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core::scoring::dssp Namespace Reference

Classes

class  Dssp
 
class  Pairing
 
class  StrandPairing
 
class  StrandPairingSet
 

Typedefs

typedef utility::vector1< PairingPairingsList
 
typedef utility::vector1< PairingPairingList
 
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 
)
void core::scoring::dssp::get_pleating ( pose::Pose const &  pose,
Size const  pos1,
Size const  pos2,
Size orientation,
Size pleating 
)
bool core::scoring::dssp::has_orientation_and_pleating ( PairingsList const &  pairings)
std::ostream & core::scoring::dssp::operator<< ( std::ostream &  out,
Pairing const &  p 
)
std::ostream & core::scoring::dssp::operator<< ( std::ostream &  out,
PairingsList const &  p 
)
std::ostream & core::scoring::dssp::operator<< ( std::ostream &  out,
const StrandPairingSet &  sp 
)
std::ostream & core::scoring::dssp::operator<< ( std::ostream &  out,
const StrandPairing &  sp 
)
std::istream& core::scoring::dssp::operator>> ( std::istream &  is,
StrandPairingSet &  set 
)
std::istream& core::scoring::dssp::operator>> ( std::istream &  is,
StrandPairing &  sp 
)
void core::scoring::dssp::read_pairing_list ( std::string  pairing_file,
PairingsList &  pairings 
)
void core::scoring::dssp::read_pairing_list ( std::istream &  pairing_stream,
PairingsList &  pairings 
)
static basic::Tracer core::scoring::dssp::tr ( "core.scoring.dssp"  )
static