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core::kinematics Namespace Reference

Namespaces

 inverse
 
 jacobian
 
 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...
 
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  Node
 
struct  TreeVizBuilder
 

Typedefs

typedef id::AtomID_Map< tree::AtomOPAtomPointer2D
 
typedef utility::vector1< tree::AtomOPAtomPointer1D
 
typedef utility::pointer::weak_ptr< AtomTreeAtomTreeAP
 
typedef utility::pointer::weak_ptr< AtomTree const > AtomTreeCAP
 
typedef utility::pointer::shared_ptr< AtomTreeAtomTreeOP
 
typedef utility::pointer::shared_ptr< AtomTree const > AtomTreeCOP
 
typedef utility::vector1< AtomWithDOFChangeAtomDOFChangeSet
 
typedef ObjexxFCL::FArray1D_int DomainMap
 
typedef utility::pointer::weak_ptr< EdgeEdgeAP
 
typedef utility::pointer::shared_ptr< EdgeEdgeOP
 
typedef utility::pointer::weak_ptr< FoldTreeFoldTreeAP
 
typedef utility::pointer::weak_ptr< FoldTree const > FoldTreeCAP
 
typedef utility::pointer::shared_ptr< FoldTreeFoldTreeOP
 
typedef utility::pointer::shared_ptr< FoldTree const > FoldTreeCOP
 
typedef utility::pointer::shared_ptr< MinimizerMapBaseMinimizerMapBaseOP
 
typedef utility::pointer::shared_ptr< MinimizerMapBase const > MinimizerMapBaseCOP
 
typedef utility::pointer::shared_ptr< MoveMapMoveMapOP
 
typedef utility::pointer::shared_ptr< MoveMap const > MoveMapCOP
 
typedef utility::pointer::shared_ptr< ResidueCoordinateChangeListResidueCoordinateChangeListOP
 
typedef utility::vector1< SizeResidueIndexList
 
typedef utility::vector1< Size >::const_iterator ResidueListIterator
 
typedef utility::pointer::weak_ptr< RTRTAP
 
typedef utility::pointer::shared_ptr< RTRTOP
 
typedef utility::pointer::weak_ptr< ShortestPathInFoldTreeShortestPathInFoldTreeAP
 
typedef utility::pointer::shared_ptr< ShortestPathInFoldTreeShortestPathInFoldTreeOP
 
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...
 
MoveMapOP deep_copy (MoveMap const &source)
 
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...
 
core::Real 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 (Stub::Matrix::identity(), Stub::Vector(0.0))
 Global default stub. More...
 

Typedef Documentation

◆ AtomDOFChangeSet

◆ AtomPointer1D

typedef utility::vector1< tree::AtomOP > core::kinematics::AtomPointer1D

◆ AtomPointer2D

◆ AtomTreeAP

typedef utility::pointer::weak_ptr< AtomTree > core::kinematics::AtomTreeAP

◆ AtomTreeCAP

typedef utility::pointer::weak_ptr< AtomTree const > core::kinematics::AtomTreeCAP

◆ AtomTreeCOP

typedef utility::pointer::shared_ptr< AtomTree const > core::kinematics::AtomTreeCOP

◆ AtomTreeOP

typedef utility::pointer::shared_ptr< AtomTree > core::kinematics::AtomTreeOP

◆ DomainMap

typedef ObjexxFCL::FArray1D_int core::kinematics::DomainMap

◆ EdgeAP

typedef utility::pointer::weak_ptr< Edge > core::kinematics::EdgeAP

◆ EdgeOP

typedef utility::pointer::shared_ptr< Edge > core::kinematics::EdgeOP

◆ FoldTreeAP

typedef utility::pointer::weak_ptr< FoldTree > core::kinematics::FoldTreeAP

◆ FoldTreeCAP

typedef utility::pointer::weak_ptr< FoldTree const > core::kinematics::FoldTreeCAP

◆ FoldTreeCOP

typedef utility::pointer::shared_ptr< FoldTree const > core::kinematics::FoldTreeCOP

◆ FoldTreeOP

typedef utility::pointer::shared_ptr< FoldTree > core::kinematics::FoldTreeOP

◆ Links

typedef utility::vector1< utility::vector1< Size > > core::kinematics::Links

◆ MinimizerMapBaseCOP

typedef utility::pointer::shared_ptr< MinimizerMapBase const > core::kinematics::MinimizerMapBaseCOP

◆ MinimizerMapBaseOP

typedef utility::pointer::shared_ptr< MinimizerMapBase > core::kinematics::MinimizerMapBaseOP

◆ MoveMapCOP

typedef utility::pointer::shared_ptr< MoveMap const > core::kinematics::MoveMapCOP

◆ MoveMapOP

typedef utility::pointer::shared_ptr< MoveMap > core::kinematics::MoveMapOP

◆ NodeAP

using core::kinematics::NodeAP = typedef utility::pointer::weak_ptr<Node>

◆ NodeOP

using core::kinematics::NodeOP = typedef utility::pointer::shared_ptr<Node>

◆ ResidueCoordinateChangeListOP

◆ ResidueIndexList

typedef utility::vector1< Size > core::kinematics::ResidueIndexList

◆ ResidueListIterator

typedef utility::vector1< Size >::const_iterator core::kinematics::ResidueListIterator

◆ RTAP

typedef utility::pointer::weak_ptr< RT > core::kinematics::RTAP

◆ RTOP

typedef utility::pointer::shared_ptr< RT > core::kinematics::RTOP

◆ ShortestPathInFoldTreeAP

◆ ShortestPathInFoldTreeCOP

typedef utility::pointer::shared_ptr< ShortestPathInFoldTree const > core::kinematics::ShortestPathInFoldTreeCOP

◆ ShortestPathInFoldTreeOP

typedef utility::pointer::shared_ptr< ShortestPathInFoldTree > core::kinematics::ShortestPathInFoldTreeOP

Function Documentation

◆ add_atom() [1/2]

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().

◆ add_atom() [2/2]

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.

◆ deep_copy()

MoveMapOP core::kinematics::deep_copy ( MoveMap const &  source)
inline

◆ dir_jump()

int const core::kinematics::dir_jump ( )

◆ distance() [1/3]

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

RT root squared deviation.

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::indexed_structure_store::FragmentStore::add_threshold_distance_allFrag(), protocols::abinitio::DomainAssembly::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::rigid::RigidBodyTransMover::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::task_operations::DesignAroundOperation::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::fldsgn::filters::StrandHelixGeometryFilter::apply(), protocols::simple_filters::ResidueDistanceFilter::apply(), protocols::simple_filters::ResidueSelectionDistanceFilter::apply(), protocols::simple_filters::StemFinder::apply(), protocols::cyclic_peptide::PeptideCyclizeMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::task_operations::RestrictToMoveMapChiOperation::apply(), protocols::simple_filters::EnergyPerResidueFilter::apply_helper(), core::chemical::MutableResidueType::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(), protocols::features::SmotifFeatures::calculate_angles(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::calculate_block(), core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor(), protocols::glycopeptide_docking::calculate_sampled_distance(), core::energy_methods::MPHelicalityEnergy::centroid_neighbors(), core::energy_methods::MPResidueLipophilicityEnergy::centroid_neighbors(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::splice::Splice::chainbreak_check(), protocols::splice::SpliceManager::chainbreak_check(), protocols::qsar::scoring_grid::ChargeGrid::charge_charge_electrostatic(), protocols::loop_grower::LoopGrower::check_coordinates(), protocols::ligand_docking::Transform::check_grid(), protocols::ligand_docking::TransformEnsemble::check_grid(), protocols::splice::SpliceManager::check_sequence_profile(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::check_voxel_distance_to_receptor(), protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::fold_from_loops::utils::Nub::closest_binder(), core::pose::rna::RNA_SuiteName::closest_by_dist4(), protocols::scoring::Interface::closest_interface_residue(), core::pose::rna::RNA_SuiteName::closest_suite(), protocols::electron_density::cluster_RBfitResultDB_fast(), protocols::enzdes::LigBurialFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::simple_filters::ChainBreak::compute(), protocols::simple_filters::HelixHelixAngleFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::ResidueSelectionDistanceFilter::compute(), protocols::simple_filters::SequenceDistance::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::enzdes::PackRotamersMoverPartGreedy::compute_designable_neighbors(), 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(), 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< PageIter >::distance(), core::fragment::picking_old::vall::scores::VallFragmentScore::distance(), core::scoring::lkball::LK_DomeEnergy::dlk_frac_sigmoid(), core::scoring::lkball::LK_DomeEnergy::dmy_lk_fraction(), protocols::frag_picker::scores::DisulfideDistance::do_caching(), protocols::frag_picker::scores::PCS_FragDistance::do_caching(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), core::conformation::membrane::membrane_geometry::DoubleVesicle::DoubleVesicle(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::denovo_design::architects::BetaSheetArchitect::enumerate_permutations(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::energy_methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::scoring::atomic_depth::AtomicDepth::fastdistancemap(), protocols::hotspot_hashing::HotspotStubSet::fill(), protocols::mpi_refinement::MultiObjective::filter_similar(), 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(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::find_network(), protocols::splice::Splice::fold_tree(), 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::vardist_solaccess::VarSolDRotamerDots::get_atom_overlap_masks(), 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::electron_density::get_gdt(), protocols::sewing::movers::LigandBindingAssemblyMover::get_min_distance(), core::scoring::sc::get_n_neighbors(), 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(), core::scoring::interface_::DDPlookup::get_potentials(), protocols::electron_density::get_rms(), protocols::qsar::scoring_grid::ShapeGrid::get_score_from_angles(), protocols::relax::RangeRelaxMover::get_spherical_repack_residues(), protocols::simple_moves::BBConRotMover::get_xyz(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), protocols::sewing::hashing::LigandBindingResPlacer::identify_possible_binders(), core::scoring::orbitals::OrbitalsStatistics::increment_histogram_bin(), protocols::nonlocal::SheetTranslate::initialize(), protocols::hydrate::is_inside(), protocols::kinematic_closure::BalancedKicMover::is_solution_trivial(), core::scoring::lkball::LK_DomeEnergy::lk_frac_sigmoid(), core::io::mmtf::make_atom_information(), protocols::flexpep_docking::FlexPepDockingProtocol::markInterfaceBySideChainContacts(), protocols::protein_interface_design::MinimizeInterface(), core::scoring::lkball::LK_DomeEnergy::my_lk_fraction(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::NC_distance_filter(), core::scoring::nv::NVscore::neighbor_weight(), core::select::residue_selector::NeighborhoodResidueSelector::NeighborhoodResidueSelector(), core::energy_methods::MPHelicalityEnergy::neighboring_atoms(), core::energy_methods::MPResidueLipophilicityEnergy::neighboring_atoms(), protocols::splice::neighbors_in_vector(), core::scoring::orbitals::OrbitalsLookup::OrbHdist_cosAOH_energy(), core::scoring::orbitals::OrbitalsLookup::OrbHdist_cosDHO_energy(), core::scoring::orbitals::OrbitalsLookup::OrbOrbDist_cosAOD_energy(), core::scoring::orbitals::OrbitalsLookup::OrbOrbDist_cosDOA_energy(), 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(), protocols::ligand_docking::Transform::randomize_ligand(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), protocols::pose_metric_calculators::CatPiCalculator::recompute(), protocols::pose_metric_calculators::PiPiCalculator::recompute(), protocols::pose_metric_calculators::SaltBridgeCalculator::recompute(), protocols::simple_filters::ResidueDistanceFilter::report(), protocols::simple_filters::ResidueSelectionDistanceFilter::report(), protocols::features::SmotifFeatures::report_features(), protocols::pose_sewing::filters::CoreScorer::report_sm(), protocols::simple_filters::ResidueDistanceFilter::report_sm(), protocols::simple_filters::ResidueSelectionDistanceFilter::report_sm(), core::energy_methods::CovalentLabelingEnergy::residue_energy(), core::energy_methods::CovalentLabelingFAEnergy::residue_energy(), core::energy_methods::HRF_MSLabelingEnergy::residue_energy(), core::energy_methods::HRFDynamicsEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::interface_::DDPscore::residue_pair_energy(), core::energy_methods::PointWaterEnergy::residue_pair_energy(), core::energy_methods::ArgCationPiEnergy::residue_pair_energy(), protocols::legacy_sewing::result_to_models(), core::energy_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::select_density_points(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D1D2(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D2D3(), core::conformation::membrane::membrane_geometry::DoubleVesicle::set_distance(), core::select::residue_selector::NeighborhoodResidueSelector::set_distance(), core::scoring::nmr::NMRGridSearch::set_distance_center_to_atom1(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::set_interface_distance(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_interface_distance(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::energy_methods::RNP_LowResEnergy::setup_for_scoring(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), core::io::mmtf::sfrs_to_sd(), 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::ligand_docking::TransformEnsemble::translate_ligand(), protocols::chemically_conjugated_docking::ubq_ras_distance(), protocols::mpi_refinement::MultiObjective::update_library_seeds(), protocols::star::update_sequence_separation(), 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().

◆ distance() [2/3]

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

root squared devitation of two RTs

◆ distance() [3/3]

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

root squared deviation between two stubs

References core::pose::motif::a(), and protocols::match::upstream::b.

◆ find_stub_transform()

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 protocols::match::upstream::b, 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().

◆ get_foldtree_which_partitions()

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

◆ get_residues_from_movemap_bb_any_torsion()

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().

◆ get_residues_from_movemap_bb_or_chi()

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(), core::kinematics::MoveMap::get_chi(), and protocols::hybridization::on.

◆ get_residues_from_movemap_with_id()

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().

◆ jump_distance()

void core::kinematics::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)

References core::pose::motif::a(), protocols::comparative_modeling::features::A, core::chemical::element::B, and protocols::match::upstream::b.

◆ jump_which_partitions()

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(), and protocols::nmr::pcs::PCSLigandTransformMover::move_ligand_close_to_surface().

◆ linearize_fold_tree()

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().

◆ operator!=() [1/2]

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

◆ operator!=() [2/2]

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

◆ operator*()

std::string core::kinematics::operator* ( std::string const &  s,
size_t  n 
)

◆ operator<()

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

◆ operator<<() [1/6]

std::ostream& core::kinematics::operator<< ( std::ostream &  os,
const Edge e 
)

◆ operator<<() [2/6]

std::ostream& core::kinematics::operator<< ( std::ostream &  os,
const Jump jump 
)

◆ operator<<() [3/6]

std::ostream& core::kinematics::operator<< ( std::ostream &  os,
const RT rt 
)

◆ operator<<() [4/6]

std::ostream& core::kinematics::operator<< ( std::ostream &  os,
FoldTree const &  t 
)

Foldtree output to stream

◆ operator<<() [5/6]

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

output operator, 3x3 matrix followed by an xyzVector

References core::pose::motif::a().

◆ operator<<() [6/6]

std::ostream& core::kinematics::operator<< ( std::ostream &  out,
MoveMap const &  mm 
)
inline

◆ operator==() [1/2]

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

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

◆ operator==() [2/2]

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

◆ operator>>() [1/4]

std::istream& core::kinematics::operator>> ( std::istream &  is,
Edge e 
)

◆ operator>>() [2/4]

std::istream& core::kinematics::operator>> ( std::istream &  is,
FoldTree t 
)

Foldtree input from stream

◆ operator>>() [3/4]

std::istream& core::kinematics::operator>> ( std::istream &  is,
Jump jump 
)

◆ operator>>() [4/4]

std::istream& core::kinematics::operator>> ( std::istream &  is,
RT rt 
)

◆ pad_dash()

std::string core::kinematics::pad_dash ( Size  npad,
std::string  s 
)

◆ pad_dash_left()

std::string core::kinematics::pad_dash_left ( Size  npad,
std::string  s 
)

◆ pad_dash_right()

std::string core::kinematics::pad_dash_right ( Size  npad,
std::string  s 
)

◆ pick_loopy_cutpoint()

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().

◆ remodel_fold_tree_to_account_for_insertion()

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.

◆ replace_substr()

void core::kinematics::replace_substr ( std::string &  str,
const std::string &  from,
const std::string &  to 
)

◆ residues_downstream_of_jump()

utility::vector1< core::Size > core::kinematics::residues_downstream_of_jump ( FoldTree const &  fold_tree,
core::Size  jump_id 
)

◆ residues_upstream_of_jump()

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().

◆ simple_visualize_fold_tree()

void core::kinematics::simple_visualize_fold_tree ( FoldTree const &  fold_tree,
std::ostream &  out 
)

◆ simple_visualize_fold_tree_and_movemap()

void core::kinematics::simple_visualize_fold_tree_and_movemap ( FoldTree const &  fold_tree,
MoveMap const &  mm,
std::ostream &  out 
)

◆ simple_visualize_fold_tree_and_movemap_bb_chi()

void core::kinematics::simple_visualize_fold_tree_and_movemap_bb_chi ( FoldTree const &  fold_tree,
MoveMap const &  mm,
std::ostream &  out 
)

◆ tr() [1/2]

static basic::Tracer core::kinematics::tr ( "core.kinematics"  )
static

◆ TR() [1/2]

static basic::Tracer core::kinematics::TR ( "core.kinematics.AtomTree"  )
static

◆ tr() [2/2]

static basic::Tracer core::kinematics::tr ( "core.kinematics.ShortestPathInFoldTree"  ,
basic::t_info   
)
static

◆ TR() [2/2]

static basic::Tracer core::kinematics::TR ( "core.kinematics.util"  )
static

◆ visualize_fold_tree() [1/4]

std::string core::kinematics::visualize_fold_tree ( FoldTree const &  ft)

sheffler

References visualize_fold_tree().

◆ visualize_fold_tree() [2/4]

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

References visualize_fold_tree().

◆ visualize_fold_tree() [3/4]

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

References visualize_fold_tree().

◆ visualize_fold_tree() [4/4]

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 
)

◆ ZERO()

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

Variable Documentation

◆ default_stub

Stub core::kinematics::default_stub ( Stub::Matrix::identity()  ,
Stub::Vector(0.0)   
)

◆ dir_jump

int const core::kinematics::dir_jump
extern