protocols::motif_hash Namespace Reference

Classes
class	MotifHash
class	MotifHashManager
struct	MotifHit
class	MotifHits
class	MotifRotamerSetOperation
struct	MyHash
struct	MyPred
class	ResPairMotif
class	ResPairMotifs
class	XformScore
class	Xfrag
class	XfragSet
class	Xfres

Typedefs
typedef numeric::xyzVector < core::Real >	Vec
typedef numeric::xyzMatrix < core::Real >	Mat
typedef numeric::xyzTransform < core::Real >	Xform
typedef utility::fixedsizearray1 < float, 20 >	float20
typedef utility::fixedsizearray1 < float, 9 >	float9
typedef boost::unordered_set < ResPairMotif, MyHash, MyPred >	MotifSet
typedef utility::pointer::owning_ptr < XfragSet >	XfragSetOP
typedef utility::pointer::owning_ptr < XfragSet const >	XfragSetCOP
typedef utility::pointer::access_ptr < XfragSet const >	XfragSetCAP
typedef utility::pointer::owning_ptr < XformScore >	XformScoreOP
typedef utility::pointer::owning_ptr < XformScore const >	XformScoreCOP
typedef utility::pointer::access_ptr < XformScore const >	XformScoreCAP
typedef utility::pointer::owning_ptr < MotifHash >	MotifHashOP
typedef utility::pointer::owning_ptr < MotifHash const >	MotifHashCOP
typedef utility::pointer::access_ptr < MotifHash const >	MotifHashCAP
typedef utility::vector1< bool >	Bools
typedef utility::pointer::owning_ptr < MotifRotamerSetOperation >	MotifRotamerSetOperationOP
typedef utility::pointer::owning_ptr < MotifRotamerSetOperation const >	MotifRotamerSetOperationCOP

Functions
Mat	random_rotation ()
std::string	tag_from_pdb_fname (std::string const &fname0)
std::ostream &	operator<< (std::ostream &out, Real6 const &r6)
Real	rt6_rt6_bb_dis2_explicit_stupid (Real6 const &x1, Real6 const &x2)
Real	rt6_rt6_dis2 (Real6 const &x1, Real6 const &x2, Real const lever)
Real	rt6_rt6_bb_dis2 (Real6 const &x1, Real6 const &x2)
Real6	inverse_rt6 (Real6 const &rt)
Real6	rt_to_real6 (core::kinematics::RT const &rt)
core::kinematics::RT	real6_to_rt (Real6 const &rt6)
Real6	get_residue_pair_rt6 (Pose const &pose1, Size ir, Pose const &pose2, Size jr)
Real6	get_residue_pair_rt6 (Pose const &pose, Size ir, Size jr)
void	set_residue_pair_rt (Real6 const &rt6, Pose &pose, Size ir, Size jr)
Real	uint16_to_real (uint16_t const &val, Real const &lb, Real const &ub)
uint16_t	real_to_uint16 (Real const &val, Real const &lb, Real const &ub)
Real	uint8_to_real (uint8_t const &val, Real const &lb, Real const &ub)
uint8_t	real_to_uint8 (Real const &val, Real const &lb, Real const &ub)
vector1< Real >	get_sasa (Pose const &pose, Real const &probesize)
vector1< Real >	get_nbrs (Pose const &pose)
void	HACK_dump_helix (core::pose::Pose const &pose, string fname, int beg, int end)
int	HACK_dump_helices (core::pose::Pose const &pose, string tag, int nres, int minlen=10)
utility::fixedsizearray1< Real, 6 >	get_bins (Real c, Real a)
Real	align_motif_pose_super (Pose &pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr)
Real	align_motif_pose_break (Pose &pose, Pose const &paln1, Size const &ir, Pose const &paln2, Size const &jr)
std::ostream &	operator<< (std::ostream &out, ResPairMotif const &x)
bool	write_motifs_binary (std::ostream &out, ResPairMotifs const &motifs)
bool	write_motifs_binary (std::string const &fname, ResPairMotifs const &motifs)
bool	read_motifs_binary (std::istream &in, ResPairMotifs &motifs)
bool	read_motifs_binary (std::string const &fname, ResPairMotifs &motifs)
bool	read_motifs_binary (vector1< string > const &fnames, ResPairMotifs &motifs)
void	load_motifs (vector1< string > const &fnames, ResPairMotifs &motifs)
void	load_motifs (string const &fname, ResPairMotifs &motifs)
std::ostream &	operator<< (std::ostream &out, Xfres const &x)
std::istream &	operator>> (std::istream &in, Xfres &x)
bool	read_xfres_binary (string const &fname, vector1< Xfres > &xfres)
bool	read_xfres_binary (std::istream &in, vector1< Xfres > &xfres)
bool	write_xfres_binary (std::ostream &out, vector1< Xfres > const &xfres)
bool	write_xfres_binary (string const &fname, vector1< Xfres > const &xfres)
bool	read_xfres_binary (vector1< string > const &fnames, vector1< Xfres > &xfres)
std::ostream &	operator<< (std::ostream &out, Xfrag const &x)
std::istream &	operator>> (std::istream &in, Xfrag &x)
bool	read_xfrag_binary (string const &fname, vector1< Xfrag > &xfrag)
bool	read_xfrag_binary (std::istream &in, vector1< Xfrag > &xfrag)
bool	write_xfrag_binary (std::ostream &out, vector1< Xfrag > const &xfrag)
bool	write_xfrag_binary (string const &fname, vector1< Xfrag > const &xfrag)
bool	read_xfrag_binary (vector1< string > const &fnames, vector1< Xfrag > &xfrag)
bool	read_xfrag_binary (string const &fname, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
bool	read_xfrag_binary (std::istream &in, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
bool	write_xfrag_binary (std::ostream &out, vector1< Xfrag > const &xfrag, vector1< Xfres > const &xfres)
bool	write_xfrag_binary (string const &fname, vector1< Xfrag > const &xfrag, vector1< Xfres > const &xfres)
bool	read_xfrag_binary (vector1< string > const &fnames, vector1< Xfrag > &xfrag, vector1< Xfres > &xfres)
std::ostream &	operator<< (std::ostream &out, MotifHash const &x)
void	print_motifs (std::ostream &out)
void	merge_motifs ()
void	dump_motif_pdbs ()
void	harvest_scores ()
void	print_scores ()
void	dump_matching_motifs ()
void	filter_motifs (ResPairMotifs const &motifs_in, ResPairMotifs &motifs_out)
Real6 &	reframe_rt_centered (Real6 &rt)
std::ostream &	operator<< (std::ostream &out, XformScore const &xh)
bool	gather_simplemotifs (ResPairMotifs &motifs, string const &tag, Pose const &pose, core::scoring::dssp::Dssp &dssp, Size const &ir, core::scoring::EnergyEdge const &edge, vector1< Real > const &occupancy, vector1< Real > const &bfactors, vector1< Real > const &rsd_sasa, vector1< Real > const &nbrs, int &nbad, int &nbadbfac, int &nbadocc, int &nbadiface, int &nbaddist)
void	harvest_motifs ()
XformScore *	get_xform_score_from_file (XformScore *xs, vector1< string > const &datfiles, XformScore *defaultval=NULL)
std::ostream &	operator<< (std::ostream &out, MotifHit const &h)
std::ostream &	operator<< (std::ostream &out, MotifHits const &h)
int	base_dump_matching_motifs (Pose const &pose1, Pose const &pose2, std::ostream &out, int &count, bool print, MotifHits const &hits)
static float	fasterlog (float x)
std::istream &	operator>> (std::istream &in, ResPairMotif &x)
std::istream &	operator>> (std::istream &in, MotifHash &x)

Variables
static basic::Tracer	TR ("protocols.motif_hash")

Typedef Documentation

typedef utility::vector1<bool> protocols::motif_hash::Bools

typedef utility::fixedsizearray1<float,20> protocols::motif_hash::float20

typedef utility::fixedsizearray1<float,9> protocols::motif_hash::float9

typedef numeric::xyzMatrix< core::Real > protocols::motif_hash::Mat

typedef utility::pointer::access_ptr< MotifHash const > protocols::motif_hash::MotifHashCAP

typedef utility::pointer::owning_ptr< MotifHash const > protocols::motif_hash::MotifHashCOP

typedef utility::pointer::owning_ptr< MotifHash > protocols::motif_hash::MotifHashOP

typedef utility::pointer::owning_ptr<MotifRotamerSetOperation const> protocols::motif_hash::MotifRotamerSetOperationCOP

typedef utility::pointer::owning_ptr<MotifRotamerSetOperation > protocols::motif_hash::MotifRotamerSetOperationOP

typedef boost::unordered_set<ResPairMotif,MyHash,MyPred> protocols::motif_hash::MotifSet

typedef numeric::xyzVector< core::Real > protocols::motif_hash::Vec

typedef numeric::xyzTransform<core::Real> protocols::motif_hash::Xform

typedef utility::pointer::access_ptr< XformScore const > protocols::motif_hash::XformScoreCAP

typedef utility::pointer::owning_ptr< XformScore const > protocols::motif_hash::XformScoreCOP

typedef utility::pointer::owning_ptr< XformScore > protocols::motif_hash::XformScoreOP

typedef utility::pointer::access_ptr< XfragSet const > protocols::motif_hash::XfragSetCAP

typedef utility::pointer::owning_ptr< XfragSet const > protocols::motif_hash::XfragSetCOP

typedef utility::pointer::owning_ptr< XfragSet > protocols::motif_hash::XfragSetOP

Function Documentation

Real protocols::motif_hash::align_motif_pose_break	(	Pose &	pose,
		Pose const &	paln1,
		Size const &	ir,
		Pose const &	paln2,
		Size const &	jr
	)

References core::scoring::bb_rmsd(), protocols::loops::start, protocols::sic_dock::xform_pose(), and core::pose::Pose::xyz().

Referenced by protocols::motif_hash::ResPairMotif::dump_aligned_motif_break().

Real protocols::motif_hash::align_motif_pose_super	(	Pose &	pose,
		Pose const &	paln1,
		Size const &	ir,
		Pose const &	paln2,
		Size const &	jr
	)

References BOGUS_ATOM_ID, core::pose::initialize_atomid_map(), ref, core::pose::Pose::residue(), and core::scoring::superimpose_pose().

Referenced by protocols::motif_hash::ResPairMotif::dump_aligned_motif_super(), protocols::motif_hash::MotifHash::get_matching_motifs(), and protocols::motif_hash::MotifRotamerSetOperation::MotifRotamerSetOperation().

int protocols::motif_hash::base_dump_matching_motifs	(	Pose const &	pose1,
		Pose const &	pose2,
		std::ostream &	out,
		int &	count,
		bool	print,
		MotifHits const &	hits
	)

References cout.

Referenced by protocols::motif_hash::MotifHash::dump_matching_motifs().

void protocols::motif_hash::dump_matching_motifs

(

)

References protocols::motif_hash::MotifHash::cart_size(), core::import_pose::centroid_pose_from_pdb(), core::pose::Pose::chain(), utility::io::ozstream::close(), cout, numeric::xyzVector< class >::distance_squared(), dssp, protocols::motif_hash::ResPairMotif::dump_aligned_motif(), mh::dump_matching_motifs, mh::dump_matching_motifs_cutoff, utility::file_basename(), get_residue_pair_rt6(), protocols::motif_hash::MotifHash::hasher(), mh::input_motifs, core::scoring::dssp::Dssp::insert_edge_ss_into_pose(), key, load_motifs(), mh, protocols::motif_hash::MotifHash::motif_hash_, motifs, o, option, numeric::geometry::hashing::SixDCoordinateBinner::radial_bin_index(), protocols::motif_hash::ResPairMotif::rt(), rt6_rt6_bb_dis2(), mh::score_across_chains_only, core::pose::Pose::total_residue(), numeric::geometry::hashing::SixDCoordinateBinner::tree_init(), and core::pose::Pose::xyz().

void protocols::motif_hash::dump_motif_pdbs

(

)

References protocols::motif_hash::ResPairMotif::aa1(), protocols::motif_hash::ResPairMotif::aa2(), mh::dump_motif_pdbs, mh::dump_motif_pdbs_min_counts, protocols::motif_hash::ResPairMotif::dump_pdb(), key, l, load_motifs(), mh, mh::motif_out_file, motifs, option, protocols::motif_hash::ResPairMotif::pdb_, protocols::motif_hash::ResPairMotif::print_header(), protocols::motif_hash::ResPairMotif::resi1_, protocols::motif_hash::ResPairMotif::resi2_, protocols::motif_hash::ResPairMotif::ss1(), protocols::motif_hash::ResPairMotif::ss2(), and user.

static float protocols::motif_hash::fasterlog ( float  x )

inlinestatic

void protocols::motif_hash::filter_motifs	(	ResPairMotifs const &	motifs_in,
		ResPairMotifs &	motifs_out
	)

Referenced by load_motifs().

bool protocols::motif_hash::gather_simplemotifs	(	ResPairMotifs &	motifs,
		string const &	tag,
		Pose const &	pose,
		core::scoring::dssp::Dssp &	dssp,
		Size const &	ir,
		core::scoring::EnergyEdge const &	edge,
		vector1< Real > const &	occupancy,
		vector1< Real > const &	bfactors,
		vector1< Real > const &	rsd_sasa,
		vector1< Real > const &	nbrs,
		int &	nbad,
		int &	nbadbfac,
		int &	nbadocc,
		int &	nbadiface,
		int &	nbaddist
	)

References core::scoring::calc_per_atom_sasa(), core::pose::Pose::chain(), mh::filter::coorderr, fa_atr, core::scoring::fa_atr, protocols::motif_hash::ResPairMotif::filter(), mh::filter::filter_harvest, get_residue_pair_rt6(), hb_bb, hb_bb_sc, hb_sc, core::scoring::hbond_bb_sc, core::scoring::hbond_lr_bb, core::scoring::hbond_sc, core::scoring::hbond_sr_bb, core::scoring::dssp::Dssp::in_paired_strands(), core::pose::initialize_atomid_map(), core::conformation::Residue::is_protein(), mh::filter::maxdist2, core::conformation::Residue::natoms(), option, core::pose::Pose::residue(), sasa, and mh::filter::seqsep.

Referenced by harvest_motifs().

utility::fixedsizearray1<Real,6> protocols::motif_hash::get_bins	(	Real	c,
		Real	a
	)

vector1<Real> protocols::motif_hash::get_nbrs

(

Pose const &

pose

)

References numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::is_protein(), core::pose::Pose::n_residue(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by harvest_motifs().

Real6 protocols::motif_hash::get_residue_pair_rt6	(	Pose const &	pose1,
		Size	ir,
		Pose const &	pose2,
		Size	jr
	)

References cout, numeric::xyzVector< class >::x(), core::pose::Pose::xyz(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by dump_matching_motifs(), gather_simplemotifs(), protocols::motif_hash::MotifHash::get_matching_motifs(), and protocols::motif_hash::MotifHash::stat_matching_motifs().

Real6 protocols::motif_hash::get_residue_pair_rt6	(	Pose const &	pose,
		Size	ir,
		Size	jr
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::get_stub_transform(), and rt_to_real6().

vector1<Real> protocols::motif_hash::get_sasa	(	Pose const &	pose,
		Real const &	probesize
	)

References core::scoring::calc_per_atom_sasa(), core::pose::Pose::n_residue(), and utility_exit_with_message.

Referenced by harvest_motifs().

XformScore* protocols::motif_hash::get_xform_score_from_file	(	XformScore *	xs,
		vector1< string > const &	datfiles,
		XformScore *	defaultval = NULL
	)

References protocols::motif_hash::XformScore::read_binary(), s, utility_exit_with_message, and protocols::motif_hash::XformScore::XformScore().

Referenced by protocols::motif_hash::MotifHashManager::xform_score_ee_from_cli(), protocols::motif_hash::MotifHashManager::xform_score_eh_from_cli(), protocols::motif_hash::MotifHashManager::xform_score_from_cli(), protocols::motif_hash::MotifHashManager::xform_score_he_from_cli(), protocols::motif_hash::MotifHashManager::xform_score_hh_from_cli(), and protocols::motif_hash::MotifHashManager::xform_score_sspair_from_cli().

int protocols::motif_hash::HACK_dump_helices	(	core::pose::Pose const &	pose,
		string	tag,
		int	nres,
		int	minlen = 10
	)

References core::pose::Pose::chain(), cout, HACK_dump_helix(), and core::pose::Pose::secstruct().

void protocols::motif_hash::HACK_dump_helix	(	core::pose::Pose const &	pose,
		string	fname,
		int	beg,
		int	end
	)

References utility::io::ozstream::close(), cout, core::io::pdb::dump_pdb_residue(), out, and core::pose::Pose::residue().

Referenced by HACK_dump_helices().

void protocols::motif_hash::harvest_motifs

(

)

References core::graph::Node::const_upper_edge_list_end(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), dssp, core::pose::Pose::energies(), utility::file::file_exists(), gather_simplemotifs(), get_nbrs(), core::graph::Edge::get_node(), get_sasa(), core::scoring::getScoreFunction(), mh::harvest_motifs, mh::harvest_motifs_min_hh_ends, core::scoring::methods::EnergyMethodOptions::hbond_options(), protocols::abinitio::abscript::I, core::scoring::dssp::Dssp::insert_edge_ss_into_pose(), core::conformation::Residue::is_protein(), basic::options::OptionKeys::mh::motif_out_file, motif_out_file, motifs, out::file::o, occupancy, basic::options::option, option, protocols::sic_dock::read_biounit(), core::pose::Pose::residue(), sf, tag_from_pdb_fname(), user, utility_exit_with_message, and write_motifs_binary().

void protocols::motif_hash::harvest_scores

(

)

References protocols::motif_hash::XformScore::add_xform_count(), mh::harvest_scores, load_motifs(), mh::motif_out_file, motifs, and option.

Real6 protocols::motif_hash::inverse_rt6

(

Real6 const &

rt

)

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

void protocols::motif_hash::load_motifs	(	vector1< string > const &	fnames,
		ResPairMotifs &	motifs
	)

References basic::options::OptionKeys::mh::filter::filter_io, filter_motifs(), protocols::motif_hash::ResPairMotifs::filter_structurally_similar_motifs(), basic::options::OptionKeys::mh::merge_similar_motifs, option, read_motifs_binary(), user, and utility_exit_with_message.

Referenced by dump_matching_motifs(), dump_motif_pdbs(), harvest_scores(), load_motifs(), merge_motifs(), protocols::motif_hash::MotifHashManager::motif_hash_from_cli(), and print_motifs().

void protocols::motif_hash::load_motifs	(	string const &	fname,
		ResPairMotifs &	motifs
	)

References load_motifs().

void protocols::motif_hash::merge_motifs

(

)

References load_motifs(), mh::merge_motifs, basic::options::OptionKeys::mh::motif_out_file, mh::motif_out_file, motifs, basic::options::option, option, user, utility_exit_with_message, and write_motifs_binary().

std::ostream& protocols::motif_hash::operator<<	(	std::ostream &	out,
		Real6 const &	r6
	)

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

References protocols::motif_hash::ResPairMotif::aa1_, protocols::motif_hash::ResPairMotif::aa2_, protocols::motif_hash::ResPairMotif::bfac1(), protocols::motif_hash::ResPairMotif::bfac2(), protocols::motif_hash::ResPairMotif::chain1_, protocols::motif_hash::ResPairMotif::chain2_, protocols::motif_hash::ResPairMotif::chi1_, protocols::motif_hash::ResPairMotif::chi2_, protocols::motif_hash::ResPairMotif::count(), protocols::motif_hash::ResPairMotif::fa_atr(), protocols::motif_hash::ResPairMotif::hb_bb(), protocols::motif_hash::ResPairMotif::hb_bb_sc(), protocols::motif_hash::ResPairMotif::hb_sc(), protocols::abinitio::abscript::I, protocols::motif_hash::ResPairMotif::nbrs(), protocols::motif_hash::ResPairMotif::pdb_, protocols::motif_hash::ResPairMotif::resi1_, protocols::motif_hash::ResPairMotif::resi2_, protocols::motif_hash::ResPairMotif::rt(), protocols::motif_hash::ResPairMotif::sasa(), protocols::motif_hash::ResPairMotif::ss1_, protocols::motif_hash::ResPairMotif::ss2_, and uint8_to_real().

std::ostream & protocols::motif_hash::operator<<	(	std::ostream &	out,
		Xfres const &	x
	)

References protocols::motif_hash::Xfres::aa(), protocols::motif_hash::Xfres::chi1(), protocols::motif_hash::Xfres::chi2(), protocols::motif_hash::Xfres::chi3(), protocols::motif_hash::Xfres::chi4(), protocols::motif_hash::Xfres::omg(), protocols::motif_hash::Xfres::phi(), protocols::motif_hash::Xfres::psi(), and protocols::motif_hash::Xfres::ss().

std::ostream & protocols::motif_hash::operator<<	(	std::ostream &	out,
		Xfrag const &	x
	)

References protocols::motif_hash::Xfrag::bfac(), protocols::motif_hash::Xfrag::burial(), protocols::motif_hash::Xfrag::ex1(), protocols::motif_hash::Xfrag::ex2(), protocols::motif_hash::Xfrag::ex3(), protocols::motif_hash::Xfrag::ex4(), protocols::abinitio::abscript::I, protocols::motif_hash::Xfrag::position(), protocols::motif_hash::Xfrag::rt6(), protocols::motif_hash::Xfrag::size(), and protocols::motif_hash::Xfrag::sscomp().

std::ostream & protocols::motif_hash::operator<<	(	std::ostream &	out,
		MotifHash const &	x
	)

References numeric::geometry::hashing::SixDCoordinateBinner::bin_widths(), numeric::geometry::hashing::SixDCoordinateBinner::bounding_box(), numeric::geometry::hashing::SixDCoordinateBinner::euler_offsets(), protocols::motif_hash::MotifHash::hasher_, and protocols::motif_hash::MotifHash::motif_hash_.

std::ostream & protocols::motif_hash::operator<<	(	std::ostream &	out,
		XformScore const &	xh
	)

References protocols::motif_hash::XformScore::angle_resl_, protocols::motif_hash::XformScore::cart_resl_, protocols::motif_hash::XformScore::cart_size_, protocols::motif_hash::XformScore::num_bins(), protocols::motif_hash::XformScore::num_samples(), and protocols::motif_hash::XformScore::print_quantiles().

std::ostream & protocols::motif_hash::operator<<	(	std::ostream &	out,
		MotifHit const &	h
	)

References protocols::abinitio::abscript::I, protocols::motif_hash::MotifHit::motif, protocols::motif_hash::MotifHit::residue1, protocols::motif_hash::MotifHit::residue2, and protocols::motif_hash::MotifHit::score.

std::ostream & protocols::motif_hash::operator<<	(	std::ostream &	out,
		MotifHits const &	h
	)

References protocols::motif_hash::MotifHits::compute_metrics(), protocols::motif_hash::MotifHits::paircover, protocols::motif_hash::MotifHits::rescover, and protocols::motif_hash::MotifHits::total_score.

std::istream& protocols::motif_hash::operator>>	(	std::istream &	in,
		ResPairMotif &	x
	)

std::istream& protocols::motif_hash::operator>>	(	std::istream &	in,
		MotifHash &	x
	)

std::istream & protocols::motif_hash::operator>>	(	std::istream &	in,
		Xfres &	x
	)

References protocols::motif_hash::Xfres::aa(), protocols::motif_hash::Xfres::chi1(), protocols::motif_hash::Xfres::chi2(), protocols::motif_hash::Xfres::chi3(), protocols::motif_hash::Xfres::chi4(), protocols::motif_hash::Xfres::omg(), protocols::motif_hash::Xfres::phi(), protocols::motif_hash::Xfres::psi(), protocols::motif_hash::Xfres::ss(), and utility_exit_with_message.

std::istream & protocols::motif_hash::operator>>	(	std::istream &	in,
		Xfrag &	x
	)

References protocols::motif_hash::Xfrag::bfac(), protocols::motif_hash::Xfrag::burial(), protocols::motif_hash::Xfrag::ex1(), protocols::motif_hash::Xfrag::ex2(), protocols::motif_hash::Xfrag::ex3(), protocols::motif_hash::Xfrag::ex4(), protocols::motif_hash::Xfrag::position(), protocols::motif_hash::Xfrag::size(), protocols::motif_hash::Xfrag::sscomp(), and utility_exit_with_message.

void protocols::motif_hash::print_motifs

(

std::ostream &

out

)

References load_motifs(), motifs, option, and mh::print_motifs.

void protocols::motif_hash::print_scores

(

)

References cout, option, mh::print_scores, and protocols::motif_hash::XformScore::read_binary().

Mat protocols::motif_hash::random_rotation

(

)

References protocols::match::upstream::b, c, numeric::xyzMatrix< class >::cols(), and uniform().

bool protocols::motif_hash::read_motifs_binary	(	std::istream &	in,
		ResPairMotifs &	motifs
	)

References basic::options::OptionKeys::mh::generate_reverse_motifs, and option.

Referenced by load_motifs(), and read_motifs_binary().

bool protocols::motif_hash::read_motifs_binary	(	std::string const &	fname,
		ResPairMotifs &	motifs
	)

References utility::io::izstream::good(), in, and read_motifs_binary().

bool protocols::motif_hash::read_motifs_binary	(	vector1< string > const &	fnames,
		ResPairMotifs &	motifs
	)

References basic::options::OptionKeys::mh::ignore_io_errors, option, read_motifs_binary(), and utility_exit_with_message.

bool protocols::motif_hash::read_xfrag_binary	(	string const &	fname,
		vector1< Xfrag > &	xfrag
	)

References utility::io::izstream::good(), and in.

Referenced by read_xfrag_binary().

bool protocols::motif_hash::read_xfrag_binary	(	std::istream &	in,
		vector1< Xfrag > &	xfrag
	)

bool protocols::motif_hash::read_xfrag_binary	(	vector1< string > const &	fnames,
		vector1< Xfrag > &	xfrag
	)

References protocols::motif_hash::ResPairMotif::count(), and read_xfrag_binary().

bool protocols::motif_hash::read_xfrag_binary	(	string const &	fname,
		vector1< Xfrag > &	xfrag,
		vector1< Xfres > &	xfres
	)

References utility::io::izstream::good(), in, and read_xfrag_binary().

bool protocols::motif_hash::read_xfrag_binary	(	std::istream &	in,
		vector1< Xfrag > &	xfrag,
		vector1< Xfres > &	xfres
	)

References read_xfrag_binary(), and read_xfres_binary().

bool protocols::motif_hash::read_xfrag_binary	(	vector1< string > const &	fnames,
		vector1< Xfrag > &	xfrag,
		vector1< Xfres > &	xfres
	)

References protocols::motif_hash::ResPairMotif::count(), and read_xfrag_binary().

bool protocols::motif_hash::read_xfres_binary	(	string const &	fname,
		vector1< Xfres > &	xfres
	)

References utility::io::izstream::good(), and in.

Referenced by read_xfrag_binary(), and read_xfres_binary().

bool protocols::motif_hash::read_xfres_binary	(	std::istream &	in,
		vector1< Xfres > &	xfres
	)

bool protocols::motif_hash::read_xfres_binary	(	vector1< string > const &	fnames,
		vector1< Xfres > &	xfres
	)

References protocols::motif_hash::ResPairMotif::count(), and read_xfres_binary().

core::kinematics::RT protocols::motif_hash::real6_to_rt

(

Real6 const &

rt6

)

References numeric::HomogeneousTransform< T >::from_euler_angles_deg(), t, numeric::HomogeneousTransform< T >::xaxis(), numeric::HomogeneousTransform< T >::yaxis(), and numeric::HomogeneousTransform< T >::zaxis().

Referenced by set_residue_pair_rt().

uint16_t protocols::motif_hash::real_to_uint16	(	Real const &	val,
		Real const &	lb,
		Real const &	ub
	)

References max(), MAX_UINT16, and min.

Referenced by protocols::motif_hash::Xfres::omg(), protocols::motif_hash::Xfres::phi(), protocols::motif_hash::Xfres::psi(), protocols::motif_hash::ResPairMotif::rt(), and protocols::motif_hash::Xfrag::rt6().

uint8_t protocols::motif_hash::real_to_uint8	(	Real const &	val,
		Real const &	lb,
		Real const &	ub
	)

References max(), MAX_UINT8, and min.

Referenced by protocols::motif_hash::Xfrag::bfac(), protocols::motif_hash::ResPairMotif::bfac1(), protocols::motif_hash::ResPairMotif::bfac2(), protocols::motif_hash::Xfrag::burial(), protocols::motif_hash::Xfres::chi1(), protocols::motif_hash::Xfres::chi2(), protocols::motif_hash::Xfres::chi3(), protocols::motif_hash::Xfres::chi4(), protocols::motif_hash::Xfrag::ex1(), protocols::motif_hash::Xfrag::ex2(), protocols::motif_hash::Xfrag::ex3(), protocols::motif_hash::Xfrag::ex4(), protocols::motif_hash::ResPairMotif::fa_atr(), protocols::motif_hash::ResPairMotif::hb_bb(), protocols::motif_hash::ResPairMotif::hb_bb_sc(), protocols::motif_hash::ResPairMotif::hb_sc(), protocols::motif_hash::ResPairMotif::nbrs(), protocols::motif_hash::ResPairMotif::ResPairMotif(), and protocols::motif_hash::ResPairMotif::sasa().

Real6& protocols::motif_hash::reframe_rt_centered

(

Real6 &

rt

)

Real protocols::motif_hash::rt6_rt6_bb_dis2	(	Real6 const &	x1,
		Real6 const &	x2
	)

References rt6_rt6_dis2().

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

Real protocols::motif_hash::rt6_rt6_bb_dis2_explicit_stupid	(	Real6 const &	x1,
		Real6 const &	x2
	)

References protocols::frag_picker::CA, protocols::frag_picker::CB, distance_squared(), numeric::HomogeneousTransform< T >::from_euler_angles_deg(), protocols::forge::build::SegmentInsertConnectionScheme::N, protocols::comparative_modeling::features::O, and numeric::HomogeneousTransform< T >::set_point().

Real protocols::motif_hash::rt6_rt6_dis2	(	Real6 const &	x1,
		Real6 const &	x2,
		Real const	lever
	)

References numeric::xyzVector< class >::distance_squared(), numeric::HomogeneousTransform< T >::from_euler_angles_deg(), numeric::HomogeneousTransform< T >::inverse(), numeric::HomogeneousTransform< T >::xx(), numeric::HomogeneousTransform< T >::yy(), and numeric::HomogeneousTransform< T >::zz().

Referenced by rt6_rt6_bb_dis2().

Real6 protocols::motif_hash::rt_to_real6

(

core::kinematics::RT const &

rt

)

References core::kinematics::RT::get_rotation(), core::kinematics::RT::get_translation(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by get_residue_pair_rt6().

void protocols::motif_hash::set_residue_pair_rt	(	Real6 const &	rt6,
		Pose &	pose,
		Size	ir,
		Size	jr
	)

References core::pose::Pose::conformation(), real6_to_rt(), and core::conformation::Conformation::set_stub_transform().

Referenced by protocols::motif_hash::ResPairMotif::fill_pose_with_motif().

std::string protocols::motif_hash::tag_from_pdb_fname

(

std::string const &

fname0

)

References utility::file_basename().

Referenced by harvest_motifs().

Real protocols::motif_hash::uint16_to_real	(	uint16_t const &	val,
		Real const &	lb,
		Real const &	ub
	)

References max(), MAX_UINT16, and min.

Referenced by protocols::motif_hash::ResPairMotif::dist2(), protocols::motif_hash::ResPairMotif::filter(), protocols::motif_hash::Xfres::omg(), protocols::motif_hash::Xfres::phi(), protocols::motif_hash::Xfres::psi(), protocols::motif_hash::ResPairMotif::rt(), and protocols::motif_hash::Xfrag::rt6().

Real protocols::motif_hash::uint8_to_real	(	uint8_t const &	val,
		Real const &	lb,
		Real const &	ub
	)

References max(), MAX_UINT8, and min.

Referenced by protocols::motif_hash::Xfrag::bfac(), protocols::motif_hash::ResPairMotif::bfac1(), protocols::motif_hash::ResPairMotif::bfac2(), protocols::motif_hash::Xfrag::burial(), protocols::motif_hash::Xfres::chi1(), protocols::motif_hash::ResPairMotif::chi11(), protocols::motif_hash::ResPairMotif::chi12(), protocols::motif_hash::ResPairMotif::chi13(), protocols::motif_hash::ResPairMotif::chi14(), protocols::motif_hash::Xfres::chi2(), protocols::motif_hash::ResPairMotif::chi21(), protocols::motif_hash::ResPairMotif::chi22(), protocols::motif_hash::ResPairMotif::chi23(), protocols::motif_hash::ResPairMotif::chi24(), protocols::motif_hash::Xfres::chi3(), protocols::motif_hash::Xfres::chi4(), protocols::motif_hash::Xfrag::ex1(), protocols::motif_hash::Xfrag::ex2(), protocols::motif_hash::Xfrag::ex3(), protocols::motif_hash::Xfrag::ex4(), protocols::motif_hash::ResPairMotif::fa_atr(), protocols::motif_hash::ResPairMotif::fill_pose_with_motif(), protocols::motif_hash::ResPairMotif::hb_bb(), protocols::motif_hash::ResPairMotif::hb_bb_sc(), protocols::motif_hash::ResPairMotif::hb_sc(), protocols::motif_hash::ResPairMotif::nbrs(), operator<<(), and protocols::motif_hash::ResPairMotif::sasa().

bool protocols::motif_hash::write_motifs_binary	(	std::ostream &	out,
		ResPairMotifs const &	motifs
	)

Referenced by harvest_motifs(), merge_motifs(), and write_motifs_binary().

bool protocols::motif_hash::write_motifs_binary	(	std::string const &	fname,
		ResPairMotifs const &	motifs
	)

References utility::io::ozstream::close(), utility::io::ozstream::good(), and write_motifs_binary().

bool protocols::motif_hash::write_xfrag_binary	(	std::ostream &	out,
		vector1< Xfrag > const &	xfrag
	)

References cout.

Referenced by write_xfrag_binary().

bool protocols::motif_hash::write_xfrag_binary	(	string const &	fname,
		vector1< Xfrag > const &	xfrag
	)

References utility::io::ozstream::close(), utility::io::ozstream::good(), and write_xfrag_binary().

bool protocols::motif_hash::write_xfrag_binary	(	std::ostream &	out,
		vector1< Xfrag > const &	xfrag,
		vector1< Xfres > const &	xfres
	)

References write_xfrag_binary(), and write_xfres_binary().

bool protocols::motif_hash::write_xfrag_binary	(	string const &	fname,
		vector1< Xfrag > const &	xfrag,
		vector1< Xfres > const &	xfres
	)

References utility::io::ozstream::close(), utility::io::ozstream::good(), and write_xfrag_binary().

bool protocols::motif_hash::write_xfres_binary	(	std::ostream &	out,
		vector1< Xfres > const &	xfres
	)

References cout.

Referenced by write_xfrag_binary(), and write_xfres_binary().

bool protocols::motif_hash::write_xfres_binary	(	string const &	fname,
		vector1< Xfres > const &	xfres
	)

References utility::io::ozstream::close(), utility::io::ozstream::good(), and write_xfres_binary().

Variable Documentation

basic::Tracer protocols::motif_hash::TR("protocols.motif_hash")

static