core::kinematics Namespace Reference

See AtomTree overview and FoldTree overview for details. More...

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 treelike 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::AtomOP >	AtomPointer2D
typedef utility::vector1 < tree::AtomOP >	AtomPointer1D
typedef utility::pointer::access_ptr < AtomTree >	AtomTreeAP
typedef utility::pointer::access_ptr < AtomTree const >	AtomTreeCAP
typedef utility::pointer::owning_ptr < AtomTree >	AtomTreeOP
typedef utility::pointer::owning_ptr < AtomTree const >	AtomTreeCOP
typedef utility::vector1 < AtomWithDOFChange >	AtomDOFChangeSet
typedef ObjexxFCL::FArray1D_int	DomainMap
typedef utility::pointer::access_ptr < Edge >	EdgeAP
typedef utility::pointer::owning_ptr < Edge >	EdgeOP
typedef utility::pointer::access_ptr < FoldTree >	FoldTreeAP
typedef utility::pointer::access_ptr < FoldTree const >	FoldTreeCAP
typedef utility::pointer::owning_ptr < FoldTree >	FoldTreeOP
typedef utility::pointer::owning_ptr < FoldTree const >	FoldTreeCOP
typedef utility::pointer::owning_ptr < MinimizerMapBase >	MinimizerMapBaseOP
typedef utility::pointer::owning_ptr < MinimizerMapBase const >	MinimizerMapBaseCOP
typedef utility::pointer::owning_ptr < MoveMap >	MoveMapOP
typedef utility::pointer::owning_ptr < MoveMap const >	MoveMapCOP
typedef utility::pointer::owning_ptr < ResidueCoordinateChangeList >	ResidueCoordinateChangeListOP
typedef utility::vector1< Size >	ResidueIndexList
typedef utility::vector1< Size > ::const_iterator	ResidueListIterator
typedef utility::pointer::access_ptr < RT >	RTAP
typedef utility::pointer::owning_ptr < RT >	RTOP
typedef utility::pointer::access_ptr < ShortestPathInFoldTree >	ShortestPathInFoldTreeAP
typedef utility::pointer::owning_ptr < ShortestPathInFoldTree >	ShortestPathInFoldTreeOP
typedef utility::pointer::owning_ptr < ShortestPathInFoldTree const >	ShortestPathInFoldTreeCOP
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)
static numeric::random::RandomGenerator	jump_RG (62454)
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 followd by an xyzVector More...
Stub	default_stub (Stub::Matrix::identity(), Stub::Vector(0.0))
	Globals. More...
double	distance (Stub const &a, Stub const &b)
	root sqared deviation between two stubs More...
static numeric::random::RandomGenerator	RG (62457)
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...
tree::AtomOP	setup_cloned_atom (tree::AtomCOP, utility::vector1< id::AtomID > const &)
	helper function for setup_backrub_atom_tree More...
tree::AtomOP	setup_backrub_atom_tree (utility::vector1< AtomID >, AtomID const &, AtomPointer2D const &, utility::vector1< std::pair< Size, Size > > const &, Size const )
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...
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
static const utility::vector1 < Real >	ZERO (6, 0.0)
Stub	default_stub
	Globals. More...

Detailed Description

See AtomTree overview and FoldTree overview for details.

Typedef Documentation

typedef utility::vector1< AtomWithDOFChange > core::kinematics::AtomDOFChangeSet

Definition at line 25 of file AtomWithDOFChange.fwd.hh.

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

Definition at line 30 of file AtomPointer.fwd.hh.

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

Definition at line 29 of file AtomPointer.fwd.hh.

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

Definition at line 27 of file AtomTree.fwd.hh.

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

Definition at line 31 of file AtomTree.fwd.hh.

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

Definition at line 34 of file AtomTree.fwd.hh.

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

Definition at line 33 of file AtomTree.fwd.hh.

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

Definition at line 27 of file DomainMap.fwd.hh.

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

Definition at line 29 of file Edge.fwd.hh.

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

Definition at line 34 of file Edge.fwd.hh.

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

Definition at line 29 of file FoldTree.fwd.hh.

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

Definition at line 33 of file FoldTree.fwd.hh.

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

Definition at line 35 of file FoldTree.fwd.hh.

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

Definition at line 34 of file FoldTree.fwd.hh.

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

Definition at line 49 of file util.hh.

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

Definition at line 30 of file MinimizerMapBase.fwd.hh.

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

Definition at line 27 of file MinimizerMapBase.fwd.hh.

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

Definition at line 27 of file MoveMap.fwd.hh.

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

Definition at line 25 of file MoveMap.fwd.hh.

typedef utility::pointer::owning_ptr< ResidueCoordinateChangeList > core::kinematics::ResidueCoordinateChangeListOP

Definition at line 32 of file ResidueCoordinateChangeList.fwd.hh.

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

Definition at line 36 of file ResidueCoordinateChangeList.fwd.hh.

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

Definition at line 37 of file ResidueCoordinateChangeList.fwd.hh.

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

Definition at line 29 of file RT.fwd.hh.

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

Definition at line 34 of file RT.fwd.hh.

typedef utility::pointer::access_ptr< ShortestPathInFoldTree > core::kinematics::ShortestPathInFoldTreeAP

Definition at line 29 of file ShortestPathInFoldTree.fwd.hh.

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

Definition at line 35 of file ShortestPathInFoldTree.fwd.hh.

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

Definition at line 34 of file ShortestPathInFoldTree.fwd.hh.

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 reside 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

Definition at line 71 of file util.cc.

Referenced by core::coarse::Translator::add_all_remaining(), core::coarse::Translator::add_atom(), core::coarse::Translator::add_remaining_sidechain(), core::conformation::build_residue_tree(), and core::coarse::Translator::Translator().

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

Globals.

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

int const core::kinematics::dir_jump

(

0

)

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

inline

root sqared deviation between two stubs

Definition at line 184 of file Stub.hh.

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

Definition at line 226 of file RT.hh.

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.

Definition at line 456 of file Jump.cc.

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

Referenced by protocols::seeded_abinitio::add_dist_constraints(), protocols::simple_filters::ResidueDistanceFilter::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::simple_filters::PredictedBurialEvaluator::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::toolbox::task_operations::DesignAroundOperation::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), core::chemical::ResidueType::assign_neighbor_atom(), core::chemical::orbitals::AssignOrbitals::assign_orbitals(), core::scoring::methods::atoms_interact(), protocols::hotspot_hashing::HotspotStubSet::autofill(), core::pack::rotamer_set::build_optimal_water_O_on_donor(), core::scoring::methods::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::build_optimal_water_Os_on_acceptor(), core::chemical::ResidueType::calculate_icoor(), core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::qsar::scoring_grid::ChargeGrid::charge_charge_electrostatic(), protocols::loops::loop_closure::ccd::check_overlap_pos(), protocols::nonlocal::chunks_by_CA_CA_distance(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::enzdes::LigBurialFilter::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::medal::cutpoint_probabilities(), protocols::relax::derive_sc_sc_restraints(), core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node(), 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(), 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(), protocols::hotspot_hashing::HotspotStubSet::fill(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), protocols::seeded_abinitio::find_nearest_residue(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), core::pack::interaction_graph::RotamerDots::get_atom_atom_coverage(), protocols::seeded_abinitio::get_closest_residue_pair(), protocols::swa::rna::get_max_centroid_to_atom_distance(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::hotspot_hashing::HotspotStubSet::get_nearest_stub(), protocols::loops::loop_closure::ccd::get_overlap_pos(), hbonded(), protocols::nonlocal::SheetTranslate::initialize(), MinimizeInterface(), protocols::sic_dock::neighbor_count(), core::scoring::nv::NVscore::neighbor_weight(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), core::scoring::disulfides::FullatomDisulfidePotential::print_score_functions(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator::recompute(), protocols::toolbox::pose_metric_calculators::CatPiCalculator::recompute(), protocols::toolbox::pose_metric_calculators::PiPiCalculator::recompute(), protocols::simple_filters::ResidueDistanceFilter::report(), protocols::features::SmotifFeatures::report_features(), protocols::simple_filters::ResidueDistanceFilter::report_sm(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::scoring::interface::DDPscore::residue_pair_energy(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), core::pack::RTMin::rtmin(), core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D1D2(), protocols::toolbox::match_enzdes_util::ExternalGeomSampler::set_dis_D2D3(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), 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
	)

void AtomTree::setup_backrub_segment( utility::vector1< AtomID > const & mainchain, AtomID const & downstream_id, // mainchain child of last atom in mainchain vector utility::vector1< std::pair< Size, Size > > const & edges, Size const first_new_pseudo_residue ) {

this assumes that the segment of mainchain has exactly one connection in and exactly one connection out, (to the downstream_id atom) and all of the atoms to be replaced are bonded atoms

for ( Size i=1; i<= mainchain.size(); ++i ) { assert( !( atom_pointer_[ mainchain[i] ]->is_jump() ) ); } AtomID const last_mainchain_id( mainchain[ mainchain.size() ] ); assert( atom_pointer_[ downstream_id ]->parent()->id() == last_mainchain_id );

operation is done "by xyz" leaving the internal coords out of date update_xyz_coords();

AtomOP subtree_root ( setup_backrub_atom_tree( mainchain, downstream_id, atom_pointer_, edges, first_new_pseudo_residue ) ); assert( subtree_root->id() == mainchain[1] );

AtomOP old_root( atom_pointer_[ mainchain[1] ] ); AtomOP anchor( old_root->parent() );

AtomOP downstream_atom( atom_pointer_[ downstream_id ] ); downstream_atom->parent()->delete_atom( downstream_atom ); // delete the old outgoing connection

update atom_pointer_ subtree_root->update_atom_pointer( atom_pointer_, true );

insert the new tree anchor->replace_atom( old_root, subtree_root ); // incoming connection atom_pointer_[ last_mainchain_id ]->insert_atom( downstream_atom ); // outoing connection

erase the old tree this call will erase and delete all of old_root's children old_root->erase(); free the last bit of old data delete old_root;

internal_coords_need_updating_ = true;

}

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

Definition at line 298 of file AtomTree.cc.

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

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

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)

Definition at line 473 of file Jump.cc.

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

static numeric::random::RandomGenerator core::kinematics::jump_RG ( 62454  )

static

Referenced by core::kinematics::Jump::gaussian_move(), core::kinematics::Jump::gaussian_move_single_rb(), and core::kinematics::Jump::random_trans().

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

Definition at line 450 of file util.cc.

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::begin(), core::sequence::end, and core::kinematics::FoldTree::end().

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

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

Definition at line 76 of file FoldTree.cc.

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

Definition at line 166 of file Edge.cc.

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
	)

Definition at line 477 of file util.cc.

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

Definition at line 139 of file Edge.cc.

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 followd by an xyzVector

Definition at line 34 of file Stub.cc.

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

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

Definition at line 51 of file Edge.cc.

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,
		const RT &	rt
	)

Definition at line 108 of file RT.cc.

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
	)

Definition at line 424 of file Jump.cc.

References 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

Definition at line 598 of file MoveMap.hh.

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

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

Foldtree output to stream

Definition at line 2338 of file FoldTree.cc.

References core::kinematics::FoldTree::begin(), and core::kinematics::FoldTree::end().

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

Checks that edges are in the same order and are equal

Definition at line 61 of file FoldTree.cc.

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

Definition at line 156 of file Edge.cc.

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
	)

Definition at line 77 of file Edge.cc.

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
	)

Definition at line 131 of file RT.cc.

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
	)

Definition at line 409 of file Jump.cc.

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

Definition at line 2357 of file FoldTree.cc.

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

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

Definition at line 484 of file util.cc.

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

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

Definition at line 491 of file util.cc.

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

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

Definition at line 497 of file util.cc.

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.

Definition at line 111 of file util.cc.

References 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

Definition at line 750 of file util.cc.

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

Referenced by protocols::grafting::insert_pose_into_pose().

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

Definition at line 469 of file util.cc.

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

static numeric::random::RandomGenerator core::kinematics::RG ( 62457  )

static

Referenced by protocols::wum::SilentStructStore::get_struct_random(), and pick_loopy_cutpoint().

tree::AtomOP core::kinematics::setup_backrub_atom_tree	(	utility::vector1< AtomID >	,
		AtomID const &	,
		AtomPointer2D const &	,
		utility::vector1< std::pair< Size, Size > > const &	,
		Size	const
	)

in principal, this should be the inverse of the build_tree function at the beginning

Definition at line 180 of file util.cc.

tree::AtomOP core::kinematics::setup_cloned_atom	(	tree::AtomCOP	,
		utility::vector1< id::AtomID > const &
	)

helper function for setup_backrub_atom_tree

Definition at line 140 of file util.cc.

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*****

Definition at line 339 of file util.cc.

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(), and protocols::abinitio::AbrelaxApplication::setup_fold().

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************************************

Definition at line 365 of file util.cc.

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************************************

Definition at line 404 of file util.cc.

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"  )

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.util"  )

static

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

static

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

static

Referenced by core::kinematics::AtomTree::bond_angle(), core::kinematics::AtomTree::bond_length(), core::kinematics::AtomTree::get_frag_local_stub(), 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::torsion_angle(), and core::kinematics::AtomTree::torsion_angle_dof_id().

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
	)

Definition at line 643 of file util.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::TreeVizBuilder::expand_node_labels_partial_by_contig(), 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 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

Definition at line 690 of file util.cc.

References visualize_fold_tree().

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

Definition at line 698 of file util.cc.

References visualize_fold_tree().

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

Definition at line 705 of file util.cc.

References visualize_fold_tree().

Variable Documentation

Stub core::kinematics::default_stub

Globals.

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(), and protocols::forge::build::SegmentInsert::modify_impl().

const utility::vector1<Real> core::kinematics::ZERO(6, 0.0)

static

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().