metrics.cc File Reference

#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <basic/Tracer.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/scoring/Interface.hh>
#include <core/conformation/Residue.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/mp.OptionKeys.gen.hh>
#include <protocols/membrane/util.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/docking/metrics.hh>
#include <utility/io/izstream.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::docking

Functions
static basic::Tracer	TR ("protocols.docking.DockingProtocol.metrics")
core::Real	protocols::docking::calc_intf_score (const core::pose::Pose &pose, const core::scoring::ScoreFunctionOP scorefxn, int const jump)
	Compute interface score between the input complex and complex with the two partners at 500A from each other. More...
core::Real	protocols::docking::calc_interaction_energy (const core::pose::Pose &pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the difference in energy between the inputted complex, and the complex with the two partners at 500A from each other. More...
core::Real	protocols::docking::calc_Lrmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, DockJumps const movable_jumps)
	Calculates C-alpha RMSD of the smaller partner after superposition of the larger partner. More...
core::Real	protocols::docking::calc_P1rmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, DockJumps const movable_jumps)
	Calculates C-alpha RMSD of the superimposed larger partner. More...
core::Real	protocols::docking::calc_P2rmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, DockJumps const movable_jumps)
	Calculates C-alpha RMSD of the superimposed smaller partner. More...
core::Real	protocols::docking::calc_Irmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the all-atom RMSD of all residues within 10A of the interface at superposition along those same atoms. More...
core::Real	protocols::docking::calc_Irmsd_legacy (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the backbone RMSD of all residues within 8A of the interface at superposition along those same atoms. More...
core::Real	protocols::docking::calc_CA_Irmsd (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	calcluates the CA-atom RMSD of all residues within 5A of the interface at superposition along those same atoms More...
core::Real	protocols::docking::calc_Fnat (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the fraction of native contacts recovered between the input and native pose. A native-contact is defined as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. More...
core::Real	protocols::docking::calc_Fnat (const core::pose::Pose &pose, std::string const &list_file, DockJumps const movable_jumps)
	Calculates the fraction of native contacts from the given native contacts pair list. More...
core::Real	protocols::docking::calc_Fnonnat (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)
	Calculates the fraction of non-native contacts recovered between the input and native pose. A native-contact is defined as defined by a residue from one partner being within 5A of a residue from the other partner in the native structure. Fnonnat = Nnon-native-contact/Nnative_contact. More...
core::Real	protocols::docking::calc_Fnonnat (const core::pose::Pose &pose, std::string const &list_file, DockJumps const movable_jumps)
	Calculates the fraction of non-native contacts from the given native contacts pari list. More...
bool	protocols::docking::calc_res_contact (conformation::ResidueOP rsd1, conformation::ResidueOP rsd2, Real dist_cutoff)
core::Size	protocols::docking::calc_CAPRI_rank (const core::pose::Pose &pose, const core::pose::Pose &native_pose, const core::scoring::ScoreFunctionCOP dock_scorefxn, DockJumps const movable_jumps)

Function Documentation

TR()

static basic::Tracer TR ( "protocols.docking.DockingProtocol.metrics"  )

static

Referenced by protocols::docking::calc_Fnat(), protocols::docking::calc_Fnonnat(), protocols::docking::calc_interaction_energy(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Irmsd_legacy(), and protocols::docking::calc_res_contact().