CartesianBondedEnergy.cc File Reference

Harmonic bondangle/bondlength/torsion constraints. More...

#include <core/scoring/methods/CartBondedParameters.hh>
#include <core/scoring/methods/CartesianBondedEnergy.hh>
#include <core/scoring/methods/CartesianBondedEnergyCreator.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/AA.hh>
#include <core/id/DOF_ID.hh>
#include <core/id/TorsionID.hh>
#include <core/chemical/AtomType.hh>
#include <core/scoring/mm/MMBondAngleLibrary.hh>
#include <core/scoring/mm/MMBondLengthLibrary.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/scoring/PeptideBondedEnergyContainer.hh>
#include <core/scoring/Energies.hh>
#include <core/pose/Pose.hh>
#include <basic/Tracer.hh>
#include <basic/basic.hh>
#include <basic/database/open.hh>
#include <utility/string_util.hh>
#include <utility/io/izstream.hh>
#include <numeric/constants.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/deriv/angle_deriv.hh>
#include <numeric/deriv/distance_deriv.hh>
#include <numeric/deriv/dihedral_deriv.hh>
#include <numeric/NumericTraits.hh>
#include <numeric/angle.functions.hh>
#include <core/scoring/DerivVectorPair.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/optE.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <iostream>
#include <boost/tuple/tuple.hpp>
#include <boost/algorithm/string.hpp>
#include <utility/vector1.hh>
#include <core/pose/PDBInfo.hh>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::scoring
	core::scoring::methods

Macros
#define	CUTOFF   1

Functions
std::string	core::scoring::methods::get_restag (core::chemical::ResidueType const &restype)
	helper function More...

Variables
static basic::Tracer	core::scoring::methods::TR ("core.scoring.CartesianBondedEnergy")
static basic::Tracer	core::scoring::methods::GEOMETRIES ("core.scoring.CartesianBondedEnergy.GEOMETRIES")
static const Real	core::scoring::methods::K_LENGTH =300.0
static const Real	core::scoring::methods::K_ANGLE =80.0
static const Real	core::scoring::methods::K_TORSION =20.0
static const Real	core::scoring::methods::K_TORSION_PROTON =10.0
static const Real	core::scoring::methods::K_TORSION_IMPROPER =40.0

Detailed Description

Harmonic bondangle/bondlength/torsion constraints.

C++ implementaion of GOAP(Generalized Orientation-dependent, All-atom statistical Potential) by Zhou H & Skolnick J, Biophys J 2011, 101(8):2043-52.

Author

Frank DiMaio modified by Vikram K. Mulligan to allow D-amino acid minimization.

Hahnbeom Park

Macro Definition Documentation

#define CUTOFF   1

Referenced by core::io::pdb::dump_connect_info(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsion_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies(), and core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies().