protocols::jumping Namespace Reference

Classes
class	BaseDisulfPairingLibrary
class	BaseJumpSetup
	virtual base class: can create a set of jumps and cuts More...
class	BasePairingLibrary
	returns relative orientation of chains at res1 and res2 this is the inner product of the respective N-C vectors. More...
class	DisulfPairing
class	DisulfPairingLibrary
class	DisulfTemplate
class	Interval
	two numbers, i.e., jump start end residue, or cut-regions... More...
class	JumpSample
class	JumpSelector
class	JumpSetup
class	JumpsFromAllPairings
class	MembraneJump
class	PairingLibrary
class	PairingTemplate
class	RandomSheetBuilder
	select jumps to build a given topology More...
class	ResiduePairJump
class	ResiduePairJumpSetup
class	ResiduePairJumpSingle
	a single residue component of a ResiduePairJump class More...
class	SameStrand
	tiny helper class that knows the relative fractions of secondary structure L,H,E so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses, More...
class	SheetBuilder
	select jumps to build a given topology More...
class	SpecificGeometryLibrary
class	StandardDisulfPairingLibrary
	The StandardDisulfPairingsLibrary initializes itself in its constructor from the sampling/disulfide_jump_database_wip.dat file in the database. Users should not in any circumstance invoke any of its non-const methods that are defined in the subclass. This class ought to be reworked to ensure that it is threadsafe. More...
class	StandardPairingLibrary
	This class is thread-unsafe, though, if perhaps none of its non-const functions were accessible, then it wouldn't be. More...

Typedefs
typedef utility::vector1 < DisulfPairing >	DisulfPairingsList
typedef utility::vector1 < DisulfPairing >	DisulfPairingList
typedef utility::vector1 < jumping::Interval >	JumpList
typedef utility::pointer::shared_ptr < BaseJumpSetup >	BaseJumpSetupOP
typedef utility::pointer::shared_ptr < BaseJumpSetup const >	BaseJumpSetupCOP
typedef utility::pointer::shared_ptr < JumpSetup >	JumpSetupOP
typedef utility::pointer::shared_ptr < JumpSetup const >	JumpSetupCOP
typedef utility::pointer::shared_ptr < JumpSelector >	JumpSelectorOP
typedef utility::pointer::shared_ptr < JumpSelector const >	JumpSelectorCOP
typedef utility::pointer::shared_ptr < MembraneJump >	MembraneJumpOP
typedef utility::pointer::owning_ptr < BasePairingLibrary >	BasePairingLibraryOP
typedef utility::pointer::owning_ptr < BasePairingLibrary const >	BasePairingLibraryCOP
typedef utility::pointer::owning_ptr < PairingLibrary >	PairingLibraryOP
typedef utility::pointer::owning_ptr < PairingLibrary const >	PairingLibraryCOP
typedef utility::pointer::owning_ptr < StandardPairingLibrary >	StandardPairingLibraryOP
typedef utility::pointer::owning_ptr < StandardPairingLibrary const >	StandardPairingLibraryCOP
typedef utility::pointer::shared_ptr < ResiduePairJumpSingle >	ResiduePairJumpSingleOP
typedef utility::pointer::shared_ptr < ResiduePairJumpSingle const >	ResiduePairJumpSingleCOP
typedef utility::pointer::shared_ptr < ResiduePairJump >	ResiduePairJumpOP
typedef utility::pointer::shared_ptr < ResiduePairJump const >	ResiduePairJumpCOP
typedef utility::pointer::shared_ptr < ResiduePairJumpSetupSingle >	ResiduePairJumpSetupSingleOP
typedef utility::pointer::shared_ptr < ResiduePairJumpSetupSingle const >	ResiduePairJumpSetupSingleCOP
typedef utility::pointer::shared_ptr < ResiduePairJumpSetup >	ResiduePairJumpSetupOP
typedef utility::pointer::shared_ptr < ResiduePairJumpSetup const >	ResiduePairJumpSetupCOP
typedef utility::pointer::shared_ptr < SameStrand >	SameStrandOP
typedef utility::pointer::shared_ptr < SameStrand const >	SameStrandCOP
typedef utility::vector1 < PointPosition >	PointList

Enumerations
enum	cstType {   disAB = 1, angleA, angleB, dihedralA,   dihedralAB, dihedralB, num_cstType = dihedralB }
enum	dofType { rot1 = 1, rot2, cstJump, num_dofType = cstJump }

Functions
void	dis_get_coordinate_system (numeric::xyzMatrix_double const &p, numeric::xyzMatrix_double &m)
void	dis_get_ncac (FArray2A_float pos, numeric::xyzMatrix_double &p)
numeric::xyzMatrix_double	dis_get_ncac (FArray2A_float pos)
RT	dis_RT_from_epos (FArray2A_float Epos1, FArray2A_float Epos2)
void	read_pairing_list (std::string disulf_pairing_file, DisulfPairingsList &disulf_pairings)
void	read_disulf_pairing_list (std::istream &is, DisulfPairingsList &disulf_pairings)
	add pairings in pairing_file to list "pairings" More...
std::ostream &	operator<< (std::ostream &out, DisulfPairing const &)
	list of pairings More...
std::ostream &	operator<< (std::ostream &out, DisulfPairingsList const &p)
static thread_local basic::Tracer	tr ("protocols.jumping")
std::ostream &	operator<< (std::ostream &os, JumpSample const &t)
	output operator More...
static thread_local basic::Tracer	tr ("protocols.jumping")
void	dump_tags_ (FArray1D_int const &tags, Size nres, std::ostream &out)
void	fill_tags_ (FArray1D_int &tags, Size fill_pos, int tag, Size nres)
static thread_local basic::Tracer	tr ("protocols.jumping.MembraneJump")
void	get_coordinate_system (numeric::xyzMatrix_double const &p, numeric::xyzMatrix_double &m)
void	get_ncac (FArray2A_float pos, numeric::xyzMatrix_double &p)
numeric::xyzMatrix_double	get_ncac (FArray2A_float pos)
RT	RT_from_epos (FArray2A_float Epos1, FArray2A_float Epos2)
static thread_local basic::Tracer	tr ("protocols.jumping")
std::ostream &	operator<< (std::ostream &os, SameStrand const &t)
	output operator More...
static thread_local basic::Tracer	tr ("protocols.jumping")
void	close_chainbreaks (loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol, Pose &open_pose, protocols::checkpoint::CheckPointer &checkpoint, const std::string &decoy_tag, core::kinematics::FoldTree const &final_fold_tree_in)
bool	remove_cut (Size cutpoint, Pose &pose, FoldTree const &final_fold_tree)
bool	remove_cut (Size cutpoint, FoldTree &new_fold_tree, FoldTree const &final_fold_tree)
void	safe_secstruct (pose::Pose &pose)
core::fragment::JumpingFrameOP	generate_empty_jump_frame (Size startpos, Size endpos, Size length)
core::fragment::JumpingFrameOP	generate_jump_frame (Size startpos, Size endpos, bool bWithTorsion)
void	get_CA_vectors (PointList const &ca1, PointList const &ca2, Vector &a, Vector &b, Vector &c)
void	get_pairing_geometry (pose::Pose const &pose, Size const res1, Size const res2, Real &orientation, Real &pleating1, Real &pleating2)
void	get_pleating (pose::Pose const &pose, Size const pos1, Size const pos2, Size &orientation, Size &pleating)
void	assign_ss_dssp (core::pose::Pose &pose)
	Assign secondary structure using DSSP. More...
bool	remove_cut (core::Size cutpoint, core::pose::Pose &pose, core::kinematics::FoldTree const &final_fold_tree=core::kinematics::FoldTree())
bool	remove_cut (core::Size cutpoint, core::kinematics::FoldTree &fold_tree, core::kinematics::FoldTree const &final_fold_tree=core::kinematics::FoldTree())

Typedef Documentation

typedef utility::pointer::shared_ptr< BaseJumpSetup const > protocols::jumping::BaseJumpSetupCOP

typedef utility::pointer::shared_ptr< BaseJumpSetup > protocols::jumping::BaseJumpSetupOP

typedef utility::pointer::owning_ptr< BasePairingLibrary const > protocols::jumping::BasePairingLibraryCOP

typedef utility::pointer::owning_ptr< BasePairingLibrary > protocols::jumping::BasePairingLibraryOP

typedef utility::vector1<DisulfPairing> protocols::jumping::DisulfPairingList

typedef utility::vector1<DisulfPairing> protocols::jumping::DisulfPairingsList

typedef utility::vector1< jumping::Interval > protocols::jumping::JumpList

typedef utility::pointer::shared_ptr< JumpSelector const > protocols::jumping::JumpSelectorCOP

typedef utility::pointer::shared_ptr< JumpSelector > protocols::jumping::JumpSelectorOP

typedef utility::pointer::shared_ptr< JumpSetup const > protocols::jumping::JumpSetupCOP

typedef utility::pointer::shared_ptr< JumpSetup > protocols::jumping::JumpSetupOP

typedef utility::pointer::shared_ptr< MembraneJump > protocols::jumping::MembraneJumpOP

typedef utility::pointer::owning_ptr< PairingLibrary const > protocols::jumping::PairingLibraryCOP

typedef utility::pointer::owning_ptr< PairingLibrary > protocols::jumping::PairingLibraryOP

typedef utility::vector1< PointPosition > protocols::jumping::PointList

some legacy code

typedef utility::pointer::shared_ptr< ResiduePairJump const > protocols::jumping::ResiduePairJumpCOP

typedef utility::pointer::shared_ptr< ResiduePairJump > protocols::jumping::ResiduePairJumpOP

typedef utility::pointer::shared_ptr< ResiduePairJumpSetup const > protocols::jumping::ResiduePairJumpSetupCOP

typedef utility::pointer::shared_ptr< ResiduePairJumpSetup > protocols::jumping::ResiduePairJumpSetupOP

typedef utility::pointer::shared_ptr< ResiduePairJumpSetupSingle const > protocols::jumping::ResiduePairJumpSetupSingleCOP

typedef utility::pointer::shared_ptr< ResiduePairJumpSetupSingle > protocols::jumping::ResiduePairJumpSetupSingleOP

typedef utility::pointer::shared_ptr< ResiduePairJumpSingle const > protocols::jumping::ResiduePairJumpSingleCOP

typedef utility::pointer::shared_ptr< ResiduePairJumpSingle > protocols::jumping::ResiduePairJumpSingleOP

typedef utility::pointer::shared_ptr< SameStrand const > protocols::jumping::SameStrandCOP

typedef utility::pointer::shared_ptr< SameStrand > protocols::jumping::SameStrandOP

typedef utility::pointer::owning_ptr< StandardPairingLibrary const > protocols::jumping::StandardPairingLibraryCOP

typedef utility::pointer::owning_ptr< StandardPairingLibrary > protocols::jumping::StandardPairingLibraryOP

Enumeration Type Documentation

enum protocols::jumping::cstType

Enumerator
disAB
angleA
angleB
dihedralA
dihedralAB
dihedralB
num_cstType

enum protocols::jumping::dofType

Enumerator
rot1
rot2
cstJump
num_dofType

Function Documentation

void protocols::jumping::assign_ss_dssp

(

core::pose::Pose &

pose

)

Assign secondary structure using DSSP.

References protocols::simple_filters::dssp(), and core::scoring::dssp::Dssp::insert_ss_into_pose().

void protocols::jumping::close_chainbreaks	(	loops::loop_closure::ccd::SlidingWindowLoopClosureOP	closure_protocol,
		Pose &	open_pose,
		protocols::checkpoint::CheckPointer &	checkpoint,
		const std::string &	decoy_tag,
		core::kinematics::FoldTree const &	final_fold_tree_in
	)

References protocols::checkpoint::CheckPointer::checkpoint(), core::kinematics::FoldTree::cutpoint(), core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get_bb(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::pose::symmetry::is_symmetric(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_cutpoint(), protocols::checkpoint::CheckPointer::recover_checkpoint(), remove_cut(), core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer(), runtime_assert, core::kinematics::FoldTree::simple_tree(), simple_visualize_fold_tree(), simple_visualize_fold_tree_and_movemap(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and tr().

Referenced by protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::abinitio::abscript::AbscriptLoopCloserCM::attempt_ccd(), protocols::abinitio::AbrelaxApplication::close_loops(), and protocols::loop_build::LoopMover_SlidingWindow::model_loop().

void protocols::jumping::dis_get_coordinate_system	(	numeric::xyzMatrix_double const &	p,
		numeric::xyzMatrix_double &	m
	)

References numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), cross(), and numeric::xyzVector< class >::normalize().

Referenced by dis_RT_from_epos().

void protocols::jumping::dis_get_ncac	(	FArray2A_float	pos,
		numeric::xyzMatrix_double &	p
	)

References c.

numeric::xyzMatrix_double protocols::jumping::dis_get_ncac

(

FArray2A_float

pos

)

References c.

Referenced by dis_RT_from_epos().

RT protocols::jumping::dis_RT_from_epos	(	FArray2A_float	Epos1,
		FArray2A_float	Epos2
	)

References dis_get_coordinate_system(), dis_get_ncac(), F, core::kinematics::RT::set_rotation(), core::kinematics::RT::set_translation(), and numeric::xyzMatrix< class >::transposed().

void protocols::jumping::dump_tags_	(	FArray1D_int const &	tags,
		Size	nres,
		std::ostream &	out
	)

Referenced by protocols::jumping::JumpSelector::create_jump_sample().

void protocols::jumping::fill_tags_	(	FArray1D_int &	tags,
		Size	fill_pos,
		int	tag,
		Size	nres
	)

References runtime_assert.

Referenced by protocols::jumping::JumpSelector::create_jump_sample().

core::fragment::JumpingFrameOP protocols::jumping::generate_empty_jump_frame	(	Size	startpos,
		Size	endpos,
		Size	length
	)

References frame(), and utility_exit_with_message.

Referenced by protocols::jumping::DisulfPairingLibrary::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::PairingLibrary::generate_jump_frags(), and generate_jump_frame().

core::fragment::JumpingFrameOP protocols::jumping::generate_jump_frame	(	Size	startpos,
		Size	endpos,
		bool	bWithTorsion
	)

References frame(), generate_empty_jump_frame(), protocols::loops::start, and protocols::loops::stop.

void protocols::jumping::get_CA_vectors	(	PointList const &	ca1,
		PointList const &	ca2,
		Vector &	a,
		Vector &	b,
		Vector &	c
	)

References numeric::xyzVector< class >::normalize().

Referenced by get_pairing_geometry().

void protocols::jumping::get_coordinate_system	(	numeric::xyzMatrix_double const &	p,
		numeric::xyzMatrix_double &	m
	)

References numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), cross(), and numeric::xyzVector< class >::normalize().

Referenced by RT_from_epos().

void protocols::jumping::get_ncac	(	FArray2A_float	pos,
		numeric::xyzMatrix_double &	p
	)

References c.

numeric::xyzMatrix_double protocols::jumping::get_ncac

(

FArray2A_float

pos

)

References c.

Referenced by RT_from_epos().

void protocols::jumping::get_pairing_geometry	(	pose::Pose const &	pose,
		Size const	res1,
		Size const	res2,
		Real &	orientation,
		Real &	pleating1,
		Real &	pleating2
	)

References cross(), dot_product(), get_CA_vectors(), numeric::xyzVector< class >::length(), core::pose::Pose::residue_type(), runtime_assert, core::pose::Pose::total_residue(), tr(), and core::pose::Pose::xyz().

Referenced by get_pleating().

void protocols::jumping::get_pleating	(	pose::Pose const &	pose,
		Size const	pos1,
		Size const	pos2,
		Size &	orientation,
		Size &	pleating
	)

References get_pairing_geometry(), and tr().

Referenced by protocols::jumping::JumpSample::steal_orientation_and_pleating().

std::ostream & protocols::jumping::operator<<	(	std::ostream &	out,
		DisulfPairing const &	p
	)

list of pairings

References protocols::jumping::DisulfPairing::pos1, protocols::jumping::DisulfPairing::pos2, protocols::jumping::DisulfPairing::seq_sep, and protocols::jumping::DisulfPairing::ss_type.

std::ostream& protocols::jumping::operator<< ( std::ostream &  os, SameStrand const &  t  )

inline

output operator

References protocols::jumping::SameStrand::show().

std::ostream & protocols::jumping::operator<<	(	std::ostream &	out,
		DisulfPairingsList const &	p
	)

std::ostream & protocols::jumping::operator<<	(	std::ostream &	os,
		JumpSample const &	t
	)

output operator

References protocols::jumping::JumpSample::cuts_, protocols::jumping::JumpSample::jumps_, and protocols::jumping::JumpSample::size().

void protocols::jumping::read_disulf_pairing_list	(	std::istream &	disulf_pairing_stream,
		DisulfPairingsList &	disulf_pairings
	)

add pairings in pairing_file to list "pairings"

References a(), protocols::match::upstream::b, c, and getline().

Referenced by read_pairing_list().

void protocols::jumping::read_pairing_list	(	std::string	disulf_pairing_file,
		DisulfPairingsList &	disulf_pairings
	)

References utility::io::izstream::close(), utility::exit(), read_disulf_pairing_list(), and tr().

Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::jumping::MembraneJump::init(), protocols::abinitio::Templates::read_pairings(), protocols::topology_broker::TemplateJumpClaimer::read_tag(), and protocols::abinitio::AbrelaxApplication::setup_jumps().

bool protocols::jumping::remove_cut	(	core::Size	cutpoint,
		core::pose::Pose &	pose,
		core::kinematics::FoldTree const &	final_fold_tree = core::kinematics::FoldTree()
	)

bool protocols::jumping::remove_cut	(	core::Size	cutpoint,
		core::kinematics::FoldTree &	fold_tree,
		core::kinematics::FoldTree const &	final_fold_tree = core::kinematics::FoldTree()
	)

bool protocols::jumping::remove_cut	(	Size	cutpoint,
		Pose &	pose,
		FoldTree const &	final_fold_tree
	)

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), and tr().

Referenced by close_chainbreaks().

bool protocols::jumping::remove_cut	(	Size	cutpoint,
		FoldTree &	new_fold_tree,
		FoldTree const &	final_fold_tree
	)

References runtime_assert, and tr().

RT protocols::jumping::RT_from_epos	(	FArray2A_float	Epos1,
		FArray2A_float	Epos2
	)

References F, get_coordinate_system(), get_ncac(), core::kinematics::RT::set_rotation(), core::kinematics::RT::set_translation(), and numeric::xyzMatrix< class >::transposed().

Referenced by protocols::jumping::PairingLibrary::read_from_file().

void protocols::jumping::safe_secstruct

(

pose::Pose &

pose

)

References core::pose::Pose::fold_tree(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), and core::pose::Pose::total_residue().

Referenced by protocols::abinitio::KinematicControl::prepare_pose_for_sampling().

static thread_local basic::Tracer protocols::jumping::tr ( "protocols.jumping.MembraneJump"  )

static

static thread_local basic::Tracer protocols::jumping::tr ( "protocols.jumping"  )

static

static thread_local basic::Tracer protocols::jumping::tr ( "protocols.jumping"  )

static

static thread_local basic::Tracer protocols::jumping::tr ( "protocols.jumping"  )

static

static thread_local basic::Tracer protocols::jumping::tr ( "protocols.jumping"  )

static

Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint(), protocols::jumping::SheetBuilder::builder_loop(), close_chainbreaks(), protocols::jumping::SheetBuilder::create_jump_sample(), protocols::jumping::JumpSelector::create_jump_sample(), protocols::jumping::RandomSheetBuilder::create_new_random_topol(), protocols::jumping::JumpSample::generate_jump_frags(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), protocols::jumping::JumpSample::generate_jump_frames(), protocols::jumping::JumpSample::generate_random_tree_from_jumps(), get_pairing_geometry(), get_pleating(), protocols::jumping::JumpSample::JumpSample(), protocols::jumping::ResiduePairJumpSetup::read_file(), protocols::jumping::JumpSetup::read_file(), protocols::jumping::JumpSelector::read_file(), remove_cut(), protocols::jumping::MembraneJump::setup_fold_tree(), protocols::jumping::JumpSample::steal_orientation_and_pleating(), and protocols::jumping::JumpSample::transfer_jumps().