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Rosetta
2020.50
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Classes | |
class | Dssp |
class | Pairing |
class | StrandPairing |
class | StrandPairingSet |
Typedefs | |
typedef utility::vector1< Pairing > | PairingsList |
typedef utility::vector1< Pairing > | PairingList |
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 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 |
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).
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 | ||
) |
References get_CA_vectors(), core::pose::Pose::residue_type(), core::pose::Pose::size(), tr(), and core::pose::Pose::xyz().
Referenced by get_pleating().
void core::scoring::dssp::get_pleating | ( | pose::Pose const & | pose, |
Size const | pos1, | ||
Size const | pos2, | ||
Size & | orientation, | ||
Size & | pleating | ||
) |
References get_pairing_geometry(), and tr().
Referenced by core::scoring::dssp::StrandPairingSet::compute(), and protocols::jumping::JumpSample::steal_orientation_and_pleating().
bool core::scoring::dssp::has_orientation_and_pleating | ( | PairingsList const & | pairings | ) |
std::ostream & core::scoring::dssp::operator<< | ( | std::ostream & | out, |
Pairing const & | p | ||
) |
list of pairings
References core::scoring::dssp::Pairing::is_inwards(), core::scoring::dssp::Pairing::is_parallel(), core::scoring::dssp::Pairing::Orientation(), core::conformation::membrane::out, core::scoring::dssp::Pairing::Pleating(), core::scoring::dssp::Pairing::Pos1(), and core::scoring::dssp::Pairing::Pos2().
std::ostream & core::scoring::dssp::operator<< | ( | std::ostream & | out, |
PairingsList const & | p | ||
) |
References core::conformation::membrane::out.
std::ostream & core::scoring::dssp::operator<< | ( | std::ostream & | out, |
const StrandPairingSet & | sp | ||
) |
std::ostream & core::scoring::dssp::operator<< | ( | std::ostream & | out, |
const StrandPairing & | sp | ||
) |
References core::scoring::dssp::StrandPairing::antipar_, core::scoring::dssp::StrandPairing::begin1_, core::scoring::dssp::StrandPairing::begin2_, core::scoring::dssp::StrandPairing::end1_, core::scoring::dssp::StrandPairing::end2_, core::scoring::dssp::StrandPairing::get_all_register_and_bulges(), core::conformation::membrane::out, core::scoring::dssp::StrandPairing::pairing1, and core::scoring::dssp::StrandPairing::pleating1.
std::istream& core::scoring::dssp::operator>> | ( | std::istream & | is, |
StrandPairingSet & | set | ||
) |
References core::scoring::dssp::StrandPairingSet::pairings_, and tr().
std::istream& core::scoring::dssp::operator>> | ( | std::istream & | is, |
StrandPairing & | sp | ||
) |
References core::scoring::dssp::StrandPairing::antipar_, core::scoring::dssp::StrandPairing::begin1_, core::scoring::dssp::StrandPairing::begin2_, core::scoring::dssp::StrandPairing::end1_, core::scoring::dssp::StrandPairing::end2_, core::scoring::dssp::StrandPairing::pairing1, core::scoring::dssp::StrandPairing::pairing2, core::scoring::dssp::StrandPairing::pleating1, core::scoring::dssp::StrandPairing::show_internals(), and tr().
void core::scoring::dssp::read_pairing_list | ( | std::string | pairing_file, |
PairingsList & | pairings | ||
) |
add pairings in pairing_file to list "pairings"
References core::scoring::TR().
Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairings(), protocols::abinitio::Templates::read_pairings(), protocols::topology_broker::TemplateJumpClaimer::read_tag(), protocols::abinitio::abscript::FragmentJumpCM::set_topology(), and protocols::abinitio::AbrelaxApplication::setup_jumps().
void core::scoring::dssp::read_pairing_list | ( | std::istream & | pairing_stream, |
PairingsList & | pairings | ||
) |
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static |
Referenced by get_pairing_geometry(), get_pleating(), core::scoring::dssp::StrandPairing::operator<(), and operator>>().