core::kinematics Namespace Reference

Namespaces
	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...
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< Size >	ResidueIndexList
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...
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...
Stub	default_stub (Stub::Matrix::identity(), Stub::Vector(0.0))
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::Size >	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. More...
utility::vector1< core::Size >	residues_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::Size >	get_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::Size >	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. More...
utility::vector1< core::Size >	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. 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< AtomWithDOFChange > core::kinematics::AtomDOFChangeSet

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

typedef id::AtomID_Map< tree::AtomOP > core::kinematics::AtomPointer2D

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::pointer::shared_ptr< ResidueCoordinateChangeList > core::kinematics::ResidueCoordinateChangeListOP

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::weak_ptr< ShortestPathInFoldTree > core::kinematics::ShortestPathInFoldTreeAP

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().

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

inline

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

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

(

0

)

core::Real 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::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(), 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(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), 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::ArgCationPiEnergy::eval_residue_pair_derivatives(), 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(), core::io::mmtf::make_atom_information(), 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::SaltBridgeCalculator::recompute(), protocols::pose_metric_calculators::CatPiCalculator::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(), core::scoring::methods::CovalentLabelingFAEnergy::residue_energy(), core::scoring::methods::CovalentLabelingEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::methods::ArgCationPiEnergy::residue_pair_energy(), 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(), 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::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::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::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(), and protocols::nmr::pcs::PCSLigandTransformMover::move_ligand_close_to_surface().

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

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
	)

compare the difference of two jumps in term of the translation (dist) and rotational angle(theta)

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

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().

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
	)

References protocols::match::upstream::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,
		const Edge &	e
	)

References core::kinematics::Edge::CHEMICAL, core::kinematics::Edge::has_atom_info(), core::kinematics::Edge::is_jump(), core::kinematics::Edge::keep_stub_in_residue(), 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 RT &	rt
	)

References core::kinematics::RT::ortho_check(), core::kinematics::RT::rotation, and core::kinematics::RT::translation.

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

References core::kinematics::Jump::get_invert_downstream(), core::kinematics::Jump::get_invert_upstream(), core::kinematics::Jump::nonzero_deltas(), core::kinematics::Jump::rb_center, core::kinematics::Jump::rb_delta, and core::kinematics::Jump::rt_.

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

inline

References core::conformation::membrane::out, and core::kinematics::MoveMap::show().

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
	)

References core::kinematics::Edge::bKeepStubInResidue_, core::kinematics::Edge::CHEMICAL, core::kinematics::Edge::is_jump(), core::kinematics::Edge::label(), core::kinematics::Edge::label_, core::kinematics::Edge::start_, core::kinematics::Edge::start_atom_, core::kinematics::Edge::stop_, core::kinematics::Edge::stop_atom_, and tr().

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

References core::kinematics::RT::ortho_check(), core::kinematics::RT::rotation, and core::kinematics::RT::translation.

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

References core::kinematics::Jump::rb_center, core::kinematics::Jump::rb_delta, core::kinematics::Jump::rt_, and ZERO().

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

Foldtree input from stream

References core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::edge_list_, core::kinematics::FoldTree::new_topology, core::kinematics::FoldTree::reorder(), protocols::hybridization::t, and TR().

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

Referenced by core::kinematics::Node::str().

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

Referenced by core::kinematics::Node::str().

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

Referenced by core::kinematics::Node::str().

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
	)

Referenced by core::kinematics::Node::str().

utility::vector1< core::Size > core::kinematics::residues_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.

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

Referenced by protocols::ligand_docking::get_ligand_grid_scores(), and protocols::analysis::InterfaceAnalyzerMover::make_separated_pose().

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
	)

prints something like this ***1***C***1*********2***C********3****C****2********3*****

References core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

Referenced by protocols::abinitio::KinematicTaskControl::apply(), protocols::jumping::close_chainbreaks(), protocols::abinitio::DoubleLayerKinematicAbinitio::inner_loop(), protocols::abinitio::KinematicTaskControl::inner_loop(), protocols::abinitio::AbrelaxApplication::setup_fold(), and protocols::fold_from_loops::movers::DisplayPoseLabelsMover::simple_visualize_fold_tree().

void core::kinematics::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************************************

References core::kinematics::MoveMap::get_bb(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

Referenced by protocols::floppy_tail::FloppyTailMover::apply(), protocols::jumping::close_chainbreaks(), protocols::topology_broker::FragmentClaimer::initialize_dofs(), protocols::abinitio::DoubleLayerKinematicAbinitio::inner_loop(), and protocols::abinitio::KinematicTaskControl::inner_loop().

void core::kinematics::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************************************

References core::kinematics::MoveMap::get_bb(), core::kinematics::MoveMap::get_chi(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

Referenced by protocols::relax::FastRelax::apply(), and protocols::relax::FastRelax::batch_apply().

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

static

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

static

Referenced by core::kinematics::ShortestPathInFoldTree::build_jumpres_distmap(), core::kinematics::ResidueCoordinateChangeList::mark_residue_moved(), and operator>>().

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

static

Referenced by core::kinematics::AtomTree::bond_angle(), core::kinematics::AtomTree::bond_length(), get_foldtree_which_partitions(), core::kinematics::AtomTree::get_frag_local_stub(), core::kinematics::jacobian::ModuleType1::get_orthogonal_wrenches_from_twists(), core::kinematics::AtomTree::insert_fragment(), pick_loopy_cutpoint(), core::kinematics::AtomTree::promote_sameresidue_nonjump_child(), protocols::wum::SilentStructStore::read_from_cmd_line(), protocols::wum::SilentStructStore::serialize(), core::kinematics::AtomTree::set_torsion_angle(), core::kinematics::AtomTree::torsion_angle(), core::kinematics::AtomTree::torsion_angle_dof_id(), and core::kinematics::jacobian::ModuleType1::update_jacobian_matrices().

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
	)

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::TreeVizBuilder::expand_node_labels_partial_by_contig(), core::kinematics::FoldTree::get_chemical_edges(), core::kinematics::TreeVizBuilder::get_ft_node_bounds(), core::kinematics::TreeVizBuilder::get_jump_num_to_contig_of_resi(), core::kinematics::TreeVizBuilder::get_res_nodenames(), core::kinematics::TreeVizBuilder::is_single(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::environment::EnvClaimBroker::broker_fold_tree(), core::conformation::symmetry::setup_symmetric_conformation(), core::conformation::symmetry::show_foldtree(), and visualize_fold_tree().

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

(

)

Referenced by core::kinematics::Jump::fold_in_rb_deltas(), core::kinematics::Jump::from_bond_cst(), core::kinematics::Jump::from_stubs(), core::kinematics::Jump::identity_transform(), operator>>(), and core::kinematics::Jump::reset().

Variable Documentation

Stub core::kinematics::default_stub

Global default stub.

Referenced by core::kinematics::tree::Atom_::get_input_stub(), protocols::hotspot_hashing::SICPatternAtTransform::Searchpoints(), protocols::hotspot_hashing::ComposeSearchPatterns::Searchpoints(), and core::kinematics::AtomTree::update_internal_coords().

int const core::kinematics::dir_jump

Referenced by core::conformation::build_residue_tree(), core::conformation::get_anchor_and_root_atoms(), core::conformation::get_anchor_atomno(), core::conformation::get_root_atomno(), core::conformation::get_root_residue_root_atomno(), core::conformation::Conformation::jump_atom_id(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::modify_impl(), and core::pack::scmin::ResidueAtomTreeCollection::ResidueAtomTreeCollection().