protocols::flexpep_docking::FlexPepDockingPoseMetrics Class Reference

#include <FlexPepDockingPoseMetrics.hh>

Public Types
typedef bool(*	t_predicate_func) (core::pose::Pose const &, core::pose::Pose const &, core::Size, core::Size)

Public Member Functions
	FlexPepDockingPoseMetrics (FlexPepDockingFlagsCOP flags)
core::Real	calc_frac_native_contacts (core::pose::Pose const &native, core::pose::Pose const &final, core::Real threashold) const
core::Real	calc_frac_atoms_kA_to_native (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &res_subset, t_predicate_func predicate, core::Real k, core::Size &ngood) const
	calculate fractions of atoms that are at the same location as native More...
core::Real	best_Kmer_rms (core::pose::Pose const &pose1, core::pose::Pose const &pose2, t_predicate_func predicate, core::Size k) const
core::Real	calc_phipsi_RMSD (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &res_subset) const
std::map< std::string, core::Real >	calc_interface_metrics (core::pose::Pose &pose, core::Size rb_jump, core::scoring::ScoreFunctionOP scorefxn)
void	calc_pep_scores (core::pose::Pose const &pose, core::Real &pepScore, core::Real &pepScore_noref) const
bool	isInContact (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Real threashold) const
void	set_flags (FlexPepDockingFlagsCOP flags)

Private Attributes
FlexPepDockingFlagsCOP	flags_

Member Typedef Documentation

t_predicate_func

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

Constructor & Destructor Documentation

FlexPepDockingPoseMetrics()

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

inline

Member Function Documentation

best_Kmer_rms()

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

References core::scoring::rmsd_no_super_subset(), and core::pose::Pose::size().

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

calc_frac_atoms_kA_to_native()

core::Real protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_atoms_kA_to_native	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	res_subset,
		t_predicate_func	predicate,
		core::Real	k,
		core::Size &	ngood
	)		const

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::size(), and core::conformation::Residue::xyz().

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

calc_frac_native_contacts()

core::Real protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_frac_native_contacts	(	core::pose::Pose const &	native,
		core::pose::Pose const &	final,
		core::Real	threashold
	)		const

References core::pose::Pose::residue(), and TR().

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

calc_interface_metrics()

std::map< std::string, core::Real > protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_interface_metrics	(	core::pose::Pose &	pose,
		core::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, core::pose::metrics::CalculatorFactory::Instance(), core::pose::Pose::metric(), core::pose::metrics::CalculatorFactory::register_calculator(), and TR().

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

calc_pep_scores()

void protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_pep_scores	(	core::pose::Pose const &	pose,
		core::Real &	pepScore,
		core::Real &	pepScore_noref
	)		const

References core::pose::Pose::energies(), core::scoring::ref, core::scoring::Energies::residue_total_energies(), and core::scoring::Energies::residue_total_energy().

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

calc_phipsi_RMSD()

core::Real protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D_bool const &	res_subset
	)		const

References core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueType::is_upper_terminus(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

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

isInContact()

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

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

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

set_flags()

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

inline

References flags_.

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

Member Data Documentation

flags_

FlexPepDockingFlagsCOP protocols::flexpep_docking::FlexPepDockingPoseMetrics::flags_

private

Referenced by set_flags().

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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