protocols::motif_hash::ResPairMotif Class Reference

#include <motif_hash_stuff.hh>

Public Member Functions
	ResPairMotif ()
	ResPairMotif (std::string const &tag, core::pose::Pose const &pose, Real6 const &xform, Size const &resi1, Size const &resi2, Real const &sasa, Real const &nbrs, Real const &fa_atr, Real const &hb_sc, Real const &hb_bb_sc, Real const &hb_bb, Real const &bfac1, Real const &bfac2, bool is_sspaired)
void	reverse_in_place ()
void	reset ()
Real6	rt () const
void	rt (Real6 const &rt)
numeric::HomogeneousTransform < Real >	ht () const
void	ht (numeric::HomogeneousTransform< Real > const &h)
Real	dist2 () const
Real	bfac1 () const
Real	bfac2 () const
Real	sasa () const
Real	fa_atr () const
Real	hb_sc () const
Real	hb_bb_sc () const
Real	hb_bb () const
Real	nbrs () 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
void	bfac1 (Real const &bfac1)
void	bfac2 (Real const &bfac2)
void	sasa (Real const &sasa)
void	fa_atr (Real const &fa_atr)
void	hb_sc (Real const &hb_sc)
void	hb_bb_sc (Real const &hb_bb_sc)
void	hb_bb (Real const &hb_bb)
void	nbrs (Real const &nbrs)
char	aa1 () const
char	aa2 () const
char	ss1 () const
char	ss2 () const
char	dssp1 () const
char	dssp2 () const
Size	count () const
void	count (Size const &count)
void	addcount ()
bool	filter () const
void	dump_pdb (std::string const &fname, std::string const &tag="1") const
void	dump_pdb (std::ostream &out, numeric::xyzTransform< Real > const &xform, std::string const &tag="1") const
Real	dump_aligned_motif (std::ostream &out, Pose const &pose1, Size const &ir, Pose const &pose2, Size const &jr, int const &num=1) const
Real	dump_aligned_motif_break (std::ostream &out, Pose const &pose1, Size const &ir, Pose const &pose2, Size const &jr, int const &num=1) const
Real	dump_aligned_motif_super (std::ostream &out, Pose const &pose1, Size const &ir, Pose const &pose2, Size const &jr, int const &num=1) const
Real	dump_aligned_motif (std::ostream &out, Pose const &pose, Size const &ir, Size const &jr, int const &num=1) const
void	fill_pose_with_motif (Pose &pose, int ir=1, int jr=2) const

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

Public Attributes
uint16_t	resi1_
uint16_t	resi2_
utility::fixedsizearray1 < unsigned char, 8 >	pdb_

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	hb_sc_
uint8_t	hb_bb_sc_
uint8_t	hb_bb_
uint8_t	sasa_
uint8_t	nbrs_
uint8_t	misc1_
uint8_t	misc2_
uint8_t	misc3_
uint8_t	misc4_
uint8_t	misc5_
uint8_t	count_
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_

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

Constructor & Destructor Documentation

protocols::motif_hash::ResPairMotif::ResPairMotif

(

)

References reset().

protocols::motif_hash::ResPairMotif::ResPairMotif	(	std::string const &	tag,
		core::pose::Pose const &	pose,
		Real6 const &	xform,
		Size const &	resi1,
		Size const &	resi2,
		Real const &	sasa,
		Real const &	nbrs,
		Real const &	fa_atr,
		Real const &	hb_sc,
		Real const &	hb_bb_sc,
		Real const &	hb_bb,
		Real const &	bfac1,
		Real const &	bfac2,
		bool	is_sspaired
	)

References aa1_, aa2_, bfac1(), bfac2(), core::pose::Pose::chain(), chain1_, chain2_, core::conformation::Residue::chi(), chi1_, chi2_, fa_atr(), basic::get_pymol_chain(), hb_bb(), hb_bb_sc(), hb_sc(), core::conformation::Residue::name1(), nbrs(), core::conformation::Residue::nchi(), pdb_, protocols::motif_hash::real_to_uint8(), reset(), resi1_, resi2_, core::pose::Pose::residue(), rt(), sasa(), core::pose::Pose::secstruct(), ss1_, ss2_, and utility_exit_with_message.

Member Function Documentation

char protocols::motif_hash::ResPairMotif::aa1

(

)

const

References aa1_.

Referenced by protocols::motif_hash::dump_motif_pdbs(), protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs(), and protocols::motif_hash::MotifHash::stat_matching_motifs().

char protocols::motif_hash::ResPairMotif::aa2

(

)

const

References aa2_.

Referenced by protocols::motif_hash::dump_motif_pdbs(), protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs(), and protocols::motif_hash::MotifHash::stat_matching_motifs().

void protocols::motif_hash::ResPairMotif::addcount ( )

inline

References count_.

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Real protocols::motif_hash::ResPairMotif::bfac1

(

)

const

References bfac1_, and protocols::motif_hash::uint8_to_real().

Referenced by filter(), protocols::motif_hash::operator<<(), and ResPairMotif().

void protocols::motif_hash::ResPairMotif::bfac1

(

Real const &

bfac1

)

References bfac1_, and protocols::motif_hash::real_to_uint8().

Real protocols::motif_hash::ResPairMotif::bfac2

(

)

const

References bfac2_, and protocols::motif_hash::uint8_to_real().

Referenced by filter(), protocols::motif_hash::operator<<(), and ResPairMotif().

void protocols::motif_hash::ResPairMotif::bfac2

(

Real const &

bfac2

)

References bfac2_, and protocols::motif_hash::real_to_uint8().

Real protocols::motif_hash::ResPairMotif::chi11

(

)

const

References chi1_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Real protocols::motif_hash::ResPairMotif::chi12

(

)

const

References chi1_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Real protocols::motif_hash::ResPairMotif::chi13

(

)

const

References chi1_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Real protocols::motif_hash::ResPairMotif::chi14

(

)

const

References chi1_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Real protocols::motif_hash::ResPairMotif::chi21

(

)

const

References chi2_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Real protocols::motif_hash::ResPairMotif::chi22

(

)

const

References chi2_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Real protocols::motif_hash::ResPairMotif::chi23

(

)

const

References chi2_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Real protocols::motif_hash::ResPairMotif::chi24

(

)

const

References chi2_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs().

Size protocols::motif_hash::ResPairMotif::count ( ) const

inline

References count_.

Referenced by protocols::motif_hash::operator<<(), protocols::motif_hash::read_xfrag_binary(), and protocols::motif_hash::read_xfres_binary().

void protocols::motif_hash::ResPairMotif::count ( Size const &  count )

inline

References count(), and count_.

Referenced by count().

Real protocols::motif_hash::ResPairMotif::dist2

(

)

const

References basic::options::OptionKeys::mh::hash_cart_size, basic::options::option, rt6_, and protocols::motif_hash::uint16_to_real().

char protocols::motif_hash::ResPairMotif::dssp1

(

)

const

References ss1_.

Referenced by filter(), and protocols::motif_hash::MotifHash::stat_matching_motifs().

char protocols::motif_hash::ResPairMotif::dssp2

(

)

const

References ss2_.

Referenced by filter(), and protocols::motif_hash::MotifHash::stat_matching_motifs().

Real protocols::motif_hash::ResPairMotif::dump_aligned_motif	(	std::ostream &	out,
		Pose const &	pose1,
		Size const &	ir,
		Pose const &	pose2,
		Size const &	jr,
		int const &	num = 1
	)		const

References dump_aligned_motif_super().

Referenced by dump_aligned_motif(), and protocols::motif_hash::dump_matching_motifs().

Real protocols::motif_hash::ResPairMotif::dump_aligned_motif	(	std::ostream &	out,
		Pose const &	pose,
		Size const &	ir,
		Size const &	jr,
		int const &	num = 1
	)		const

References dump_aligned_motif().

Real protocols::motif_hash::ResPairMotif::dump_aligned_motif_break	(	std::ostream &	out,
		Pose const &	pose1,
		Size const &	ir,
		Pose const &	pose2,
		Size const &	jr,
		int const &	num = 1
	)		const

References protocols::motif_hash::align_motif_pose_break(), core::io::pdb::dump_pdb(), fill_pose_with_motif(), core::pose::Pose::n_residue(), and rms.

Real protocols::motif_hash::ResPairMotif::dump_aligned_motif_super	(	std::ostream &	out,
		Pose const &	pose1,
		Size const &	ir,
		Pose const &	pose2,
		Size const &	jr,
		int const &	num = 1
	)		const

References protocols::motif_hash::align_motif_pose_super(), core::io::pdb::dump_pdb(), fill_pose_with_motif(), core::pose::Pose::n_residue(), and rms.

Referenced by dump_aligned_motif().

void protocols::motif_hash::ResPairMotif::dump_pdb	(	std::string const &	fname,
		std::string const &	tag = "1"
	)		const

References utility::io::ozstream::close(), and out.

Referenced by protocols::motif_hash::dump_motif_pdbs().

void protocols::motif_hash::ResPairMotif::dump_pdb	(	std::ostream &	out,
		numeric::xyzTransform< Real > const &	xform,
		std::string const &	tag = "1"
	)		const

Real protocols::motif_hash::ResPairMotif::fa_atr

(

)

const

References fa_atr_, and protocols::motif_hash::uint8_to_real().

Referenced by filter(), protocols::motif_hash::operator<<(), and ResPairMotif().

void protocols::motif_hash::ResPairMotif::fa_atr

(

Real const &

fa_atr

)

References fa_atr_, and protocols::motif_hash::real_to_uint8().

void protocols::motif_hash::ResPairMotif::fill_pose_with_motif	(	Pose &	pose,
		int	ir = 1,
		int	jr = 2
	)		const

References aa1_, aa2_, chi1_, chi2_, core::pose::Pose::fold_tree(), jumps, core::pose::make_pose_from_sequence(), core::conformation::Residue::nchi(), core::pose::Pose::pdb_info(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), rt(), seq, core::pose::Pose::set_chi(), protocols::motif_hash::set_residue_pair_rt(), and protocols::motif_hash::uint8_to_real().

Referenced by dump_aligned_motif_break(), dump_aligned_motif_super(), and protocols::motif_hash::MotifRotamerSetOperation::MotifRotamerSetOperation().

bool protocols::motif_hash::ResPairMotif::filter

(

)

const

References aa1_, aa2_, bfac1(), bfac2(), chain1_, chain2_, dssp1(), dssp2(), fa_atr(), basic::options::OptionKeys::mh::hash_cart_size, hb_bb(), hb_bb_sc(), hb_sc(), option, basic::options::option, resi1_, resi2_, rt6_, sasa(), ss1(), ss1_, ss2(), ss2_, protocols::motif_hash::uint16_to_real(), and user.

Referenced by protocols::motif_hash::gather_simplemotifs().

Real protocols::motif_hash::ResPairMotif::hb_bb

(

)

const

References hb_bb_, and protocols::motif_hash::uint8_to_real().

Referenced by filter(), protocols::motif_hash::operator<<(), and ResPairMotif().

void protocols::motif_hash::ResPairMotif::hb_bb

(

Real const &

hb_bb

)

References hb_bb_, and protocols::motif_hash::real_to_uint8().

Real protocols::motif_hash::ResPairMotif::hb_bb_sc

(

)

const

References hb_bb_sc_, and protocols::motif_hash::uint8_to_real().

Referenced by filter(), protocols::motif_hash::operator<<(), and ResPairMotif().

void protocols::motif_hash::ResPairMotif::hb_bb_sc

(

Real const &

hb_bb_sc

)

References hb_bb_sc_, and protocols::motif_hash::real_to_uint8().

Real protocols::motif_hash::ResPairMotif::hb_sc

(

)

const

References hb_sc_, and protocols::motif_hash::uint8_to_real().

Referenced by filter(), protocols::motif_hash::operator<<(), and ResPairMotif().

void protocols::motif_hash::ResPairMotif::hb_sc

(

Real const &

hb_sc

)

References hb_sc_, and protocols::motif_hash::real_to_uint8().

HomogeneousTransform< Real > protocols::motif_hash::ResPairMotif::ht

(

)

const

References numeric::HomogeneousTransform< T >::from_euler_angles_deg(), rt(), and numeric::HomogeneousTransform< T >::set_point().

Referenced by reverse_in_place().

void protocols::motif_hash::ResPairMotif::ht

(

numeric::HomogeneousTransform< Real > const &

h

)

References numeric::HomogeneousTransform< T >::euler_angles_deg(), numeric::HomogeneousTransform< T >::px(), numeric::HomogeneousTransform< T >::py(), numeric::HomogeneousTransform< T >::pz(), rt(), utility_exit_with_message, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Real protocols::motif_hash::ResPairMotif::nbrs

(

)

const

References nbrs_, and protocols::motif_hash::uint8_to_real().

Referenced by protocols::motif_hash::operator<<(), and ResPairMotif().

void protocols::motif_hash::ResPairMotif::nbrs

(

Real const &

nbrs

)

References nbrs_, and protocols::motif_hash::real_to_uint8().

void protocols::motif_hash::ResPairMotif::print_header ( std::ostream &  out )

static

Referenced by protocols::motif_hash::dump_motif_pdbs().

void protocols::motif_hash::ResPairMotif::reset

(

void

)

References aa1_, aa2_, bfac1_, bfac2_, chain1_, chain2_, chi1_, chi2_, count_, fa_atr_, hb_bb_, hb_bb_sc_, hb_sc_, lg1x_, lg1y_, lg1z_, lg2x_, lg2y_, lg2z_, misc1_, misc2_, misc3_, misc4_, misc5_, nbrs_, pdb_, resi1_, resi2_, rt6_, sasa_, ss1_, and ss2_.

Referenced by ResPairMotif().

void protocols::motif_hash::ResPairMotif::reverse_in_place

(

)

References aa1_, aa2_, bfac1_, bfac2_, chain1_, chain2_, chi1_, chi2_, ht(), inverse(), resi1_, resi2_, ss1_, ss2_, and protocols::jd2::utility::pointer::swap().

Real6 protocols::motif_hash::ResPairMotif::rt

(

)

const

References rt6_, and protocols::motif_hash::uint16_to_real().

Referenced by protocols::motif_hash::MotifHash::add_motif(), protocols::motif_hash::MotifHash::add_motif_shift(), protocols::motif_hash::MotifHash::bin_index(), protocols::motif_hash::dump_matching_motifs(), fill_pose_with_motif(), protocols::motif_hash::MotifHash::find_motifs_with_radius(), ht(), protocols::motif_hash::operator<<(), ResPairMotif(), and protocols::motif_hash::MotifHash::stat_matching_motifs().

void protocols::motif_hash::ResPairMotif::rt

(

Real6 const &

rt

)

References protocols::motif_hash::real_to_uint16(), and rt6_.

Real protocols::motif_hash::ResPairMotif::sasa

(

)

const

References sasa_, and protocols::motif_hash::uint8_to_real().

Referenced by filter(), protocols::motif_hash::operator<<(), and ResPairMotif().

void protocols::motif_hash::ResPairMotif::sasa

(

Real const &

sasa

)

References protocols::motif_hash::real_to_uint8(), and sasa_.

char protocols::motif_hash::ResPairMotif::ss1

(

)

const

References ss1_, and utility_exit_with_message.

Referenced by protocols::motif_hash::dump_motif_pdbs(), filter(), protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs(), and protocols::motif_hash::MotifHash::stat_matching_motifs().

char protocols::motif_hash::ResPairMotif::ss2

(

)

const

References ss2_, and utility_exit_with_message.

Referenced by protocols::motif_hash::dump_motif_pdbs(), filter(), protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs(), and protocols::motif_hash::MotifHash::stat_matching_motifs().

Friends And Related Function Documentation

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

friend

Member Data Documentation

char protocols::motif_hash::ResPairMotif::aa1_

private

Referenced by aa1(), fill_pose_with_motif(), filter(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), and reverse_in_place().

char protocols::motif_hash::ResPairMotif::aa2_

private

Referenced by aa2(), fill_pose_with_motif(), filter(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), and reverse_in_place().

uint8_t protocols::motif_hash::ResPairMotif::bfac1_

private

Referenced by bfac1(), reset(), and reverse_in_place().

uint8_t protocols::motif_hash::ResPairMotif::bfac2_

private

Referenced by bfac2(), reset(), and reverse_in_place().

char protocols::motif_hash::ResPairMotif::chain1_

private

Referenced by filter(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), and reverse_in_place().

char protocols::motif_hash::ResPairMotif::chain2_

private

Referenced by filter(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), and reverse_in_place().

utility::fixedsizearray1<uint8_t,4> protocols::motif_hash::ResPairMotif::chi1_

private

Referenced by chi11(), chi12(), chi13(), chi14(), fill_pose_with_motif(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), and reverse_in_place().

utility::fixedsizearray1<uint8_t,4> protocols::motif_hash::ResPairMotif::chi2_

private

Referenced by chi21(), chi22(), chi23(), chi24(), fill_pose_with_motif(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), and reverse_in_place().

uint8_t protocols::motif_hash::ResPairMotif::count_

private

Referenced by addcount(), count(), and reset().

uint8_t protocols::motif_hash::ResPairMotif::fa_atr_

private

Referenced by fa_atr(), and reset().

uint8_t protocols::motif_hash::ResPairMotif::hb_bb_

private

Referenced by hb_bb(), and reset().

uint8_t protocols::motif_hash::ResPairMotif::hb_bb_sc_

private

Referenced by hb_bb_sc(), and reset().

uint8_t protocols::motif_hash::ResPairMotif::hb_sc_

private

Referenced by hb_sc(), and reset().

uint16_t protocols::motif_hash::ResPairMotif::lg1x_

private

Referenced by reset().

uint16_t protocols::motif_hash::ResPairMotif::lg1y_

private

Referenced by reset().

uint16_t protocols::motif_hash::ResPairMotif::lg1z_

private

Referenced by reset().

uint16_t protocols::motif_hash::ResPairMotif::lg2x_

private

Referenced by reset().

uint16_t protocols::motif_hash::ResPairMotif::lg2y_

private

Referenced by reset().

uint16_t protocols::motif_hash::ResPairMotif::lg2z_

private

Referenced by reset().

uint8_t protocols::motif_hash::ResPairMotif::misc1_

private

Referenced by reset().

uint8_t protocols::motif_hash::ResPairMotif::misc2_

private

Referenced by reset().

uint8_t protocols::motif_hash::ResPairMotif::misc3_

private

Referenced by reset().

uint8_t protocols::motif_hash::ResPairMotif::misc4_

private

Referenced by reset().

uint8_t protocols::motif_hash::ResPairMotif::misc5_

private

Referenced by reset().

uint8_t protocols::motif_hash::ResPairMotif::nbrs_

private

Referenced by nbrs(), and reset().

utility::fixedsizearray1<unsigned char,8> protocols::motif_hash::ResPairMotif::pdb_

Referenced by protocols::motif_hash::dump_motif_pdbs(), protocols::motif_hash::operator<<(), reset(), and ResPairMotif().

uint16_t protocols::motif_hash::ResPairMotif::resi1_

Referenced by protocols::motif_hash::dump_motif_pdbs(), filter(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), and reverse_in_place().

uint16_t protocols::motif_hash::ResPairMotif::resi2_

Referenced by protocols::motif_hash::dump_motif_pdbs(), filter(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), and reverse_in_place().

utility::fixedsizearray1<uint16_t,6> protocols::motif_hash::ResPairMotif::rt6_

private

Referenced by dist2(), filter(), reset(), rt(), and protocols::motif_hash::Xfrag::rt6().

uint8_t protocols::motif_hash::ResPairMotif::sasa_

private

Referenced by reset(), and sasa().

char protocols::motif_hash::ResPairMotif::ss1_

private

Referenced by dssp1(), filter(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), reverse_in_place(), and ss1().

char protocols::motif_hash::ResPairMotif::ss2_

private

Referenced by dssp2(), filter(), protocols::motif_hash::operator<<(), reset(), ResPairMotif(), reverse_in_place(), and ss2().

---

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

• src/protocols/motif_hash/motif_hash_stuff.hh
• src/protocols/motif_hash/motif_hash_stuff.cc