#include <NumberHBondsCalculator.hh>
◆ NumberHBondsCalculator() [1/2]
protocols::simple_pose_metric_calculators::NumberHBondsCalculator::NumberHBondsCalculator |
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◆ NumberHBondsCalculator() [2/2]
protocols::simple_pose_metric_calculators::NumberHBondsCalculator::NumberHBondsCalculator |
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bool const |
generous, |
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std::set< core::Size > |
special_region = std::set< core::Size >() |
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◆ ~NumberHBondsCalculator()
protocols::simple_pose_metric_calculators::NumberHBondsCalculator::~NumberHBondsCalculator |
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◆ clone()
◆ compute_Hbonds_for_residue()
References protocols::simple_pose_metric_calculators::choose_hbond_parameter_set(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::hbonds::HBondDatabase::get_database(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::hbonds::HBondSet::nhbonds(), core::pose::Pose::residue(), residue_Hbonds_, special_region_, special_region_Hbonds_, core::scoring::Energies::tenA_neighbor_graph(), and use_generous_hbonds_.
Referenced by recompute().
◆ determine_res_to_recompute()
void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::determine_res_to_recompute |
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core::pose::Pose const & |
pose, |
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utility::vector1< bool > & |
res_to_recompute |
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function to figure out which residues to recompute the hydrogen bonds for
strategy: for each residue, we check whether the internally cached total energies
correspond to the energies found in the pose for that residue. If they do,
this means that the number of H-bonds hasn't changed.
References atom_Hbonds_, core::id::AtomID_Map< T >::clear(), core::pose::Pose::energies(), ref_residue_total_energies_, residue_Hbonds_, core::scoring::Energies::residue_total_energies(), core::id::AtomID_Map< T >::resize(), core::pose::Pose::size(), special_region_, and core::scoring::total_score.
Referenced by recompute().
◆ get_residue_hbonds()
utility::vector1< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::get_residue_hbonds |
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◆ get_special_region()
std::set< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::get_special_region |
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◆ get_total_hbonds()
core::Size protocols::simple_pose_metric_calculators::NumberHBondsCalculator::get_total_hbonds |
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◆ lookup()
void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::lookup |
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std::string const & |
key, |
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basic::MetricValueBase * |
valptr |
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◆ print()
std::string protocols::simple_pose_metric_calculators::NumberHBondsCalculator::print |
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std::string const & |
key | ) |
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◆ recompute()
void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute |
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core::pose::Pose const & |
this_pose | ) |
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Implements core::pose::metrics::EnergyDependentCalculator.
References all_Hbonds_, atom_Hbonds_, core::conformation::Residue::atom_type(), core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check(), compute_Hbonds_for_residue(), cumul_hbonds_, core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), determine_res_to_recompute(), core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(), core::scoring::hbonds::HBondOptions::exclude_intra_res_protein(), core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA(), core::scoring::hbonds::HBondOptions::exclude_self_hbonds(), core::scoring::hbonds::HBondSet::hbond_options(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::scoring::hbonds::HBondOptions::max_hb_energy(), max_hb_energy_, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), residue_Hbonds_, core::id::AtomID_Map< T >::set(), core::pose::Pose::size(), core::conformation::Residue::type(), use_generous_hbonds_, and core::scoring::hbonds::HBondOptions::use_hb_env_dep().
◆ set_cumul_hbonds()
void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::set_cumul_hbonds |
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bool |
cumul_hbonds | ) |
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◆ set_generous()
void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::set_generous |
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bool |
generous | ) |
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◆ set_max_hb_energy()
void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::set_max_hb_energy |
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core::Real |
energy | ) |
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◆ set_special_region()
void protocols::simple_pose_metric_calculators::NumberHBondsCalculator::set_special_region |
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std::set< core::Size > |
selection | ) |
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◆ sum_Hbond_terms()
◆ all_Hbonds_
core::Size protocols::simple_pose_metric_calculators::NumberHBondsCalculator::all_Hbonds_ |
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◆ atom_Hbonds_
◆ cumul_hbonds_
bool protocols::simple_pose_metric_calculators::NumberHBondsCalculator::cumul_hbonds_ |
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◆ max_hb_energy_
core::Real protocols::simple_pose_metric_calculators::NumberHBondsCalculator::max_hb_energy_ |
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◆ ref_residue_total_energies_
utility::vector1< core::Real > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::ref_residue_total_energies_ |
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◆ residue_Hbonds_
utility::vector1< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::residue_Hbonds_ |
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◆ special_region_
std::set< core::Size > protocols::simple_pose_metric_calculators::NumberHBondsCalculator::special_region_ |
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◆ special_region_Hbonds_
core::Size protocols::simple_pose_metric_calculators::NumberHBondsCalculator::special_region_Hbonds_ |
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◆ use_generous_hbonds_
bool protocols::simple_pose_metric_calculators::NumberHBondsCalculator::use_generous_hbonds_ |
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The documentation for this class was generated from the following files: