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Rosetta 3.5
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Rosetta 3.5
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#include <FlexPepDockingPoseMetrics.hh>
Public Types | |
| typedef bool(* | t_predicate_func )(Pose const &, Pose const &, core::Size, core::Size) |
Public Member Functions | |
| FlexPepDockingPoseMetrics (FlexPepDockingFlagsCOP flags) | |
| core::Real | calc_frac_native_contacts (Pose const &native, Pose const &final, core::Real threashold) const |
| core::Real | calc_frac_atoms_kA_to_native (Pose const &pose1, Pose const &pose2, ObjexxFCL::FArray1D_bool const &res_subset, t_predicate_func predicate, double k, core::Size &ngood) const |
| calculate fractions of atoms that are at the same location as native More... | |
| core::Real | best_Kmer_rms (Pose const &pose1, Pose const &pose2, t_predicate_func predicate, core::Size k) const |
| core::Real | calc_phipsi_RMSD (Pose const &pose1, Pose const &pose2, ObjexxFCL::FArray1D_bool const &res_subset) const |
| std::map< std::string, core::Real > | calc_interface_metrics (core::pose::Pose &pose, Size rb_jump, core::scoring::ScoreFunctionOP scorefxn) |
| void | calc_pep_scores (core::pose::Pose const &pose, Real &pepScore, Real &pepScore_noref) const |
| void | set_flags (FlexPepDockingFlagsCOP flags) |
Private Member Functions | |
| bool | isInContact (core::conformation::Residue const res1, core::conformation::Residue const res2, core::Real threashold) const |
Private Attributes | |
| FlexPepDockingFlagsCOP | flags_ |
Definition at line 38 of file FlexPepDockingPoseMetrics.hh.
| typedef bool(* protocols::flexpep_docking::FlexPepDockingPoseMetrics::t_predicate_func)(Pose const &, Pose const &, core::Size, core::Size) |
Definition at line 41 of file FlexPepDockingPoseMetrics.hh.
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inline |
Definition at line 44 of file FlexPepDockingPoseMetrics.hh.
| core::Real protocols::flexpep_docking::FlexPepDockingPoseMetrics::best_Kmer_rms | ( | Pose const & | pose1, |
| Pose const & | pose2, | ||
| t_predicate_func | predicate, | ||
| core::Size | k | ||
| ) | const |
Definition at line 179 of file FlexPepDockingPoseMetrics.cc.
References flags_, core::scoring::rmsd_no_super_subset(), and core::pose::Pose::total_residue().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| core::Real protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native | ( | Pose const & | pose1, |
| Pose const & | pose2, | ||
| ObjexxFCL::FArray1D_bool const & | res_subset, | ||
| t_predicate_func | predicate, | ||
| double | k, | ||
| core::Size & | ngood | ||
| ) | const |
calculate fractions of atoms that are at the same location as native
calculate fractions of atoms that are at the same location as native
Definition at line 129 of file FlexPepDockingPoseMetrics.cc.
References core::scoring::is_heavyatom(), core::scoring::is_ligand_heavyatom(), core::scoring::is_polymer_heavyatom(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| core::Real protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_native_contacts | ( | Pose const & | native, |
| Pose const & | final, | ||
| core::Real | threashold | ||
| ) | const |
Definition at line 71 of file FlexPepDockingPoseMetrics.cc.
References flags_, isInContact(), core::pose::Pose::residue(), and protocols::TR().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| std::map< std::string, core::Real > protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_interface_metrics | ( | core::pose::Pose & | pose, |
| Size | rb_jump, | ||
| core::scoring::ScoreFunctionOP | scorefxn | ||
| ) |
Definition at line 260 of file FlexPepDockingPoseMetrics.cc.
References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, flags_, core::pose::metrics::CalculatorFactory::Instance(), core::pose::Pose::metric(), core::pose::metrics::CalculatorFactory::register_calculator(), and protocols::TR().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply(), and protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| void protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores | ( | core::pose::Pose const & | pose, |
| Real & | pepScore, | ||
| Real & | pepScore_noref | ||
| ) | const |
Definition at line 420 of file FlexPepDockingPoseMetrics.cc.
References core::pose::Pose::energies(), flags_, core::scoring::ref, core::scoring::Energies::residue_total_energies(), and core::scoring::Energies::residue_total_energy().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
| core::Real protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD | ( | Pose const & | pose1, |
| Pose const & | pose2, | ||
| ObjexxFCL::FArray1D_bool const & | res_subset | ||
| ) | const |
calculate phi/psi torsion-RMSD over peptide
Definition at line 224 of file FlexPepDockingPoseMetrics.cc.
References core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::storeJobStatistics().
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private |
Definition at line 107 of file FlexPepDockingPoseMetrics.cc.
References core::conformation::Residue::natoms(), and core::conformation::Residue::xyz().
Referenced by calc_frac_native_contacts().
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inline |
Definition at line 124 of file FlexPepDockingPoseMetrics.hh.
Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply().
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private |
Definition at line 131 of file FlexPepDockingPoseMetrics.hh.
Referenced by best_Kmer_rms(), calc_frac_native_contacts(), calc_interface_metrics(), and calc_pep_scores().
1.8.4