core::scoring::dssp Namespace Reference

Classes
class	Dssp
class	Pairing
class	StrandPairing
class	StrandPairingSet

Typedefs
typedef utility::vector1< Pairing >	PairingsList
typedef utility::vector1< Pairing >	PairingList
typedef utility::pointer::shared_ptr < StrandPairing >	StrandPairingOP
typedef utility::pointer::shared_ptr < StrandPairing const >	StrandPairingCOP
typedef utility::pointer::shared_ptr < StrandPairingSet >	StrandPairingSetOP
typedef utility::pointer::shared_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 with dssp energies. 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

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

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

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

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

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

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

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 with dssp energies.

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::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 $

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::size(), 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
	)

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
	)

References get_CA_vectors(), core::pose::Pose::residue_type(), core::pose::Pose::size(), 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
	)

References get_pairing_geometry(), and tr().

Referenced by core::scoring::dssp::StrandPairingSet::compute(), and protocols::jumping::JumpSample::steal_orientation_and_pleating().

bool core::scoring::dssp::has_orientation_and_pleating

(

PairingsList const &

pairings

)

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

References core::scoring::dssp::Pairing::is_inwards(), core::scoring::dssp::Pairing::is_parallel(), core::scoring::dssp::Pairing::Orientation(), core::conformation::membrane::out, 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
	)

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

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

References core::conformation::membrane::out, and core::scoring::dssp::StrandPairingSet::pairings_.

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

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::conformation::membrane::out, core::scoring::dssp::StrandPairing::pairing1, and core::scoring::dssp::StrandPairing::pleating1.

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

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

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

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"

References core::scoring::TR().

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

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

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

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

static

Referenced by get_pairing_geometry(), get_pleating(), core::scoring::dssp::StrandPairing::operator<(), and operator>>().