Rosetta 3.4
Classes | Typedefs | Functions
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::owning_ptr
< StrandPairing
StrandPairingOP
typedef
utility::pointer::owning_ptr
< StrandPairing const > 
StrandPairingCOP
typedef
utility::pointer::owning_ptr
< StrandPairingSet
StrandPairingSetOP
typedef
utility::pointer::owning_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.
void read_pairing_list (std::string pairing_file, PairingsList &pairings)
 add pairings in pairing_file to list "pairings"
void read_pairing_list (std::istream &pairing_stream, PairingsList &pairings)
std::ostream & operator<< (std::ostream &out, Pairing const &)
 list of pairings
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


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.

fill_hbond_bb_pair_score_

Detailed:
Uses the rosetta hydrogen bond energies computed in hbonds::hbond_set to fill the hbond_bb_pair_score_ array. The hbond_set data structure must already be populated, by (e.g.) full atom scoring. Entry (i,j) is the backbone hydrogen bond energy between residues i (acceptor) and j (donor).
Global Read:
hbonds::hbond_set
Global Write:
dssp_ns::hbond_bb_pair_score_
Remarks:
References:
Author:
olange: ported from original bblum-rosetta++ version $
Last Modified:
fill_hbond_bb_pair_score__dssp

Populates the hbond_bb_pair_score_ array with dssp energies

Detailed:
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::Sizes::total_residue_ 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 $
Last Modified:

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::total_residue(), and core::pose::Pose::xyz().

Referenced by 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,
const StrandPairing &  sp 
)
std::ostream & core::scoring::dssp::operator<< ( std::ostream &  out,
Pairing const &  p 
)
std::ostream & core::scoring::dssp::operator<< ( std::ostream &  out,
const StrandPairingSet &  sp 
)
std::ostream & core::scoring::dssp::operator<< ( std::ostream &  out,
PairingsList const &  p 
)
std::istream& core::scoring::dssp::operator>> ( std::istream &  is,
StrandPairing &  sp 
)
std::istream& core::scoring::dssp::operator>> ( std::istream &  is,
StrandPairingSet &  set 
)

References tr().

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

add pairings in pairing_file to list "pairings"

References tr().

Referenced by protocols::abinitio::Templates::read_pairings(), and protocols::topology_broker::TemplateJumpClaimer::read_tag().

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