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Rosetta
2020.50
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#include <PairingLibrary.hh>
Public Types | |
typedef std::vector < PairingTemplate > | PairingTemplateList |
typedef std::map< std::pair < int, int > , PairingTemplateList > | PairingTemplateMap |
Public Member Functions | |
PairingLibrary () | |
void | read_from_file (std::string const &fn) |
void | read_from_file_no_filters (std::string const &fn) |
core::kinematics::RT | get_random_beta_sheet_jump (int const orientation, int const pleating) const |
classic rosetta++ accessor More... | |
core::kinematics::RT | get_random_tmh_jump (int const orientation, int const pos1, int const pos2) const |
classic rosetta++ accessor More... | |
void | set_tmh_jump (core::pose::Pose pose, int const jump_number, int const orientation, int const pos1, int const pos2) const |
void | create_jump_fragments (int const orientation, int const pleating, bool bWithTorsion, core::fragment::FragDataOPs &) const override |
puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is noTorsion 1 withTorsion 3 bWithTorsion = true length of single FragData is 3 start jump end More... | |
core::Size | size () const |
void | generate_jump_frags (core::scoring::dssp::PairingsList const &pairings, core::kinematics::MoveMap const &mm, bool bWithTorsion, core::fragment::FragSet &frags_accumulator) override |
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~BasePairingLibrary () override | |
Private Attributes | |
PairingTemplateMap | pairings_ |
core::Size | num_of_pairings_ |
typedef std::vector< PairingTemplate > protocols::jumping::PairingLibrary::PairingTemplateList |
typedef std::map< std::pair< int, int >, PairingTemplateList > protocols::jumping::PairingLibrary::PairingTemplateMap |
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inline |
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overridevirtual |
puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating This creates Fragments with single JumpSRFD — PairingLibrary also stores phi/psi/omega of start and end residue use bWithTorsion = true to get FragData with BBTorsionSRFD and JumpSRFD length of single FragData is noTorsion 1 withTorsion 3 bWithTorsion = true length of single FragData is 3 start jump end
puts all jump-geometries that fit the orientation and pleating into list of FragData's. Try to reuse these FragData for different Frames that have same orientation and pleating
Implements protocols::jumping::BasePairingLibrary.
References pairings_, protocols::loops::start, and protocols::loops::stop.
Referenced by generate_jump_frags(), and protocols::jumping::JumpSample::generate_jump_frags().
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overridevirtual |
kinematics::RT protocols::jumping::PairingLibrary::get_random_beta_sheet_jump | ( | int const | orientation, |
int const | pleating | ||
) | const |
classic rosetta++ accessor
References pairings_, core::scoring::rg, protocols::jumping::PairingTemplate::rt_, and protocols::hybridization::t.
kinematics::RT protocols::jumping::PairingLibrary::get_random_tmh_jump | ( | int const | orientation, |
int const | pos1, | ||
int const | pos2 | ||
) | const |
classic rosetta++ accessor
References pairings_, core::scoring::rg, protocols::jumping::PairingTemplate::rt_, and protocols::hybridization::t.
void protocols::jumping::PairingLibrary::read_from_file | ( | std::string const & | fn | ) |
References protocols::abinitio::filename(), num_of_pairings_, protocols::jumping::PairingTemplate::omega, pairings_, protocols::jumping::PairingTemplate::phi, protocols::jumping::PairingTemplate::psi, core::kinematics::RT::reverse(), protocols::jumping::PairingTemplate::rt_, protocols::jumping::RT_from_epos(), and protocols::hybridization::t.
Referenced by protocols::jumping::StandardPairingLibrary::StandardPairingLibrary().
void protocols::jumping::PairingLibrary::read_from_file_no_filters | ( | std::string const & | fn | ) |
References protocols::abinitio::filename(), num_of_pairings_, protocols::jumping::PairingTemplate::omega, pairings_, protocols::jumping::PairingTemplate::phi, protocols::jumping::PairingTemplate::psi, protocols::jumping::PairingTemplate::rt_, protocols::jumping::PairingTemplate::secstruct, and protocols::hybridization::t.
void protocols::jumping::PairingLibrary::set_tmh_jump | ( | core::pose::Pose | pose, |
int const | jump_number, | ||
int const | orientation, | ||
int const | pos1, | ||
int const | pos2 | ||
) | const |
References core::pose::Pose::conformation(), core::pose::named_stub_id_to_stub_id(), protocols::jumping::PairingTemplate::omega, pairings_, protocols::jumping::PairingTemplate::phi, protocols::jumping::PairingTemplate::psi, core::scoring::rg, protocols::jumping::PairingTemplate::rt_, protocols::jumping::PairingTemplate::secstruct, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), core::conformation::Conformation::set_stub_transform(), and protocols::hybridization::t.
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References num_of_pairings_.
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private |
Referenced by read_from_file(), read_from_file_no_filters(), and size().
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private |