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Rosetta
2020.50
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#include <StrandPairing.hh>
Static Public Attributes | |
static core::Size | BIG_BULGE_LIMIT |
static core::Size | SMALL_BULGE_LIMIT |
Private Types | |
typedef utility::vector1 < core::Size > | SizeList |
Private Attributes | |
core::Size | begin1_ |
core::Size | end1_ |
core::Size | begin2_ |
core::Size | end2_ |
std::vector< core::Size > | pairing1 |
std::vector< core::Size > | pleating1 |
std::vector< core::Size > | pairing2 |
bool | antipar_ |
Friends | |
std::ostream & | operator<< (std::ostream &out, StrandPairing const &sp) |
std::istream & | operator>> (std::istream &in, StrandPairing &sp) |
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core::scoring::dssp::StrandPairing::StrandPairing | ( | ) |
core::scoring::dssp::StrandPairing::StrandPairing | ( | core::Size | res1, |
core::Size | res2, | ||
bool | antiparallel, | ||
core::Size | pleating | ||
) |
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bool core::scoring::dssp::StrandPairing::antiparallel | ( | ) | const |
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References begin1_.
Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), and protocols::abinitio::AlternativePairings::compatible().
bool core::scoring::dssp::StrandPairing::check_pleat | ( | ) | const |
core::Size core::scoring::dssp::StrandPairing::contact_order | ( | ) | const |
Referenced by protocols::abinitio::PairingStatEntry::contact_order().
bool core::scoring::dssp::StrandPairing::contains | ( | core::Size | res | ) | const |
References begin1_, begin2_, end1_, and end2_.
Referenced by is_bulge().
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References end1_.
Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), and protocols::abinitio::AlternativePairings::compatible().
bool core::scoring::dssp::StrandPairing::extend | ( | core::Size | res, |
core::Size | res2, | ||
bool | antiparallel, | ||
core::Size | pleating | ||
) |
If possible, extend this pairing by the given residues.
If one of res1 or res2 is within 2 residues of the beginning or end of one of the strands of the pairing, and the other is within 5 residues, extend the pairing. This is the dssp definition of allowable beta bulges. Return true if the pairing was extended.
par Global Read: |
References protocols::mean_field::max(), protocols::mean_field::min(), and tr().
void core::scoring::dssp::StrandPairing::extend_to | ( | core::Size | res | ) |
References protocols::loops::extend.
Referenced by merge(), and mergeable().
void core::scoring::dssp::StrandPairing::get_all_register_and_bulges | ( | SizeList & | regs, |
SizeList & | bulges | ||
) | const |
References antipar_, begin1_, and pairing1.
Referenced by core::scoring::dssp::operator<<().
void core::scoring::dssp::StrandPairing::get_beta_pairs | ( | core::scoring::dssp::PairingList & | beta_pairs | ) | const |
Size core::scoring::dssp::StrandPairing::get_pair | ( | core::Size | res | ) | const |
References begin1_, begin2_, end1_, end2_, pairing1, and pairing2.
Referenced by protocols::fldsgn::topology::calc_strand_pairing_set(), and is_bulge().
Size core::scoring::dssp::StrandPairing::get_pleating | ( | core::Size | res | ) | const |
Referenced by protocols::fldsgn::topology::calc_strand_pairing_set().
Size core::scoring::dssp::StrandPairing::get_register | ( | ) | const |
References antipar_, begin1_, and pairing1.
Referenced by protocols::abinitio::AlternativePairings::compatible().
bool core::scoring::dssp::StrandPairing::has_common_pairing | ( | StrandPairing const & | other | ) | const |
bool core::scoring::dssp::StrandPairing::has_pairing | ( | core::scoring::dssp::Pairing const & | p | ) | const |
References core::scoring::dssp::Pairing::is_anti(), core::scoring::dssp::Pairing::Pos1(), and core::scoring::dssp::Pairing::Pos2().
Referenced by has_common_pairing().
std::size_t core::scoring::dssp::StrandPairing::hash_value | ( | ) | const |
References boost::tuples::hash_value(), and protocols::kinmatch::str().
Referenced by protocols::abinitio::hash_value().
bool core::scoring::dssp::StrandPairing::is_bulge | ( | core::Size | res | ) | const |
References contains(), and get_pair().
bool core::scoring::dssp::StrandPairing::is_ladder | ( | ) | const |
bool core::scoring::dssp::StrandPairing::merge | ( | StrandPairing const & | other, |
bool | domerge = false |
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References begin1_, begin2_, end1_, extend_to(), protocols::mean_field::max(), protocols::mean_field::min(), pairing1, pairing2, pleating1, and valid_ends().
Referenced by protocols::abinitio::PairingStatEntry::add_pairing().
bool core::scoring::dssp::StrandPairing::mergeable | ( | StrandPairing const & | other | ) | const |
References antipar_, begin1_, begin2_, end1_, end2_, extend_to(), pairing1, pairing2, pleating1, and tr().
Referenced by protocols::abinitio::PairingStatEntry::compatible(), core::scoring::dssp::StrandPairingSet::has_pairing(), protocols::abinitio::PairingStatEntry::operator!=(), protocols::abinitio::_MergableEntries::operator()(), and protocols::abinitio::PairingStatEntry::operator==().
Size core::scoring::dssp::StrandPairing::operator< | ( | const StrandPairing & | rhs | ) | const |
Size core::scoring::dssp::StrandPairing::operator== | ( | const StrandPairing & | rhs | ) | const |
bool core::scoring::dssp::StrandPairing::paired | ( | core::Size | res1, |
core::Size | res2, | ||
bool | anti | ||
) | const |
References protocols::sparta::contains().
bool core::scoring::dssp::StrandPairing::range_check | ( | ) | const |
References begin1_, begin2_, end1_, end2_, pairing1, and pairing2.
Referenced by core::scoring::dssp::StrandPairingSet::add_pairing(), and protocols::abinitio::PairingStatEntry::show().
void core::scoring::dssp::StrandPairing::show_internals | ( | std::ostream & | out | ) | const |
Referenced by core::scoring::dssp::operator>>().
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References begin1_, and end1_.
Referenced by protocols::abinitio::PairingStatEntry::size().
bool core::scoring::dssp::StrandPairing::valid_ends | ( | ) | const |
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Referenced by begin1(), contains(), get_all_register_and_bulges(), get_beta_pairs(), get_pair(), get_register(), has_common_pairing(), is_ladder(), merge(), mergeable(), operator<(), core::scoring::dssp::operator<<(), operator==(), core::scoring::dssp::operator>>(), range_check(), size(), and StrandPairing().
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Referenced by get_pair(), merge(), mergeable(), operator==(), core::scoring::dssp::operator>>(), range_check(), and StrandPairing().
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