Classes
class	Dssp

class	Pairing

class	StrandPairing

class	StrandPairingSet

Typedefs
typedef utility::vector1< Pairing >	PairingsList

typedef utility::vector1< Pairing >	PairingList

typedef utility::pointer::owning_ptr < StrandPairing >	StrandPairingOP

typedef utility::pointer::owning_ptr < StrandPairing const >	StrandPairingCOP

typedef utility::pointer::owning_ptr < StrandPairingSet >	StrandPairingSetOP

typedef utility::pointer::owning_ptr < StrandPairingSet const >	StrandPairingSetCOP

typedef utility::vector1 < PointPosition >	PointList

Functions
void	fill_hbond_bb_pair_score_dssp (pose::Pose const &pose, ObjexxFCL::FArray2D_float &hbond_bb_pair_score)
	Populates the hbond_bb_pair_score_ array. More...

void	read_pairing_list (std::string pairing_file, PairingsList &pairings)
	add pairings in pairing_file to list "pairings" More...

void	read_pairing_list (std::istream &pairing_stream, PairingsList &pairings)

std::ostream &	operator<< (std::ostream &out, Pairing const &)
	list of pairings More...

std::ostream &	operator<< (std::ostream &out, PairingsList const &p)

bool	has_orientation_and_pleating (PairingsList const &pairings)

std::istream &	operator>> (std::istream &is, StrandPairingSet &set)

std::ostream &	operator<< (std::ostream &out, const StrandPairingSet &sp)

std::istream &	operator>> (std::istream &is, StrandPairing &sp)

std::ostream &	operator<< (std::ostream &out, const StrandPairing &sp)

static basic::Tracer	tr ("core.scoring.dssp")

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)

Typedef Documentation

typedef utility::vector1<Pairing> core::scoring::dssp::PairingList

Definition at line 38 of file PairingsList.fwd.hh.

typedef utility::vector1<Pairing> core::scoring::dssp::PairingsList

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

typedef utility::vector1< PointPosition > core::scoring::dssp::PointList

Definition at line 33 of file util.hh.

typedef utility::pointer::owning_ptr< StrandPairing const > core::scoring::dssp::StrandPairingCOP

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

typedef utility::pointer::owning_ptr< StrandPairing > core::scoring::dssp::StrandPairingOP

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

typedef utility::pointer::owning_ptr< StrandPairingSet const > core::scoring::dssp::StrandPairingSetCOP

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

typedef utility::pointer::owning_ptr< StrandPairingSet > core::scoring::dssp::StrandPairingSetOP

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

Function Documentation

void core::scoring::dssp::fill_hbond_bb_pair_score_dssp	(	pose::Pose const &	pose,
		ObjexxFCL::FArray2D_float &	hbond_bb_pair_score
	)

Populates the hbond_bb_pair_score_ array.

fill_hbond_bb_pair_score_

Detailed:: Uses the rosetta hydrogen bond energies computed in hbonds::hbond_set to fill the hbond_bb_pair_score_ array. The hbond_set data structure must already be populated, by (e.g.) full atom scoring. Entry (i,j) is the backbone hydrogen bond energy between residues i (acceptor) and j (donor).

Global Read:: hbonds::hbond_set

Global Write:: dssp_ns::hbond_bb_pair_score_

Remarks

References:

Author: olange: ported from original bblum-rosetta++ version $

Last Modified:: fill_hbond_bb_pair_score__dssp

Populates the hbond_bb_pair_score_ array with dssp energies

Detailed:: Uses hydrogen bond energies computed a la dssp to fill the hbond_bb_pair_score_ array. Entry (i,j) is the backbone hydrogen bond energy between residues i (acceptor) and j (donor).

Global Read:: misc::Sizes::total_residue_ misc::current_pose::Eposition misc::current_pose::full_coord misc::Sizes::res misc::current_pose::res_variant aaproperties_pack::properties_per_aa_aav::HNpos aaproperties_pack::properties_per_aa_aav::HNpos param_aa::aa_pro termini_ns::is_N_terminus termini_ns::is_C_terminus

Global Write:: dssp_ns::hbond_bb_pair_score_

Remarks

References:

Author: olange: ported from original bblum-rosetta++ version $

Last Modified:

Definition at line 186 of file Dssp.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, protocols::comparative_modeling::features::E, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by core::scoring::dssp::Dssp::compute(), and core::scoring::dssp::StrandPairingSet::StrandPairingSet().

void core::scoring::dssp::get_CA_vectors	(	PointList const &	ca1,
		PointList const &	ca2,
		Vector &	a,
		Vector &	b,
		Vector &	c
	)

Definition at line 62 of file util.cc.

Referenced by get_pairing_geometry().

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

Definition at line 87 of file util.cc.

References get_CA_vectors(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), tr(), and core::pose::Pose::xyz().

Referenced by get_pleating().

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

Definition at line 149 of file util.cc.

References get_pairing_geometry(), and tr().

Referenced by core::scoring::dssp::StrandPairingSet::compute().

bool core::scoring::dssp::has_orientation_and_pleating ( PairingsList const & pairings)

Definition at line 155 of file PairingsList.cc.

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

std::ostream & core::scoring::dssp::operator<<	(	std::ostream &	out,
		Pairing const &	p
	)

list of pairings

Definition at line 140 of file PairingsList.cc.

References core::scoring::dssp::Pairing::is_inwards(), core::scoring::dssp::Pairing::is_parallel(), core::scoring::dssp::Pairing::Orientation(), core::scoring::dssp::Pairing::Pleating(), core::scoring::dssp::Pairing::Pos1(), and core::scoring::dssp::Pairing::Pos2().

std::ostream & core::scoring::dssp::operator<<	(	std::ostream &	out,
		PairingsList const &	p
	)

Definition at line 147 of file PairingsList.cc.

std::ostream & core::scoring::dssp::operator<<	(	std::ostream &	out,
		const StrandPairingSet &	sp
	)

Definition at line 162 of file StrandPairing.cc.

References core::scoring::dssp::StrandPairingSet::pairings_.

std::ostream & core::scoring::dssp::operator<<	(	std::ostream &	out,
		const StrandPairing &	sp
	)

Definition at line 884 of file StrandPairing.cc.

References core::scoring::dssp::StrandPairing::antipar, core::scoring::dssp::StrandPairing::begin1_, core::scoring::dssp::StrandPairing::begin2_, core::scoring::dssp::StrandPairing::end1_, core::scoring::dssp::StrandPairing::end2_, core::scoring::dssp::StrandPairing::get_all_register_and_bulges(), core::scoring::dssp::StrandPairing::pairing1, and core::scoring::dssp::StrandPairing::pleating1.

std::istream& core::scoring::dssp::operator>>	(	std::istream &	is,
		StrandPairingSet &	set
	)

Definition at line 143 of file StrandPairing.cc.

References core::scoring::dssp::StrandPairingSet::pairings_, and tr().

std::istream& core::scoring::dssp::operator>>	(	std::istream &	is,
		StrandPairing &	sp
	)

Definition at line 731 of file StrandPairing.cc.

References core::scoring::dssp::StrandPairing::antipar, core::scoring::dssp::StrandPairing::begin1_, core::scoring::dssp::StrandPairing::begin2_, core::scoring::dssp::StrandPairing::end1_, core::scoring::dssp::StrandPairing::end2_, core::scoring::dssp::StrandPairing::pairing1, core::scoring::dssp::StrandPairing::pairing2, core::scoring::dssp::StrandPairing::pleating1, core::scoring::dssp::StrandPairing::show_internals(), and tr().

void core::scoring::dssp::read_pairing_list	(	std::string	pairing_file,
		PairingsList &	pairings
	)

add pairings in pairing_file to list "pairings"

Definition at line 80 of file PairingsList.cc.

References tr().

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

void core::scoring::dssp::read_pairing_list	(	std::istream &	pairing_stream,
		PairingsList &	pairings
	)

Definition at line 92 of file PairingsList.cc.

References protocols::match::upstream::b, core::pack::dunbrack::c, and core::scoring::dssp::Pairing::reverse().

static basic::Tracer core::scoring::dssp::tr ( "core.scoring.dssp" )

static

Referenced by get_pairing_geometry(), get_pleating(), operator>>(), and read_pairing_list().

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation