core::scoring::motif::ResPairMotif Class Reference

#include <motif_hash_stuff.hh>

Public Member Functions
	ResPairMotif ()
	ResPairMotif (std::string const &tag, core::pose::Pose const &pose, Real6 const &rt6, Size const &resi1, Size const &resi2, Real const &nbrs1, Real const &nbrs2, Real const &fa_atr, Real const &fa_atr_sc_bb, Real const &fa_atr_bb, Real const &hb_sc, Real const &hb_bb_sc, Real const &hb_bb, Real const &bfac1, Real const &bfac2, bool is_sspaired, RPM_Type _type)
bool	is_reversible () const
ResPairMotif &	reverse_in_place ()
ResPairMotif &	reverse_in_place_unsafe ()
ResPairMotif	reversed () const
void	reset ()
bool	valid () const
Xform	xform () const
void	xform (Xform const &_xform)
Real6	rt () const
void	rt (Real6 const &rt)
Real	dist2 () const
Real	bfac1 () const
Real	bfac2 () const
Real	fa_atr () const
Real	fa_atr_sc_bb () const
Real	fa_atr_bb () const
Real	hb_sc () const
Real	hb_bb_sc () const
Real	hb_bb () const
Real	nbrs1 () const
Real	nbrs2 () const
Real	chi11 () const
Real	chi12 () const
Real	chi13 () const
Real	chi14 () const
Real	chi21 () const
Real	chi22 () const
Real	chi23 () const
Real	chi24 () const
Real	chi1 (Size const &ichi) const
Real	chi2 (Size const &ichi) const
std::string	pdb () const
bool	check_pdb_code (std::string const &qpdb) const
bool	check_lig_code (std::string const &qlig) const
void	bfac1 (Real const &bfac1)
void	bfac2 (Real const &bfac2)
void	fa_atr (Real const &fa_atr)
void	fa_atr_sc_bb (Real const &fa_atr_sc_bb)
void	fa_atr_bb (Real const &fa_atr_bb)
void	hb_sc (Real const &hb_sc)
void	hb_bb_sc (Real const &hb_bb_sc)
void	hb_bb (Real const &hb_bb)
void	nbrs1 (Real const &nbrs)
void	nbrs2 (Real const &nbrs)
char	aa1 () const
char	aa2 () const
char	ss1 () const
char	ss2 () const
char	dssp1 () const
char	dssp2 () const
Real	score () const
RPM_Type	type () const
RM_Type	type1 () const
RM_Type	type2 () const
void	type (RPM_Type const &type)
Size	resi1 () const
Size	resi2 () const
Size	count () const
void	count (Size const &count)
void	addcount ()
std::string	tag () const
bool	filter (RPM_FilterStats *stat=nullptr) const
void	dump_pdb (std::ostream &out, numeric::xyzTransform< Real > const &xform=Xform::identity(), std::string tag="1") const
void	dump_pdb (std::string const &fname="", std::string const &tag="1") const
Real	dump_aligned_motif (std::ostream &out, core::pose::Pose const &pose1, Size const &ir, core::pose::Pose const &pose2, Size const &jr, Size &aotmno, int const &num=1, numeric::Xforms const &xforms=XsI) const
Real	dump_aligned_motif (std::ostream &out, core::pose::Pose const &pose, Size const &ir, Size const &jr, Size &aotmno, int const &num=1, numeric::Xforms const &xforms=XsI) const
Real	dump_aligned_motif (std::string const &fn, core::pose::Pose const &pose1, Size const &ir, core::pose::Pose const &pose2, Size const &jr, Size &aotmno, int const &num=1, numeric::Xforms const &xforms=XsI) const
Real	dump_aligned_motif (std::string const &fn, core::pose::Pose const &pose, Size const &ir, Size const &jr, Size &aotmno, int const &num=1, numeric::Xforms const &xforms=XsI) const
Real	dump_aligned_motif (std::ostream &out, core::pose::Pose const &pose1, Size const &ir, core::pose::Pose const &pose2, Size const &jr, int const &num=1, numeric::Xforms const &xforms=XsI) const
Real	dump_aligned_motif (std::ostream &out, core::pose::Pose const &pose, Size const &ir, Size const &jr, int const &num=1, numeric::Xforms const &xforms=XsI) const
Real	dump_aligned_motif (std::string const &fn, core::pose::Pose const &pose1, Size const &ir, core::pose::Pose const &pose2, Size const &jr, int const &num=1, numeric::Xforms const &xforms=XsI) const
Real	dump_aligned_motif (std::string const &fn, core::pose::Pose const &pose, Size const &ir, Size const &jr, int const &num=1, numeric::Xforms const &xforms=XsI) const
void	fill_pose_with_motif (core::pose::Pose &pose, int const &ir=1, int const &jr=2) const
core::pose::Pose	get_pose (int const &ir=1, int const &jr=2) const
bool	operator< (ResPairMotif const &other) const
bool	operator== (ResPairMotif const &other) const

Static Public Member Functions
static void	print_header (std::ostream &out)

Private Attributes
char	ss1_
char	ss2_
char	aa1_
char	aa2_
utility::fixedsizearray1< uint16_t, 6 >	rt6_
utility::fixedsizearray1< uint8_t, 4 >	chi1_
utility::fixedsizearray1< uint8_t, 4 >	chi2_
uint8_t	fa_atr_
uint8_t	fa_atr_sc_bb_
uint8_t	fa_atr_bb_
uint8_t	hb_sc_
uint8_t	hb_bb_sc_
uint8_t	hb_bb_
uint8_t	nbrs1_
uint8_t	nbrs2_
uint8_t	count_
uint8_t	type_
uint8_t	misc1_
uint16_t	lg1x_
uint16_t	lg1y_
uint16_t	lg1z_
uint16_t	lg2x_
uint16_t	lg2y_
uint16_t	lg2z_
uint8_t	bfac1_
uint8_t	bfac2_
char	chain1_
char	chain2_
uint16_t	resi1_
uint16_t	resi2_
utility::fixedsizearray1< unsigned char, 8 >	pdb_

Friends
std::ostream &	operator<< (std::ostream &out, ResPairMotif const &x)

Constructor & Destructor Documentation

ResPairMotif() [1/2]

core::scoring::motif::ResPairMotif::ResPairMotif

(

)

ResPairMotif() [2/2]

core::scoring::motif::ResPairMotif::ResPairMotif	(	std::string const &	tag,
		core::pose::Pose const &	pose,
		Real6 const &	rt6,
		Size const &	resi1,
		Size const &	resi2,
		Real const &	nbrs1,
		Real const &	nbrs2,
		Real const &	fa_atr,
		Real const &	fa_atr_sc_bb,
		Real const &	fa_atr_bb,
		Real const &	hb_sc,
		Real const &	hb_bb_sc,
		Real const &	hb_bb,
		Real const &	bfac1,
		Real const &	bfac2,
		bool	is_sspaired,
		RPM_Type	_type
	)

References core::pose::Pose::chain(), core::conformation::Residue::chi(), core::scoring::fa_atr, core::conformation::Residue::name1(), core::scoring::motif::real_to_uint8(), core::pose::Pose::residue(), and core::pose::Pose::secstruct().

Member Function Documentation

aa1()

char core::scoring::motif::ResPairMotif::aa1

(

)

const

Referenced by core::scoring::motif::ResPairMotifMetaBinner::motif_bin_hash(), core::scoring::motif::ResPairMotifMetaBinner::motif_bin_label(), and core::scoring::motif::MotifHits::stat_motifs().

aa2()

char core::scoring::motif::ResPairMotif::aa2

(

)

const

Referenced by core::scoring::motif::ResPairMotifMetaBinner::motif_bin_hash(), core::scoring::motif::ResPairMotifMetaBinner::motif_bin_label(), and core::scoring::motif::MotifHits::stat_motifs().

addcount()

void core::scoring::motif::ResPairMotif::addcount ( )

inline

References count_.

bfac1() [1/2]

Real core::scoring::motif::ResPairMotif::bfac1

(

)

const

References core::scoring::motif::uint8_to_real().

bfac1() [2/2]

void core::scoring::motif::ResPairMotif::bfac1

(

Real const &

bfac1

)

References core::scoring::motif::real_to_uint8().

bfac2() [1/2]

Real core::scoring::motif::ResPairMotif::bfac2

(

)

const

References core::scoring::motif::uint8_to_real().

bfac2() [2/2]

void core::scoring::motif::ResPairMotif::bfac2

(

Real const &

bfac2

)

References core::scoring::motif::real_to_uint8().

check_lig_code()

bool core::scoring::motif::ResPairMotif::check_lig_code ( std::string const &  qlig ) const

inline

References pdb_.

Referenced by core::scoring::motif::ResPairMotifs::add_reverse_motifs().

check_pdb_code()

bool core::scoring::motif::ResPairMotif::check_pdb_code ( std::string const &  qpdb ) const

inline

References pdb_.

chi1()

Real core::scoring::motif::ResPairMotif::chi1

(

Size const &

ichi

)

const

chi11()

Real core::scoring::motif::ResPairMotif::chi11

(

)

const

References core::scoring::motif::uint8_to_real().

chi12()

Real core::scoring::motif::ResPairMotif::chi12

(

)

const

References core::scoring::motif::uint8_to_real().

chi13()

Real core::scoring::motif::ResPairMotif::chi13

(

)

const

References core::scoring::motif::uint8_to_real().

chi14()

Real core::scoring::motif::ResPairMotif::chi14

(

)

const

References core::scoring::motif::uint8_to_real().

chi2()

Real core::scoring::motif::ResPairMotif::chi2

(

Size const &

ichi

)

const

chi21()

Real core::scoring::motif::ResPairMotif::chi21

(

)

const

References core::scoring::motif::uint8_to_real().

chi22()

Real core::scoring::motif::ResPairMotif::chi22

(

)

const

References core::scoring::motif::uint8_to_real().

chi23()

Real core::scoring::motif::ResPairMotif::chi23

(

)

const

References core::scoring::motif::uint8_to_real().

chi24()

Real core::scoring::motif::ResPairMotif::chi24

(

)

const

References core::scoring::motif::uint8_to_real().

count() [1/2]

Size core::scoring::motif::ResPairMotif::count ( ) const

inline

References count_.

count() [2/2]

void core::scoring::motif::ResPairMotif::count ( Size const &  count )

inline

References count(), and count_.

Referenced by count().

dist2()

Real core::scoring::motif::ResPairMotif::dist2

(

)

const

References core::scoring::motif::MOTIF_HASH_CART_SIZE, and core::scoring::motif::uint16_to_real().

dssp1()

char core::scoring::motif::ResPairMotif::dssp1

(

)

const

dssp2()

char core::scoring::motif::ResPairMotif::dssp2

(

)

const

dump_aligned_motif() [1/8]

Real core::scoring::motif::ResPairMotif::dump_aligned_motif	(	std::ostream &	out,
		core::pose::Pose const &	pose,
		Size const &	ir,
		Size const &	jr,
		int const &	num = 1,
		numeric::Xforms const &	xforms = XsI
	)		const

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

dump_aligned_motif() [2/8]

Real core::scoring::motif::ResPairMotif::dump_aligned_motif	(	std::ostream &	out,
		core::pose::Pose const &	pose,
		Size const &	ir,
		Size const &	jr,
		Size &	aotmno,
		int const &	num = 1,
		numeric::Xforms const &	xforms = XsI
	)		const

dump_aligned_motif() [3/8]

Real core::scoring::motif::ResPairMotif::dump_aligned_motif	(	std::ostream &	out,
		core::pose::Pose const &	pose1,
		Size const &	ir,
		core::pose::Pose const &	pose2,
		Size const &	jr,
		int const &	num = 1,
		numeric::Xforms const &	xforms = XsI
	)		const

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

dump_aligned_motif() [4/8]

Real core::scoring::motif::ResPairMotif::dump_aligned_motif	(	std::ostream &	out,
		core::pose::Pose const &	pose1,
		Size const &	ir,
		core::pose::Pose const &	pose2,
		Size const &	jr,
		Size &	aotmno,
		int const &	num = 1,
		numeric::Xforms const &	xforms = XsI
	)		const

dump_aligned_motif() [5/8]

Real core::scoring::motif::ResPairMotif::dump_aligned_motif	(	std::string const &	fn,
		core::pose::Pose const &	pose,
		Size const &	ir,
		Size const &	jr,
		int const &	num = 1,
		numeric::Xforms const &	xforms = XsI
	)		const

dump_aligned_motif() [6/8]

Real core::scoring::motif::ResPairMotif::dump_aligned_motif	(	std::string const &	fn,
		core::pose::Pose const &	pose,
		Size const &	ir,
		Size const &	jr,
		Size &	aotmno,
		int const &	num = 1,
		numeric::Xforms const &	xforms = XsI
	)		const

dump_aligned_motif() [7/8]

Real core::scoring::motif::ResPairMotif::dump_aligned_motif	(	std::string const &	fn,
		core::pose::Pose const &	pose1,
		Size const &	ir,
		core::pose::Pose const &	pose2,
		Size const &	jr,
		int const &	num = 1,
		numeric::Xforms const &	xforms = XsI
	)		const

dump_aligned_motif() [8/8]

Real core::scoring::motif::ResPairMotif::dump_aligned_motif	(	std::string const &	fn,
		core::pose::Pose const &	pose1,
		Size const &	ir,
		core::pose::Pose const &	pose2,
		Size const &	jr,
		Size &	aotmno,
		int const &	num = 1,
		numeric::Xforms const &	xforms = XsI
	)		const

dump_pdb() [1/2]

void core::scoring::motif::ResPairMotif::dump_pdb	(	std::ostream &	out,
		numeric::xyzTransform< Real > const &	xform = Xform::identity(),
		std::string	tag = "1"
	)		const

dump_pdb() [2/2]

void core::scoring::motif::ResPairMotif::dump_pdb	(	std::string const &	fname = "",
		std::string const &	tag = "1"
	)		const

References core::io::pdb::dump_pdb(), and core::conformation::membrane::out.

fa_atr() [1/2]

Real core::scoring::motif::ResPairMotif::fa_atr

(

)

const

References core::scoring::motif::uint8_to_real().

fa_atr() [2/2]

void core::scoring::motif::ResPairMotif::fa_atr

(

Real const &

fa_atr

)

References core::scoring::motif::real_to_uint8().

fa_atr_bb() [1/2]

Real core::scoring::motif::ResPairMotif::fa_atr_bb

(

)

const

References core::scoring::motif::uint8_to_real().

fa_atr_bb() [2/2]

void core::scoring::motif::ResPairMotif::fa_atr_bb

(

Real const &

fa_atr_bb

)

References core::scoring::motif::real_to_uint8().

fa_atr_sc_bb() [1/2]

Real core::scoring::motif::ResPairMotif::fa_atr_sc_bb

(

)

const

References core::scoring::motif::uint8_to_real().

fa_atr_sc_bb() [2/2]

void core::scoring::motif::ResPairMotif::fa_atr_sc_bb

(

Real const &

fa_atr_sc_bb

)

References core::scoring::motif::real_to_uint8().

fill_pose_with_motif()

void core::scoring::motif::ResPairMotif::fill_pose_with_motif	(	core::pose::Pose &	pose,
		int const &	ir = 1,
		int const &	jr = 2
	)		const

References core::chemical::aa_from_oneletter_code(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::conformation::ResidueFactory::create_residue(), core::chemical::FULL_ATOM_t, core::chemical::name_from_aa(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::set_chi(), core::scoring::motif::set_residue_pair_xform(), core::pose::Pose::size(), and core::scoring::motif::uint8_to_real().

filter()

bool core::scoring::motif::ResPairMotif::filter

(

RPM_FilterStats *

stat = nullptr

)

const

References core::scoring::motif::aa_trustworthiness(), core::scoring::motif::BB_BB, core::scoring::motif::BB_PH, core::scoring::motif::BB_PO, core::scoring::motif::RPM_FilterStats::F_aa1, core::scoring::motif::RPM_FilterStats::F_aa2, core::scoring::motif::RPM_FilterStats::F_coorderr, core::scoring::motif::RPM_FilterStats::F_dssp1, core::scoring::motif::RPM_FilterStats::F_dssp2, core::scoring::motif::RPM_FilterStats::F_faatr, core::scoring::motif::RPM_FilterStats::F_faatr_or_hb, core::scoring::motif::RPM_FilterStats::F_faatr_or_hbbb, core::scoring::motif::RPM_FilterStats::F_hb_bb, core::scoring::motif::RPM_FilterStats::F_hb_bb_sc, core::scoring::motif::RPM_FilterStats::F_hb_sc, core::scoring::motif::RPM_FilterStats::F_lig, core::scoring::motif::RPM_FilterStats::F_max_seqsep, core::scoring::motif::RPM_FilterStats::F_maxdist2, core::scoring::motif::RPM_FilterStats::F_mindist2, core::scoring::motif::RPM_FilterStats::F_no_hb_bb, core::scoring::motif::RPM_FilterStats::F_nodisulf, core::scoring::motif::RPM_FilterStats::F_noloops, core::scoring::motif::RPM_FilterStats::F_not_restype, core::scoring::motif::RPM_FilterStats::F_not_restype_one, core::scoring::motif::RPM_FilterStats::F_oneloop, core::scoring::motif::RPM_FilterStats::F_pdb, core::scoring::motif::RPM_FilterStats::F_restype, core::scoring::motif::RPM_FilterStats::F_restype1, core::scoring::motif::RPM_FilterStats::F_restype2, core::scoring::motif::RPM_FilterStats::F_restype_one, core::scoring::motif::RPM_FilterStats::F_score, core::scoring::motif::RPM_FilterStats::F_seqsep, core::scoring::motif::RPM_FilterStats::F_ss1, core::scoring::motif::RPM_FilterStats::F_ss2, core::scoring::motif::RPM_FilterStats::F_type_BB_BB, core::scoring::motif::RPM_FilterStats::F_type_BB_PH, core::scoring::motif::RPM_FilterStats::F_type_BB_PO, core::scoring::motif::RPM_FilterStats::F_type_PH_PO, core::scoring::motif::RPM_FilterStats::F_type_SC_BB, core::scoring::motif::RPM_FilterStats::F_type_SC_PH, core::scoring::motif::RPM_FilterStats::F_type_SC_PO, core::scoring::motif::RPM_FilterStats::F_type_SC_SC, core::scoring::motif::RPM_FilterStats::F_uniformfrag, core::scoring::fa_atr, core::scoring::motif::MOTIF_HASH_CART_SIZE, core::chemical::element::N, core::scoring::motif::RPM_FilterStats::P_aa1, core::scoring::motif::RPM_FilterStats::P_aa2, core::scoring::motif::RPM_FilterStats::P_coorderr, core::scoring::motif::RPM_FilterStats::P_dssp1, core::scoring::motif::RPM_FilterStats::P_dssp2, core::scoring::motif::RPM_FilterStats::P_faatr, core::scoring::motif::RPM_FilterStats::P_faatr_or_hb, core::scoring::motif::RPM_FilterStats::P_faatr_or_hbbb, core::scoring::motif::RPM_FilterStats::P_hb_bb, core::scoring::motif::RPM_FilterStats::P_hb_bb_sc, core::scoring::motif::RPM_FilterStats::P_hb_sc, core::scoring::motif::RPM_FilterStats::P_lig, core::scoring::motif::RPM_FilterStats::P_max_seqsep, core::scoring::motif::RPM_FilterStats::P_maxdist2, core::scoring::motif::RPM_FilterStats::P_mindist2, core::scoring::motif::RPM_FilterStats::P_no_hb_bb, core::scoring::motif::RPM_FilterStats::P_nodisulf, core::scoring::motif::RPM_FilterStats::P_noloops, core::scoring::motif::RPM_FilterStats::P_not_restype, core::scoring::motif::RPM_FilterStats::P_not_restype_one, core::scoring::motif::RPM_FilterStats::P_oneloop, core::scoring::motif::RPM_FilterStats::P_pdb, core::scoring::motif::RPM_FilterStats::P_restype, core::scoring::motif::RPM_FilterStats::P_restype1, core::scoring::motif::RPM_FilterStats::P_restype2, core::scoring::motif::RPM_FilterStats::P_restype_one, core::scoring::motif::RPM_FilterStats::P_score, core::scoring::motif::RPM_FilterStats::P_seqsep, core::scoring::motif::RPM_FilterStats::P_ss1, core::scoring::motif::RPM_FilterStats::P_ss2, core::scoring::motif::RPM_FilterStats::P_type_BB_BB, core::scoring::motif::RPM_FilterStats::P_type_BB_PH, core::scoring::motif::RPM_FilterStats::P_type_BB_PO, core::scoring::motif::RPM_FilterStats::P_type_PH_PO, core::scoring::motif::RPM_FilterStats::P_type_SC_BB, core::scoring::motif::RPM_FilterStats::P_type_SC_PH, core::scoring::motif::RPM_FilterStats::P_type_SC_PO, core::scoring::motif::RPM_FilterStats::P_type_SC_SC, core::scoring::motif::RPM_FilterStats::P_uniformfrag, core::scoring::motif::PH_PO, core::scoring::motif::SC_BB, core::scoring::motif::SC_PH, core::scoring::motif::SC_PO, core::scoring::motif::SC_SC, protocols::hybridization::score, and core::scoring::motif::uint16_to_real().

get_pose()

core::pose::Pose core::scoring::motif::ResPairMotif::get_pose	(	int const &	ir = 1,
		int const &	jr = 2
	)		const

hb_bb() [1/2]

Real core::scoring::motif::ResPairMotif::hb_bb

(

)

const

References core::scoring::motif::uint8_to_real().

hb_bb() [2/2]

void core::scoring::motif::ResPairMotif::hb_bb

(

Real const &

hb_bb

)

References core::scoring::motif::real_to_uint8().

hb_bb_sc() [1/2]

Real core::scoring::motif::ResPairMotif::hb_bb_sc

(

)

const

References core::scoring::motif::uint8_to_real().

hb_bb_sc() [2/2]

void core::scoring::motif::ResPairMotif::hb_bb_sc

(

Real const &

hb_bb_sc

)

References core::scoring::motif::real_to_uint8().

hb_sc() [1/2]

Real core::scoring::motif::ResPairMotif::hb_sc

(

)

const

References core::scoring::motif::uint8_to_real().

hb_sc() [2/2]

void core::scoring::motif::ResPairMotif::hb_sc

(

Real const &

hb_sc

)

References core::scoring::motif::real_to_uint8().

is_reversible()

bool core::scoring::motif::ResPairMotif::is_reversible ( ) const

inline

References type1(), and type2().

Referenced by core::scoring::motif::ResPairMotifs::filter_structurally_identical_motifs().

nbrs1() [1/2]

Real core::scoring::motif::ResPairMotif::nbrs1

(

)

const

References core::scoring::motif::uint8_to_real().

nbrs1() [2/2]

void core::scoring::motif::ResPairMotif::nbrs1

(

Real const &

nbrs

)

References core::scoring::motif::real_to_uint8().

nbrs2() [1/2]

Real core::scoring::motif::ResPairMotif::nbrs2

(

)

const

References core::scoring::motif::uint8_to_real().

nbrs2() [2/2]

void core::scoring::motif::ResPairMotif::nbrs2

(

Real const &

nbrs

)

References core::scoring::motif::real_to_uint8().

operator<()

bool core::scoring::motif::ResPairMotif::operator<

(

ResPairMotif const &

other

)

const

operator==()

bool core::scoring::motif::ResPairMotif::operator==

(

ResPairMotif const &

other

)

const

pdb()

std::string core::scoring::motif::ResPairMotif::pdb ( ) const

inline

References pdb_.

print_header()

void core::scoring::motif::ResPairMotif::print_header ( std::ostream &  out )

static

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

reset()

void core::scoring::motif::ResPairMotif::reset

(

)

resi1()

Size core::scoring::motif::ResPairMotif::resi1 ( ) const

inline

References resi1_.

Referenced by core::scoring::motif::ResPairMotifs::filter_structurally_identical_motifs().

resi2()

Size core::scoring::motif::ResPairMotif::resi2 ( ) const

inline

References resi2_.

Referenced by core::scoring::motif::ResPairMotifs::filter_structurally_identical_motifs().

reverse_in_place()

ResPairMotif & core::scoring::motif::ResPairMotif::reverse_in_place

(

)

Referenced by core::scoring::motif::ResPairMotifs::filter_structurally_identical_motifs(), and reversed().

reverse_in_place_unsafe()

ResPairMotif & core::scoring::motif::ResPairMotif::reverse_in_place_unsafe

(

)

References core::id::swap().

reversed()

ResPairMotif core::scoring::motif::ResPairMotif::reversed

(

)

const

References reverse_in_place().

Referenced by core::scoring::motif::ResPairMotifs::add_reverse_motifs().

rt() [1/2]

Real6 core::scoring::motif::ResPairMotif::rt

(

)

const

References core::scoring::motif::MOTIF_HASH_CART_SIZE, and core::scoring::motif::uint16_to_real().

Referenced by core::scoring::motif::MotifHash::add_motif(), core::scoring::motif::MotifHash::bin_index(), and core::scoring::motif::MotifHash::find_motifs_with_radius().

rt() [2/2]

void core::scoring::motif::ResPairMotif::rt

(

Real6 const &

rt

)

References core::scoring::motif::MOTIF_HASH_CART_SIZE, and core::scoring::motif::real_to_uint16().

score()

Real core::scoring::motif::ResPairMotif::score

(

)

const

References core::scoring::motif::BB_BB, core::scoring::motif::BB_PH, core::scoring::motif::BB_PO, core::scoring::fa_atr, core::scoring::motif::PH_PO, core::scoring::motif::SC_BB, core::scoring::motif::SC_PH, core::scoring::motif::SC_PO, and core::scoring::motif::SC_SC.

Referenced by core::scoring::motif::MotifHash::get_motif_summary().

ss1()

char core::scoring::motif::ResPairMotif::ss1

(

)

const

Referenced by core::scoring::motif::ResPairMotifMetaBinner::motif_bin_hash(), core::scoring::motif::ResPairMotifMetaBinner::motif_bin_label(), and core::scoring::motif::MotifHits::stat_motifs().

ss2()

char core::scoring::motif::ResPairMotif::ss2

(

)

const

Referenced by core::scoring::motif::ResPairMotifMetaBinner::motif_bin_hash(), core::scoring::motif::ResPairMotifMetaBinner::motif_bin_label(), and core::scoring::motif::MotifHits::stat_motifs().

tag()

std::string core::scoring::motif::ResPairMotif::tag

(

)

const

type() [1/2]

RPM_Type core::scoring::motif::ResPairMotif::type

(

)

const

References core::scoring::motif::RPM_Type_NONE.

Referenced by core::scoring::motif::MotifHash::add_motif(), and type().

type() [2/2]

void core::scoring::motif::ResPairMotif::type ( RPM_Type const &  type )

inline

References type(), and type_.

type1()

RM_Type core::scoring::motif::ResPairMotif::type1

(

)

const

References core::scoring::motif::rpm_type1().

Referenced by core::scoring::motif::ResPairMotifs::add_reverse_motifs(), and is_reversible().

type2()

RM_Type core::scoring::motif::ResPairMotif::type2

(

)

const

References core::scoring::motif::rpm_type2().

Referenced by core::scoring::motif::ResPairMotifs::add_reverse_motifs(), and is_reversible().

valid()

bool core::scoring::motif::ResPairMotif::valid

(

)

const

References core::scoring::motif::RPM_Type_NONE.

Referenced by core::scoring::motif::MotifHash::get_motif_summary().

xform() [1/2]

Xform core::scoring::motif::ResPairMotif::xform

(

)

const

xform() [2/2]

void core::scoring::motif::ResPairMotif::xform

(

Xform const &

_xform

)

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  out, ResPairMotif const &  x  )

friend

Member Data Documentation

aa1_

char core::scoring::motif::ResPairMotif::aa1_

private

aa2_

char core::scoring::motif::ResPairMotif::aa2_

private

bfac1_

uint8_t core::scoring::motif::ResPairMotif::bfac1_

private

bfac2_

uint8_t core::scoring::motif::ResPairMotif::bfac2_

private

chain1_

char core::scoring::motif::ResPairMotif::chain1_

private

chain2_

char core::scoring::motif::ResPairMotif::chain2_

private

chi1_

utility::fixedsizearray1<uint8_t,4> core::scoring::motif::ResPairMotif::chi1_

private

chi2_

utility::fixedsizearray1<uint8_t,4> core::scoring::motif::ResPairMotif::chi2_

private

count_

uint8_t core::scoring::motif::ResPairMotif::count_

private

Referenced by addcount(), and count().

fa_atr_

uint8_t core::scoring::motif::ResPairMotif::fa_atr_

private

fa_atr_bb_

uint8_t core::scoring::motif::ResPairMotif::fa_atr_bb_

private

fa_atr_sc_bb_

uint8_t core::scoring::motif::ResPairMotif::fa_atr_sc_bb_

private

hb_bb_

uint8_t core::scoring::motif::ResPairMotif::hb_bb_

private

hb_bb_sc_

uint8_t core::scoring::motif::ResPairMotif::hb_bb_sc_

private

hb_sc_

uint8_t core::scoring::motif::ResPairMotif::hb_sc_

private

lg1x_

uint16_t core::scoring::motif::ResPairMotif::lg1x_

private

lg1y_

uint16_t core::scoring::motif::ResPairMotif::lg1y_

private

lg1z_

uint16_t core::scoring::motif::ResPairMotif::lg1z_

private

lg2x_

uint16_t core::scoring::motif::ResPairMotif::lg2x_

private

lg2y_

uint16_t core::scoring::motif::ResPairMotif::lg2y_

private

lg2z_

uint16_t core::scoring::motif::ResPairMotif::lg2z_

private

misc1_

uint8_t core::scoring::motif::ResPairMotif::misc1_

private

nbrs1_

uint8_t core::scoring::motif::ResPairMotif::nbrs1_

private

nbrs2_

uint8_t core::scoring::motif::ResPairMotif::nbrs2_

private

pdb_

utility::fixedsizearray1<unsigned char,8> core::scoring::motif::ResPairMotif::pdb_

private

Referenced by check_lig_code(), check_pdb_code(), and pdb().

resi1_

uint16_t core::scoring::motif::ResPairMotif::resi1_

private

Referenced by resi1().

resi2_

uint16_t core::scoring::motif::ResPairMotif::resi2_

private

Referenced by resi2().

rt6_

utility::fixedsizearray1<uint16_t,6> core::scoring::motif::ResPairMotif::rt6_

private

ss1_

char core::scoring::motif::ResPairMotif::ss1_

private

ss2_

char core::scoring::motif::ResPairMotif::ss2_

private

type_

uint8_t core::scoring::motif::ResPairMotif::type_

private

Referenced by type().

---

The documentation for this class was generated from the following files:

• src/core/scoring/motif/motif_hash_stuff.hh
• src/core/scoring/motif/motif_hash_stuff.cc