protocols::flexpep_docking::FlexPepDockingPoseMetrics Class Reference

#include <FlexPepDockingPoseMetrics.hh>

Collaboration diagram for protocols::flexpep_docking::FlexPepDockingPoseMetrics:

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_

Member Typedef Documentation

typedef bool(* protocols::flexpep_docking::FlexPepDockingPoseMetrics::t_predicate_func)(Pose const &, Pose const &, core::Size, core::Size)

Constructor & Destructor Documentation

protocols::flexpep_docking::FlexPepDockingPoseMetrics::FlexPepDockingPoseMetrics ( FlexPepDockingFlagsCOP  flags)

inline

Member Function Documentation

core::Real protocols::flexpep_docking::FlexPepDockingPoseMetrics::best_Kmer_rms	(	Pose const &	pose1,
		Pose const &	pose2,
		t_predicate_func	predicate,
		core::Size	k
	)		const

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

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

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
	)

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

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

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().

bool protocols::flexpep_docking::FlexPepDockingPoseMetrics::isInContact ( core::conformation::Residue const  res1, core::conformation::Residue const  res2, core::Real  threashold  ) const

private

References core::conformation::Residue::natoms(), and core::conformation::Residue::xyz().

Referenced by calc_frac_native_contacts().

void protocols::flexpep_docking::FlexPepDockingPoseMetrics::set_flags ( FlexPepDockingFlagsCOP  flags)

inline

Referenced by protocols::flexpep_docking::FlexPepDockingProtocol::apply().

Member Data Documentation

FlexPepDockingFlagsCOP protocols::flexpep_docking::FlexPepDockingPoseMetrics::flags_

private

Referenced by best_Kmer_rms(), calc_frac_native_contacts(), calc_interface_metrics(), and calc_pep_scores().

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The documentation for this class was generated from the following files:

• src/protocols/flexpep_docking/FlexPepDockingPoseMetrics.hh
• src/protocols/flexpep_docking/FlexPepDockingPoseMetrics.cc