &  os,
const RT &  rt 
)
std::ostream& core::kinematics::operator<< ( std::ostream &  os,
const Jump &  jump 
)
std::ostream& core::kinematics::operator<< ( std::ostream &  out,
MoveMap const &  mm 
)
inline
std::ostream& core::kinematics::operator<< ( std::ostream &  os,
FoldTree const &  t 
)

Foldtree output to stream

bool core::kinematics::operator== ( FoldTree const &  a,
FoldTree const &  b 
)

Checks that edges are in the same order and are equal That is, the order of the edges in the edge list is important to equality here

References core::kinematics::FoldTree::edge_list_.

bool core::kinematics::operator== ( Edge const &  a,
Edge const &  b 
)

when start residue number, stop residue number and label index number are all equal

References core::kinematics::Edge::label(), core::kinematics::Edge::start(), core::kinematics::Edge::start_atom(), core::kinematics::Edge::stop(), and core::kinematics::Edge::stop_atom().

std::istream& core::kinematics::operator>> ( std::istream &  is,
Edge &  e 
)
std::istream& core::kinematics::operator>> ( std::istream &  is,
RT &  rt 
)
std::istream& core::kinematics::operator>> ( std::istream &  is,
Jump &  jump 
)
std::istream& core::kinematics::operator>> ( std::istream &  is,
FoldTree &  t 
)
std::string core::kinematics::pad_dash ( Size  npad,
std::string  s 
)
std::string core::kinematics::pad_dash_left ( Size  npad,
std::string  s 
)
std::string core::kinematics::pad_dash_right ( Size  npad,
std::string  s 
)
int core::kinematics::pick_loopy_cutpoint ( Size const  n_res,
ObjexxFCL::FArray1D_float const &  cut_bias_sum 
)

pick a postion in n_res as the cutpoint

this is done based on probability info stored in cut_bias_sum. This function is used during fold_tree construction.

References core::scoring::rg, and TR().

Referenced by core::kinematics::FoldTree::cut_random_edge().

core::kinematics::FoldTree core::kinematics::remodel_fold_tree_to_account_for_insertion ( core::kinematics::FoldTree const &  input_tree,
core::Size  insert_after,
core::Size  insert_size 
)

remodel a fold tree to account for a large insertion by adding the size of the insert to upstream positions

Author
Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om as a favor for Jared

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::is_jump_point(), protocols::loops::start, and protocols::loops::stop.

void core::kinematics::replace_substr ( std::string &  str,
const std::string &  from,
const std::string &  to 
)
utility::vector1< core::Size > core::kinematics::residues_downstream_of_jump ( FoldTree const &  fold_tree,
core::Size  jump_id 
)
utility::vector1< core::Size > core::kinematics::residues_upstream_of_jump ( FoldTree const &  fold_tree,
core::Size  jump_id 
)

Return a list of residue numbers which are on the upstream side of the jump.

References core::kinematics::FoldTree::partition_by_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

void core::kinematics::simple_visualize_fold_tree ( FoldTree const &  fold_tree,
std::ostream &  out 
)
void core::kinematics::simple_visualize_fold_tree_and_movemap ( FoldTree const &  fold_tree,
MoveMap const &  mm,
std::ostream &  out 
)
void core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi ( FoldTree const &  fold_tree,
MoveMap const &  mm,
std::ostream &  out 
)
static basic::Tracer core::kinematics::TR ( "core.kinematics.util"  )
static
static basic::Tracer core::kinematics::tr ( "core.kinematics"  )
static
static basic::Tracer core::kinematics::TR ( "core.kinematics.AtomTree"  )
static
static basic::Tracer core::kinematics::tr ( "core.kinematics.ShortestPathInFoldTree"  ,
basic::t_info   
)
static
std::string core::kinematics::visualize_fold_tree ( FoldTree const &  ft,
std::map< Size, std::string > const &  node_labels_partial_in,
std::map< Size, char > const &  mark_jump_to_res,
std::map< Size, Size > const &  jump_follows 
)
std::string core::kinematics::visualize_fold_tree ( FoldTree const &  ft)

sheffler

References visualize_fold_tree().

std::string core::kinematics::visualize_fold_tree ( FoldTree const &  ft,
std::map< Size, std::string > const &  node_labels_partial 
)

References visualize_fold_tree().

std::string core::kinematics::visualize_fold_tree ( FoldTree const &  ft,
std::map< Size, char > const &  mark_jump_to_res 
)

References visualize_fold_tree().

utility::vector1< Real > const & core::kinematics::ZERO ( )

Variable Documentation

Stub core::kinematics::default_stub
int const core::kinematics::dir_jump