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hbonds_geom.cc File Reference
#include <core/scoring/hbonds/hbonds_geom.hh>
#include <core/scoring/hbonds/types.hh>
#include <core/scoring/hbonds/constants.hh>
#include <core/scoring/hbonds/FadeInterval.hh>
#include <core/scoring/hbonds/HBEvalTuple.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/hbonds/HBondTypeManager.hh>
#include <core/scoring/hbonds/polynomial.hh>
#include <core/scoring/DerivVectorPair.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/rna/RNA_Info.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <numeric/constants.hh>
#include <numeric/conversions.hh>
#include <numeric/deriv/distance_deriv.hh>
#include <numeric/deriv/angle_deriv.hh>
#include <numeric/deriv/dihedral_deriv.hh>
#include <ObjexxFCL/format.hh>
#include <cmath>
#include <iostream>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/corrections.OptionKeys.gen.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/sys_util.hh>
#include <utility/py/PyAssert.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/hbtrie/HBAtom.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/FArray3D.hh>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::scoring
 
 core::scoring::hbonds
 

Functions

static basic::Tracer core::scoring::hbonds::tr ("core.scoring.hbonds.hbonds_geom")
 
Real core::scoring::hbonds::DUMMY_DERIV (0.0)
 
bool core::scoring::hbonds::DUMMY_BOOL (false)
 
HBGeoDimType core::scoring::hbonds::DUMMY_HBGEODIMTYPE (hbgd_NONE)
 
void core::scoring::hbonds::fade_energy (Real &energy, Real &dE_dr, Real &dE_dxD, Real &dE_dxH, Real &dE_dxH2, Real &dE_dBAH, Real &dE_dchi)
 Fade the energy smoothly to zero over the energy range [-0.1, 0.1] Because of the additive functional form, in order to make derivative continuous at the boundary of definition, we fade the energy function smoothly to zero. More...
 
void core::scoring::hbonds::bah_chi_compute_energy_sp2 (Real const d, Real const m, Real const l, Real const xH, Real const chi, Real const acc_don_scale, Real &energy, Real &dE_dBAH, Real &dE_dchi)
 Evaluate the Base-Acceptor-Hydrogen angle and Base-Acceptor torsion portion of the hydrogen bond energy and derivatives. More...
 
void core::scoring::hbonds::bah_chi_compute_energy_sp3 (Real const xH, Real const chi, Real const acc_don_scale, Real &energy, Real &dE_dBAH, Real &dE_dchi)
 
HBDonChemType core::scoring::hbonds::get_hb_don_chem_type (Size const datm, conformation::Residue const &don_rsd)
 
HBAccChemType core::scoring::hbonds::get_hb_acc_chem_type (Size const aatm, conformation::Residue const &acc_rsd)
 
HBSeqSep core::scoring::hbonds::get_seq_sep (HBDonChemType const &don_chem_type, HBAccChemType const &acc_chem_type, int const &sep)
 
hbonds::HBEvalTuple core::scoring::hbonds::hbond_evaluation_type (hbtrie::HBAtom const &datm, Size const don_rsd, hbtrie::HBAtom const &aatm, Size const acc_rsd)
 
hbonds::HBEvalTuple core::scoring::hbonds::hbond_evaluation_type (Size const datm, conformation::Residue const &don_rsd, Size const aatm, conformation::Residue const &acc_rsd)
 
void core::scoring::hbonds::hbond_compute_energy (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple const &hbt, Real const AHdis, Real const xD, Real const xH, Real const xH2, Real const chi, Real &energy, bool &apply_chi_torsion_penalty, HBGeoDimType &AHD_geometric_dimension, Real &dE_dr, Real &dE_dxD, Real &dE_dxH, Real &dE_dxH2, Real &dE_dBAH, Real &dE_dchi)
 
void core::scoring::hbonds::hb_energy_deriv_u (HBondDatabase const &database, HBondOptions const &hbondoptions, hbonds::HBEvalTuple const &hbt, Vector const &Hxyz, Vector const &Dxyz, Vector const &HDunit, Vector const &Axyz, Vector const &Bxyz, Vector const &BAunit, Vector const &B2xyz, Vector const &B2Aunit, Real &energy, bool const evaluate_deriv, HBondDerivs &deriv)
 car Evaluate the energy and derivative components for a hydrogen bond More...
 
void core::scoring::hbonds::hb_energy_deriv_u2 (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple const &hbt,HBDerivType const deriv_type, Vector const &Hxyz,Vector const &Dxyz,Vector const &HDunit,Vector const &Axyz,Vector const &Bxyz,Vector const &BAunit,Vector const &B2xyz,Vector const &B2Aunit,Real &energy, HBondDerivs &deriv=DUMMY_DERIVS)
 Evaluate the hydrogen bond energy and derivatives after having first calculated the HD and BA *u*nit vectors; deriv type must have been chosen (why does this exist?) More...
 
void core::scoring::hbonds::hb_energy_deriv (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple const &hbt, Vector const &Dxyz, Vector const &Hxyz, Vector const &Axyz, Vector const &Bxyz, Vector const &B2xyz, Real &energy, bool const evaluate_deriv, HBondDerivs &deriv)
 
void core::scoring::hbonds::hb_energy_deriv (HBondDatabase const &database, HBondOptions const &hbondoptions, HBEvalTuple const &hbt, Vector const &Dxyz, Vector const &Hxyz, Vector const &Axyz, Vector const &Bxyz, Vector const &B2xyz, Real &energy, HBDerivType const deriv_type, HBondDerivs &deriv)
 
Vector core::scoring::hbonds::create_acc_orientation_vector (HBondOptions const &hbondoptions, conformation::Residue const &residue, int atom_id)
 
void core::scoring::hbonds::make_hbBasetoAcc_unitvector (HBondOptions const &hbondoptions, chemical::Hybridization const &acc_hybrid, Vector const &Axyz, Vector const &Bxyz, Vector const &B2xyz, Vector &PBxyz, Vector &BAunit, Vector &B2Aunit)
 
void core::scoring::hbonds::assign_abase_derivs (HBondOptions const &hbondoptions, conformation::Residue const &acc_rsd, Size acc_atom, chemical::Hybridization const &acc_hybrid, DerivVectorPair const &abase_deriv, Real weighted_energy, utility::vector1< DerivVectorPair > &acc_atom_derivs)
 
void core::scoring::hbonds::assign_abase_derivs (HBondOptions const &hbondoptions, conformation::Residue const &acc_rsd, Size acc_atom, HBEvalTuple const &hbt, DerivVectorPair const &abase_deriv, Real weighted_energy, utility::vector1< DerivVectorPair > &acc_atom_derivs)
 
Vector core::scoring::hbonds::create_don_orientation_vector (conformation::Residue const &residue, int atom_id)
 create a unit vector pointing from the hydrogen toward the donor The atom_id is the atom id of the hydrogen atom More...
 

Variables

HBondDerivs core::scoring::hbonds::DUMMY_DERIVS
 
HBondDerivs const core::scoring::hbonds::ZERO_DERIV2D = { DerivVectorPair(), DerivVectorPair(), DerivVectorPair(), DerivVectorPair(), DerivVectorPair() }
 

Detailed Description

Author
Modified by Vikram K. Mulligan to allow scoring of D-amino acids on 27 June 2013.