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core::scoring::GenericBondedPotential Class Reference

Potential for core/scoring/methods/GenericBondedEnergy method. More...

#include <GenericBondedPotential.hh>

Inheritance diagram for core::scoring::GenericBondedPotential:
Inheritance graph
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Public Member Functions

 GenericBondedPotential ()
 Default Constructor. More...
 
void setup_for_scoring (pose::Pose &pose, scoring::ScoreFunction const &sfxn, bool const &score_full=false, bool const &score_hybrid=true) const
 Constructor with exclusion behaviors. More...
 
void residue_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap, bool const &score_full, bool const &score_hybrid) const
 interface with same named function in GenericBondedEnergy More...
 
void residue_derivatives (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs, bool const &score_full, bool const &score_hybrid) const
 interface with same named function in GenericBondedEnergy More...
 
void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap, bool const &score_full, bool const &score_hybrid) const
 interface with same named function in GenericBondedEnergy More...
 
void residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, bool const &score_full, bool const &score_hybrid) const
 interface with same named function in GenericBondedEnergy More...
 

Private Member Functions

void modify_tors_params (std::string const atm1, std::string const atm2, std::string bondtype, std::string const atm3, std::string const atm4, core::Real k1_in, core::Real k2_in, core::Real k3_in, core::Real k4_in, core::Real f1_in=0.0, core::Real f2_in=0.0, core::Real f3_in=0.0, core::Real f4_in=0.0)
 modify torsional parameters "after the fact" More...
 
void read_database (std::string filename)
 read database file located at database/scoring/score_function/generic_potential More...
 
void modify_torsion_params_from_cmd_line ()
 read flags or command line and apply modify_tors_params funciton More...
 
SpringParams const & lookup_bond_params (Size type1, Size type2) const
 fast database lookup; bond/angles (currently) keyed on type only More...
 
SpringParams const & lookup_angle_params (Size type1, Size type2, Size type3) const
 
GenTorsionParams const & lookup_tors_params (core::chemical::BondName bn, core::chemical::BondRingness br, Size type1, Size type2, Size type3, Size type4) const
 fast database lookup; torsions conditioned on types + 2-3 bond More...
 
SpringParams const & lookup_improper_params (Size type1, Size type2, Size type3, Size type4, int &idx2, int &idx3, int &idx4) const
 fast database lookup; improper keyed on types only More...
 
Real eval_residue_energy_and_derivative_bond (conformation::Residue const &rsd, utility::vector1< DerivVectorPair > &atom_derivs, Real const weight=0.0, bool const calc_deriv=false) const
 evaluate each component (1-body) for bond-length term More...
 
Real eval_residue_energy_and_derivative_angle (conformation::Residue const &rsd, utility::vector1< DerivVectorPair > &atom_derivs, Real const weight=0.0, bool const calc_deriv=false) const
 evaluate each component (1-body) for bond-angle term More...
 
Real eval_residue_energy_and_derivative_torsion (conformation::Residue const &rsd, utility::vector1< DerivVectorPair > &atom_derivs, ResidueExclParamsCOP excl_params, Real const weight=0.0, bool const calc_deriv=false) const
 evaluate each component (1-body) for regular torsion term More...
 
Real eval_residue_energy_and_derivative_improper (conformation::Residue const &rsd, utility::vector1< DerivVectorPair > &atom_derivs, ResidueExclParamsCOP excl_params, Real const weight=0.0, bool const calc_deriv=false) const
 evaluate each component (1-body) for improper-torsion term More...
 
Real eval_residue_pair_energy_and_derivative_bond (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, Real const weight=0.0, bool const calc_deriv=false) const
 evaluate each component (2-body) for bond-length term More...
 
Real eval_residue_pair_energy_and_derivative_angle (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, Real const weight=0.0, bool const calc_deriv=false) const
 evaluate each component (2-body) for bond-angle term More...
 
Real eval_residue_pair_energy_and_derivative_torsion (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, ResidueExclParamsCOP excl_info_res1, ResidueExclParamsCOP excl_info_res2, Real const weight=0.0, bool const calc_deriv=false) const
 evaluate each component (2-body) for regular torsion term More...
 
Real eval_residue_pair_energy_and_derivative_improper (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, ResidueExclParamsCOP excl_info_res1, ResidueExclParamsCOP excl_info_res2, Real const weight=0.0, bool const calc_deriv=false) const
 evaluate each component (2-body) for improper-torsion term More...
 

Private Attributes

utility::vector1< int > defined_atom_types_
 
std::map< std::string,
utility::vector1< core::Size > > 
name_index_map
 
core::Size natomtypes
 
utility::vector1< SpringParamsbond_pot_
 
utility::vector1< SpringParamsangle_pot_
 
utility::vector1< SpringParamsimproper_pot_
 
utility::vector1
< GenTorsionParams
tors_pot_
 
std::unordered_map< uint64_t,
Size
bond_lookup_
 
std::unordered_map< uint64_t,
Size
angle_lookup_
 
std::unordered_map< uint64_t,
Size
improper_lookup_
 
std::unordered_map< uint64_t,
Size
tors_lookup_
 

Static Private Attributes

static const SpringParams null_sp_param
 
static const GenTorsionParams null_tors_param
 

Detailed Description

Potential for core/scoring/methods/GenericBondedEnergy method.

Main class calculating gen_bonded energy term. Consists of energy terms of bond-length, -angle, torsion, and improper torsions. Reads in database/scoring/score_function/generic_bonded/generic_bonded.XX.txt and stores it as SpringParams or GenTorsionParams as local variables for score enumeration.

Constructor & Destructor Documentation

core::scoring::GenericBondedPotential::GenericBondedPotential ( )

Default Constructor.

Member Function Documentation

Real core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle ( conformation::Residue const &  rsd,
utility::vector1< DerivVectorPair > &  atom_derivs,
Real const  weight = 0.0,
bool const  calc_deriv = false 
) const
private
Real core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond ( conformation::Residue const &  rsd,
utility::vector1< DerivVectorPair > &  atom_derivs,
Real const  weight = 0.0,
bool const  calc_deriv = false 
) const
private
Real core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper ( conformation::Residue const &  rsd,
utility::vector1< DerivVectorPair > &  atom_derivs,
ResidueExclParamsCOP  excl_params,
Real const  weight = 0.0,
bool const  calc_deriv = false 
) const
private
Real core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion ( conformation::Residue const &  rsd,
utility::vector1< DerivVectorPair > &  atom_derivs,
ResidueExclParamsCOP  excl_params,
Real const  weight = 0.0,
bool const  calc_deriv = false 
) const
private
Real core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
utility::vector1< DerivVectorPair > &  atom_derivs_r1,
utility::vector1< DerivVectorPair > &  atom_derivs_r2,
Real const  weight = 0.0,
bool const  calc_deriv = false 
) const
private
Real core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
utility::vector1< DerivVectorPair > &  atom_derivs_r1,
utility::vector1< DerivVectorPair > &  atom_derivs_r2,
Real const  weight = 0.0,
bool const  calc_deriv = false 
) const
private
Real core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
utility::vector1< DerivVectorPair > &  atom_derivs_r1,
utility::vector1< DerivVectorPair > &  atom_derivs_r2,
ResidueExclParamsCOP  excl_info_res1,
ResidueExclParamsCOP  excl_info_res2,
Real const  weight = 0.0,
bool const  calc_deriv = false 
) const
private
Real core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
utility::vector1< DerivVectorPair > &  atom_derivs_r1,
utility::vector1< DerivVectorPair > &  atom_derivs_r2,
ResidueExclParamsCOP  excl_info_res1,
ResidueExclParamsCOP  excl_info_res2,
Real const  weight = 0.0,
bool const  calc_deriv = false 
) const
private
SpringParams const & core::scoring::GenericBondedPotential::lookup_angle_params ( Size  type1,
Size  type2,
Size  type3 
) const
private
SpringParams const & core::scoring::GenericBondedPotential::lookup_bond_params ( Size  type1,
Size  type2 
) const
private

fast database lookup; bond/angles (currently) keyed on type only

References core::scoring::get_parameter_hash().

SpringParams const & core::scoring::GenericBondedPotential::lookup_improper_params ( Size  type1,
Size  type2,
Size  type3,
Size  type4,
int &  idx2,
int &  idx3,
int &  idx4 
) const
private

fast database lookup; improper keyed on types only

References core::scoring::get_parameter_hash().

GenTorsionParams const & core::scoring::GenericBondedPotential::lookup_tors_params ( core::chemical::BondName  bn,
core::chemical::BondRingness  br,
Size  type1,
Size  type2,
Size  type3,
Size  type4 
) const
private

fast database lookup; torsions conditioned on types + 2-3 bond

References core::scoring::bin_from_bond(), and core::scoring::get_parameter_hash().

void core::scoring::GenericBondedPotential::modify_tors_params ( std::string const  atm1,
std::string const  atm2,
std::string  bondtype,
std::string const  atm3,
std::string const  atm4,
core::Real  k1_in,
core::Real  k2_in,
core::Real  k3_in,
core::Real  k4_in,
core::Real  f1_in = 0.0,
core::Real  f2_in = 0.0,
core::Real  f3_in = 0.0,
core::Real  f4_in = 0.0 
)
private

modify torsional parameters "after the fact"

References core::scoring::bondorders_map(), core::scoring::get_parameter_hash(), and core::scoring::TR().

void core::scoring::GenericBondedPotential::modify_torsion_params_from_cmd_line ( )
private

read flags or command line and apply modify_tors_params funciton

References core::scoring::TR().

void core::scoring::GenericBondedPotential::read_database ( std::string  filename)
private
void core::scoring::GenericBondedPotential::residue_derivatives ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  atom_derivs,
bool const &  score_full,
bool const &  score_hybrid 
) const
void core::scoring::GenericBondedPotential::residue_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap emap,
bool const &  score_full,
bool const &  score_hybrid 
) const
void core::scoring::GenericBondedPotential::residue_pair_derivatives ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
EnergyMap const &  weights,
utility::vector1< DerivVectorPair > &  atom_derivs_r1,
utility::vector1< DerivVectorPair > &  atom_derivs_r2,
bool const &  score_full,
bool const &  score_hybrid 
) const
void core::scoring::GenericBondedPotential::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
EnergyMap emap,
bool const &  score_full,
bool const &  score_hybrid 
) const
void core::scoring::GenericBondedPotential::setup_for_scoring ( pose::Pose pose,
scoring::ScoreFunction const &  sfxn,
bool const &  score_full = false,
bool const &  score_hybrid = true 
) const

Member Data Documentation

std::unordered_map< uint64_t, Size > core::scoring::GenericBondedPotential::angle_lookup_
private
utility::vector1< SpringParams > core::scoring::GenericBondedPotential::angle_pot_
private
std::unordered_map< uint64_t, Size > core::scoring::GenericBondedPotential::bond_lookup_
private
utility::vector1< SpringParams > core::scoring::GenericBondedPotential::bond_pot_
private
utility::vector1< int > core::scoring::GenericBondedPotential::defined_atom_types_
private
std::unordered_map< uint64_t, Size > core::scoring::GenericBondedPotential::improper_lookup_
private
utility::vector1< SpringParams > core::scoring::GenericBondedPotential::improper_pot_
private
std::map< std::string, utility::vector1< core::Size > > core::scoring::GenericBondedPotential::name_index_map
private
core::Size core::scoring::GenericBondedPotential::natomtypes
private
const SpringParams core::scoring::GenericBondedPotential::null_sp_param
staticprivate
const GenTorsionParams core::scoring::GenericBondedPotential::null_tors_param
staticprivate
std::unordered_map< uint64_t, Size > core::scoring::GenericBondedPotential::tors_lookup_
private
utility::vector1< GenTorsionParams > core::scoring::GenericBondedPotential::tors_pot_
private

The documentation for this class was generated from the following files: