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Rosetta Core
2014.35
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#include <EnvPairPotential.hh>
Public Member Functions | |
EnvPairPotential () | |
void | compute_centroid_environment (pose::Pose &pose) const |
void | finalize (pose::Pose &pose) const |
void | evaluate_env_and_cbeta_scores (pose::Pose const &pose, conformation::Residue const &rsd, Real &env_score, Real &cb_score6, Real &cb_score12) const |
void | evaluate_pair_and_cenpack_score (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const cendist, Real &pair_contribution, Real &cenpack_contribution) const |
Protected Member Functions | |
CenListInfo const & | cenlist_from_pose (pose::Pose const &) const |
CenListInfo & | nonconst_cenlist_from_pose (pose::Pose &) const |
Protected Attributes | |
Real const | cen_dist_cutoff2 |
Private Member Functions | |
void | fill_cenlist (CenListInfo &cenlist, Size const res1, Size const res2, Real const cendist) const |
fill the cenlist using interpolation More... | |
void | truncate_cenlist_values (CenListInfo &cenlist) const |
Private Attributes | |
ObjexxFCL::FArray2D< Real > | env_log_ |
ObjexxFCL::FArray1D< Real > | cbeta_den6_ |
ObjexxFCL::FArray1D< Real > | cbeta_den12_ |
ObjexxFCL::FArray3D< Real > | pair_log_ |
ObjexxFCL::FArray1D< Real > | cenpack_log_ |
Real const | cen_dist5_pad |
Real const | cen_dist6_pad |
Real const | cen_dist7_pad |
Real const | cen_dist10_pad |
Real const | cen_dist12_pad |
Real const | cen_dist5_pad_plus |
Real const | cen_dist6_pad_plus |
Real const | cen_dist7_pad_plus |
Real const | cen_dist10_pad_plus |
Real const | cen_dist12_pad_plus |
Real const | cen_dist5_pad_minus |
Real const | cen_dist7_pad_minus |
Real const | cen_dist10_pad_minus |
Real const | cen_dist12_pad_minus |
Real const | cen_dist5_pad_hinv |
Real const | cen_dist6_pad_hinv |
Real const | cen_dist7_pad_hinv |
Real const | cen_dist10_pad_hinv |
Real const | cen_dist12_pad_hinv |
Real const | cen_dist_cutoff_12_pad |
core::scoring::EnvPairPotential::EnvPairPotential | ( | ) |
References cbeta_den12_, cbeta_den6_, cenpack_log_, env_log_, getline(), l, basic::database::open(), pair_log_, tag, and utility_exit_with_message.
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Pose must already contain a cenlist object or this method will fail.
References core::pose::Pose::data(), and basic::datacache::BasicDataCache::get_const_ptr().
Referenced by core::scoring::MembranePotential::evaluate_cbeta(), core::scoring::MembranePotential::evaluate_env(), and evaluate_env_and_cbeta_scores().
void core::scoring::EnvPairPotential::compute_centroid_environment | ( | pose::Pose & | pose | ) | const |
References core::scoring::CenListInfo::calculated(), cen_dist_cutoff_12_pad, core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), fill_cenlist(), core::graph::Edge::get_node(), core::graph::Edge::get_second_node_ind(), core::scoring::CenListInfo::initialize(), nonconst_cenlist_from_pose(), nres, core::pose::Pose::residue(), core::scoring::EnergyEdge::square_distance(), and truncate_cenlist_values().
Referenced by core::scoring::methods::EnvEnergy::setup_for_scoring(), core::scoring::methods::MembraneCenPairEnergy::setup_for_scoring(), core::scoring::methods::CenPairEnergy::setup_for_scoring(), core::scoring::methods::MembraneCbetaEnergy::setup_for_scoring(), core::scoring::methods::MembraneLipo::setup_for_scoring(), core::scoring::membrane::MPPairEnergy::setup_for_scoring(), core::scoring::methods::MembraneEnvEnergy::setup_for_scoring(), core::scoring::membrane::MPCbetaEnergy::setup_for_scoring(), core::scoring::membrane::MPLipoEnergy::setup_for_scoring(), and core::scoring::membrane::MPEnvEnergy::setup_for_scoring().
void core::scoring::EnvPairPotential::evaluate_env_and_cbeta_scores | ( | pose::Pose const & | pose, |
conformation::Residue const & | rsd, | ||
Real & | env_score, | ||
Real & | cb_score6, | ||
Real & | cb_score12 | ||
) | const |
References core::conformation::Residue::aa(), cbeta_den12_, cbeta_den6_, cenlist_from_pose(), env_log_, core::scoring::CenListInfo::fcen10(), core::scoring::CenListInfo::fcen12(), core::scoring::CenListInfo::fcen6(), core::conformation::Residue::is_protein(), and core::conformation::Residue::seqpos().
Referenced by core::scoring::methods::EnvEnergy::residue_energy().
void core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score | ( | conformation::Residue const & | rsd1, |
conformation::Residue const & | rsd2, | ||
Real const | cendist, | ||
Real & | pair_contribution, | ||
Real & | cenpack_contribution | ||
) | const |
References core::conformation::Residue::aa(), aa1, aa2, core::chemical::aa_cys, cen_dist10_pad_hinv, cen_dist10_pad_minus, cen_dist10_pad_plus, cen_dist12_pad_hinv, cen_dist12_pad_minus, cen_dist5_pad_hinv, cen_dist5_pad_minus, cen_dist5_pad_plus, cen_dist7_pad_hinv, cen_dist7_pad_minus, cen_dist7_pad_plus, cenpack_log_, core::chemical::DISULFIDE, core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_protein(), pair_log_, and core::conformation::Residue::polymeric_sequence_distance().
Referenced by core::scoring::methods::CenPairEnergy::residue_pair_energy().
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fill the cenlist using interpolation
References cen_dist10_pad_hinv, cen_dist10_pad_plus, cen_dist12_pad_hinv, cen_dist12_pad_plus, cen_dist6_pad_hinv, cen_dist6_pad_plus, core::scoring::CenListInfo::fcen10(), core::scoring::CenListInfo::fcen12(), core::scoring::CenListInfo::fcen6(), and one.
Referenced by compute_centroid_environment().
void core::scoring::EnvPairPotential::finalize | ( | pose::Pose & | pose | ) | const |
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Either returns a non-const reference to the cenlist object already stored in the pose, or creates a new cenist object, places it in the pose, and returns a non-const reference to it.
References core::pose::datacache::CacheableDataType::CEN_LIST_INFO, core::pose::Pose::data(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), and basic::datacache::BasicDataCache::set().
Referenced by compute_centroid_environment(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::membrane::MembraneData::finalize(), core::scoring::Membrane_FAPotential::finalize(), finalize(), and core::scoring::MembranePotential::finalize().
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Referenced by EnvPairPotential(), and evaluate_env_and_cbeta_scores().
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Referenced by EnvPairPotential(), and evaluate_env_and_cbeta_scores().
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Referenced by evaluate_pair_and_cenpack_score(), and fill_cenlist().
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Referenced by evaluate_pair_and_cenpack_score().
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Referenced by evaluate_pair_and_cenpack_score(), and fill_cenlist().
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Referenced by evaluate_pair_and_cenpack_score(), and fill_cenlist().
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Referenced by evaluate_pair_and_cenpack_score().
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Referenced by fill_cenlist().
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Referenced by evaluate_pair_and_cenpack_score().
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Referenced by evaluate_pair_and_cenpack_score().
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Referenced by evaluate_pair_and_cenpack_score().
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Referenced by fill_cenlist().
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Referenced by fill_cenlist().
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Referenced by evaluate_pair_and_cenpack_score().
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Referenced by evaluate_pair_and_cenpack_score().
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Referenced by evaluate_pair_and_cenpack_score().
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Referenced by compute_centroid_environment().
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Referenced by EnvPairPotential(), and evaluate_pair_and_cenpack_score().
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Referenced by EnvPairPotential(), and evaluate_env_and_cbeta_scores().
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Referenced by EnvPairPotential(), and evaluate_pair_and_cenpack_score().