protocols::jumping Namespace Reference

Classes
class	DisulfTemplate
class	BaseDisulfPairingLibrary
class	DisulfPairingLibrary
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	DisulfPairing
class	ChainbreakDistFunc
class	JumpSample
class	Interval
	two numbers, i.e., jump start end residue, or cut-regions... More...
class	BaseJumpSetup
	virtual base class: can create a set of jumps and cuts More...
class	JumpSetup
class	JumpsFromAllPairings
class	JumpSelector
class	MembraneJump
class	PairingTemplate
class	BasePairingLibrary
	returns relative orientation of chains at res1 and res2 this is the inner product of the respective N-C vectors. More...
class	PairingLibrary
class	SpecificGeometryLibrary
class	StandardPairingLibrary
	This class is thread-unsafe, though, if perhaps none of its non-const functions were accessible, then it wouldn't be. More...
class	RandomSheetBuilder
	select jumps to build a given topology @detail this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++ More...
class	ResiduePairJumpSingle
	a single residue component of a ResiduePairJump class More...
class	ResiduePairJump
class	ResiduePairJumpSetup
class	SameStrand
	tiny helper class that knows the relative fractions of secondary structure L,H,E @detail 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 @detail this class encapsulates the functionality of choose_random_pairings in jumping_pairings.cc of Rosetta++ 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::shared_ptr< BasePairingLibrary >	BasePairingLibraryOP
typedef utility::pointer::shared_ptr< BasePairingLibrary const >	BasePairingLibraryCOP
typedef utility::pointer::shared_ptr< PairingLibrary >	PairingLibraryOP
typedef utility::pointer::shared_ptr< PairingLibrary const >	PairingLibraryCOP
typedef utility::pointer::shared_ptr< StandardPairingLibrary >	StandardPairingLibraryOP
typedef utility::pointer::shared_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
using	PointList = utility::vector1< PointPosition >

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 basic::Tracer	tr ("protocols.jumping")
std::ostream &	operator<< (std::ostream &os, JumpSample const &t)
	output operator More...
static basic::Tracer	tr ("protocols.jumping")
void	dump_tags_ (FArray1D_int const &tags, core::Size nres, std::ostream &out)
void	fill_tags_ (FArray1D_int &tags, core::Size fill_pos, int tag, core::Size nres)
static 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 basic::Tracer	tr ("protocols.jumping")
std::ostream &	operator<< (std::ostream &os, SameStrand const &t)
	output operator More...
static 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 (core::Size cutpoint, Pose &pose, FoldTree const &final_fold_tree)
bool	remove_cut (core::Size cutpoint, FoldTree &new_fold_tree, FoldTree const &final_fold_tree)
void	safe_secstruct (pose::Pose &pose)
core::fragment::JumpingFrameOP	generate_empty_jump_frame (core::Size startpos, core::Size endpos, core::Size length)
core::fragment::JumpingFrameOP	generate_jump_frame (core::Size startpos, core::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, core::Size const res1, core::Size const res2, Real &orientation, Real &pleating1, Real &pleating2)
void	get_pleating (pose::Pose const &pose, core::Size const pos1, core::Size const pos2, core::Size &orientation, core::Size &pleating)
void	assign_ss_dssp (core::pose::Pose &pose)
	Assign secondary structure using DSSP. More...

Typedef Documentation

BaseJumpSetupCOP

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

BaseJumpSetupOP

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

BasePairingLibraryCOP

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

BasePairingLibraryOP

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

DisulfPairingList

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

DisulfPairingsList

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

JumpList

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

JumpSelectorCOP

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

JumpSelectorOP

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

JumpSetupCOP

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

JumpSetupOP

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

MembraneJumpOP

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

PairingLibraryCOP

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

PairingLibraryOP

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

PointList

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

some legacy code

ResiduePairJumpCOP

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

ResiduePairJumpOP

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

ResiduePairJumpSetupCOP

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

ResiduePairJumpSetupOP

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

ResiduePairJumpSetupSingleCOP

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

ResiduePairJumpSetupSingleOP

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

ResiduePairJumpSingleCOP

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

ResiduePairJumpSingleOP

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

SameStrandCOP

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

SameStrandOP

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

StandardPairingLibraryCOP

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

StandardPairingLibraryOP

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

Enumeration Type Documentation

cstType

enum protocols::jumping::cstType

Enumerator
disAB
angleA
angleB
dihedralA
dihedralAB
dihedralB
num_cstType

dofType

enum protocols::jumping::dofType

Enumerator
rot1
rot2
cstJump
num_dofType

Function Documentation

assign_ss_dssp()

void protocols::jumping::assign_ss_dssp

(

core::pose::Pose &

pose

)

Assign secondary structure using DSSP.

References protocols::simple_filters::dssp().

close_chainbreaks()

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(), core::kinematics::FoldTree::simple_tree(), core::kinematics::simple_visualize_fold_tree(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), and tr().

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

dis_get_coordinate_system()

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

Referenced by dis_RT_from_epos().

dis_get_ncac() [1/2]

numeric::xyzMatrix_double protocols::jumping::dis_get_ncac

(

FArray2A_float

pos

)

Referenced by dis_RT_from_epos().

dis_get_ncac() [2/2]

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

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(), core::kinematics::RT::set_rotation(), and core::kinematics::RT::set_translation().

dump_tags_()

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

References core::conformation::membrane::out.

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

fill_tags_()

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

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

generate_empty_jump_frame()

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

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

generate_jump_frame()

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

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

get_CA_vectors()

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

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

Referenced by get_pairing_geometry().

get_coordinate_system()

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

Referenced by RT_from_epos().

get_ncac() [1/2]

numeric::xyzMatrix_double protocols::jumping::get_ncac

(

FArray2A_float

pos

)

Referenced by RT_from_epos().

get_ncac() [2/2]

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

get_pairing_geometry()

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

References core::chemical::ResidueType::atom_index(), get_CA_vectors(), core::pose::Pose::residue_type(), core::pose::Pose::size(), tr(), and core::pose::Pose::xyz().

Referenced by get_pleating().

get_pleating()

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

References get_pairing_geometry(), and tr().

operator<<() [1/4]

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

output operator

operator<<() [2/4]

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

inline

output operator

References protocols::hybridization::t.

operator<<() [3/4]

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

list of pairings

References core::conformation::membrane::out, protocols::jumping::DisulfPairing::pos1, protocols::jumping::DisulfPairing::pos2, protocols::jumping::DisulfPairing::seq_sep, and protocols::jumping::DisulfPairing::ss_type.

operator<<() [4/4]

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

References core::conformation::membrane::out.

read_disulf_pairing_list()

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

add pairings in pairing_file to list "pairings"

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

Referenced by read_pairing_list().

read_pairing_list()

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

References read_disulf_pairing_list(), and tr().

Referenced by protocols::jumping::MembraneJump::init().

remove_cut() [1/2]

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

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::connected(), core::kinematics::FoldTree::delete_extra_vertices(), core::kinematics::FoldTree::delete_unordered_edge(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::kinematics::FoldTree::jump_point(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::renumber_jumps(), core::kinematics::FoldTree::reorder(), tr(), and core::kinematics::FoldTree::update_edge_label().

remove_cut() [2/2]

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

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

Referenced by close_chainbreaks().

RT_from_epos()

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

References get_coordinate_system(), get_ncac(), core::kinematics::RT::set_rotation(), and core::kinematics::RT::set_translation().

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

safe_secstruct()

void protocols::jumping::safe_secstruct

(

pose::Pose &

pose

)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::jump_edge(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), core::kinematics::Edge::start(), and core::kinematics::Edge::stop().

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

tr() [1/5]

static 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(), protocols::jumping::JumpSetup::clean_jumps(), protocols::jumping::JumpSelector::clean_jumps(), close_chainbreaks(), protocols::jumping::JumpSelector::create_jump_sample(), protocols::jumping::SheetBuilder::create_jump_sample(), protocols::jumping::RandomSheetBuilder::create_new_random_topol(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), protocols::jumping::JumpSample::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::JumpSetup::read_file(), protocols::jumping::JumpSelector::read_file(), protocols::jumping::ResiduePairJumpSetup::read_file(), remove_cut(), protocols::jumping::MembraneJump::setup_fold_tree(), protocols::jumping::JumpSample::steal_orientation_and_pleating(), and protocols::jumping::JumpSample::transfer_jumps().

tr() [2/5]

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

static

tr() [3/5]

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

static

tr() [4/5]

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

static

tr() [5/5]

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

static