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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/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/RestypeDestructionEvent.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.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.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/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/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 <ObjexxFCL/string.functions.hh>
#include <core/pose/PDBInfo.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

constexpr int CUTOFF = -1