CartesianBondedEnergy.cc File Reference

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

#include <core/scoring/methods/CartBondedParameters.hh>
#include <core/energy_methods/CartesianBondedEnergy.hh>
#include <core/energy_methods/CartesianBondedEnergyCreator.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/RestypeDestructionEvent.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/Patch.hh>
#include <core/chemical/Element.hh>
#include <core/chemical/rings/RingConformerSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/chemical/AA.hh>
#include <core/id/DOF_ID.fwd.hh>
#include <core/id/TorsionID.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/scoring/PolymerBondedEnergyContainer.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/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/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/corrections.OptionKeys.gen.hh>
#include <iostream>
#include <boost/tuple/tuple.hpp>
#include <boost/algorithm/string.hpp>
#include <utility/vector1.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/pose/PDBInfo.hh>
#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>

Namespaces
	boost
	boost::tuples
	core
	A class for reading in the atom type properties.
	core::energy_methods

Functions
std::size_t	boost::tuples::hash_value (atm_name_quad const &e)
std::size_t	boost::tuples::hash_value (atm_name_triple const &e)
std::size_t	boost::tuples::hash_value (atm_name_pair const &e)
std::size_t	boost::tuples::hash_value (atm_name_single const &e)
bool	boost::tuples::operator== (atm_name_quad const &a, atm_name_quad const &b)
bool	boost::tuples::operator== (atm_name_triple const &a, atm_name_triple const &b)
bool	boost::tuples::operator== (atm_name_pair const &a, atm_name_pair const &b)
bool	boost::tuples::operator== (atm_name_single const &a, atm_name_single const &b)
static basic::Tracer	core::energy_methods::TR ("core.energy_methods.CartesianBondedEnergy")
static basic::Tracer	core::energy_methods::GEOMETRIES ("core.energy_methods.CartesianBondedEnergy.GEOMETRIES")
std::string	core::energy_methods::get_restag (core::chemical::ResidueType const &restype)
	helper function More...

Variables
constexpr int	CUTOFF = -1
static const Real	core::energy_methods::K_LENGTH =300.0
static const Real	core::energy_methods::K_ANGLE =80.0
static const Real	core::energy_methods::K_TORSION =80.0
static const Real	core::energy_methods::K_TORSION_PROTON =10.0
static const Real	core::energy_methods::K_TORSION_IMPROPER =80.0

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 and cyclic geometry.

Hahnbeom Park

Variable Documentation

CUTOFF

constexpr int CUTOFF = -1

constexpr

Referenced by core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_ring_energy(), core::energy_methods::CartesianBondedEnergy::eval_singleres_angle_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_length_energies(), core::energy_methods::CartesianBondedEnergy::eval_singleres_ring_energies(), and core::scoring::fiber_diffraction::rootj().