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core::energy_methods::ResidueCartBondedParameters Class Reference

#include <CartesianBondedEnergy.hh>

Inheritance diagram for core::energy_methods::ResidueCartBondedParameters:
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Public Types

typedef
utility::fixedsizearray1< Size, 2 > 
Size2
 
typedef
utility::fixedsizearray1< Size, 3 > 
Size3
 
typedef
utility::fixedsizearray1< Size, 4 > 
Size4
 
typedef std::pair< Size2,
core::scoring::methods::CartBondedParametersCOP
length_parameter
 
typedef std::pair< Size3,
core::scoring::methods::CartBondedParametersCOP
angle_parameter
 
typedef std::pair< Size4,
core::scoring::methods::CartBondedParametersCOP
torsion_parameter
 

Public Member Functions

 ResidueCartBondedParameters ()
 
 ~ResidueCartBondedParameters () override
 
void add_length_parameter (Size2 atom_inds, core::scoring::methods::CartBondedParametersCOP)
 
void add_angle_parameter (Size3 atom_inds, core::scoring::methods::CartBondedParametersCOP)
 
void add_torsion_parameter (Size4 atom_inds, core::scoring::methods::CartBondedParametersCOP)
 
void add_improper_parameter (Size4 atom_inds, core::scoring::methods::CartBondedParametersCOP)
 
void add_bbdep_length_parameter (Size2 atom_inds, core::scoring::methods::CartBondedParametersCOP)
 
void add_bbdep_angle_parameter (Size3 atom_inds, core::scoring::methods::CartBondedParametersCOP)
 
void add_lower_connect_angle_params (Size3 atom_inds, core::scoring::methods::CartBondedParametersCOP)
 
void add_upper_connect_angle_params (Size3 atom_inds, core::scoring::methods::CartBondedParametersCOP)
 
void bb_N_index (Size index)
 
void bb_CA_index (Size index)
 
void bb_C_index (Size index)
 
void bb_O_index (Size index)
 
void bb_H_index (Size index)
 
void pro_CD_index (Size index)
 
void ca_cprev_n_h_interres_improper_params (core::scoring::methods::CartBondedParametersCOP)
 
void oprev_cprev_n_h_interres_improper_params (core::scoring::methods::CartBondedParametersCOP)
 
void ca_nnext_c_o_interres_improper_params (core::scoring::methods::CartBondedParametersCOP)
 
void pro_cd_cprev_n_ca_interres_improper_params (core::scoring::methods::CartBondedParametersCOP)
 
void cprev_n_bond_length_params (core::scoring::methods::CartBondedParametersCOP)
 
utility::vector1
< length_parameter > const & 
length_parameters () const
 
utility::vector1
< angle_parameter > const & 
angle_parameters () const
 
utility::vector1
< torsion_parameter > const & 
torsion_parameters () const
 
utility::vector1
< torsion_parameter > const & 
improper_parameters () const
 Exactly the same as proper torsion parameters, but parceled out into their own section so that debugging information can be given for these torsions in particular. More...
 
utility::vector1
< length_parameter > const & 
bbdep_length_parameters () const
 just the list of length parameters that are dependent on phi and psi; used for calculating dE/dphi and dE/dpsi More...
 
utility::vector1
< angle_parameter > const & 
bbdep_angle_parameters () const
 just the list of angle parameters that are dependent on phi and psi; used for calculating dE/dphi and dE/dpsi More...
 
utility::vector1
< angle_parameter > const & 
lower_connect_angle_params () const
 
utility::vector1
< angle_parameter > const & 
upper_connect_angle_params () const
 
Size bb_N_index () const
 
Size bb_CA_index () const
 
Size bb_C_index () const
 
Size bb_O_index () const
 
Size bb_H_index () const
 
Size pro_CD_index () const
 
core::scoring::methods::CartBondedParametersCOP ca_cprev_n_h_interres_improper_params () const
 
core::scoring::methods::CartBondedParametersCOP oprev_cprev_n_h_interres_improper_params () const
 
core::scoring::methods::CartBondedParametersCOP ca_nnext_c_o_interres_improper_params () const
 
core::scoring::methods::CartBondedParametersCOP pro_cd_cprev_n_ca_interres_improper_params () const
 
core::scoring::methods::CartBondedParametersCOP cprev_n_bond_length_params () const
 

Private Attributes

utility::vector1
< length_parameter
length_params_
 
utility::vector1< angle_parameterangle_params_
 
utility::vector1
< torsion_parameter
torsion_params_
 
utility::vector1
< torsion_parameter
improper_params_
 
utility::vector1
< length_parameter
bbdep_length_params_
 
utility::vector1< angle_parameterbbdep_angle_params_
 
utility::vector1< angle_parameterlower_connect_angle_params_
 
utility::vector1< angle_parameterupper_connect_angle_params_
 
Size bb_N_index_
 
Size bb_CA_index_
 
Size bb_C_index_
 
Size bb_O_index_
 
Size bb_H_index_
 
Size pro_CD_index_
 
core::scoring::methods::CartBondedParametersCOP ca_cprev_n_h_interres_improper_params_
 
core::scoring::methods::CartBondedParametersCOP oprev_cprev_n_h_interres_improper_params_
 
core::scoring::methods::CartBondedParametersCOP ca_nnext_c_o_interres_improper_params_
 
core::scoring::methods::CartBondedParametersCOP pro_cd_cprev_n_ca_interres_improper_params_
 
core::scoring::methods::CartBondedParametersCOP cprev_n_bond_length_params_
 

Member Typedef Documentation

typedef utility::fixedsizearray1< Size, 2 > core::energy_methods::ResidueCartBondedParameters::Size2
typedef utility::fixedsizearray1< Size, 3 > core::energy_methods::ResidueCartBondedParameters::Size3
typedef utility::fixedsizearray1< Size, 4 > core::energy_methods::ResidueCartBondedParameters::Size4

Constructor & Destructor Documentation

core::energy_methods::ResidueCartBondedParameters::ResidueCartBondedParameters ( )
core::energy_methods::ResidueCartBondedParameters::~ResidueCartBondedParameters ( )
overridedefault

Member Function Documentation

void core::energy_methods::ResidueCartBondedParameters::add_angle_parameter ( Size3  atom_inds,
core::scoring::methods::CartBondedParametersCOP  params 
)

References angle_params_.

void core::energy_methods::ResidueCartBondedParameters::add_bbdep_angle_parameter ( Size3  atom_inds,
core::scoring::methods::CartBondedParametersCOP  params 
)

References bbdep_angle_params_.

void core::energy_methods::ResidueCartBondedParameters::add_bbdep_length_parameter ( Size2  atom_inds,
core::scoring::methods::CartBondedParametersCOP  params 
)

References bbdep_length_params_.

void core::energy_methods::ResidueCartBondedParameters::add_improper_parameter ( Size4  atom_inds,
core::scoring::methods::CartBondedParametersCOP  params 
)

References improper_params_.

void core::energy_methods::ResidueCartBondedParameters::add_length_parameter ( Size2  atom_inds,
core::scoring::methods::CartBondedParametersCOP  params 
)

References length_params_.

void core::energy_methods::ResidueCartBondedParameters::add_lower_connect_angle_params ( Size3  atom_inds,
core::scoring::methods::CartBondedParametersCOP  params 
)
void core::energy_methods::ResidueCartBondedParameters::add_torsion_parameter ( Size4  atom_inds,
core::scoring::methods::CartBondedParametersCOP  params 
)

References torsion_params_.

void core::energy_methods::ResidueCartBondedParameters::add_upper_connect_angle_params ( Size3  atom_inds,
core::scoring::methods::CartBondedParametersCOP  params 
)
utility::vector1< angle_parameter > const& core::energy_methods::ResidueCartBondedParameters::angle_parameters ( ) const
inline
void core::energy_methods::ResidueCartBondedParameters::bb_C_index ( Size  index)
Size core::energy_methods::ResidueCartBondedParameters::bb_C_index ( ) const
inline

References bb_C_index_.

void core::energy_methods::ResidueCartBondedParameters::bb_CA_index ( Size  index)
Size core::energy_methods::ResidueCartBondedParameters::bb_CA_index ( ) const
inline

References bb_CA_index_.

void core::energy_methods::ResidueCartBondedParameters::bb_H_index ( Size  index)
Size core::energy_methods::ResidueCartBondedParameters::bb_H_index ( ) const
inline

References bb_H_index_.

void core::energy_methods::ResidueCartBondedParameters::bb_N_index ( Size  index)
Size core::energy_methods::ResidueCartBondedParameters::bb_N_index ( ) const
inline

References bb_N_index_.

void core::energy_methods::ResidueCartBondedParameters::bb_O_index ( Size  index)
Size core::energy_methods::ResidueCartBondedParameters::bb_O_index ( ) const
inline

References bb_O_index_.

utility::vector1< angle_parameter > const& core::energy_methods::ResidueCartBondedParameters::bbdep_angle_parameters ( ) const
inline

just the list of angle parameters that are dependent on phi and psi; used for calculating dE/dphi and dE/dpsi

References bbdep_angle_params_.

Referenced by core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative().

utility::vector1< length_parameter > const& core::energy_methods::ResidueCartBondedParameters::bbdep_length_parameters ( ) const
inline

just the list of length parameters that are dependent on phi and psi; used for calculating dE/dphi and dE/dpsi

References bbdep_length_params_.

Referenced by core::energy_methods::CartesianBondedEnergy::eval_intraresidue_dof_derivative().

void core::energy_methods::ResidueCartBondedParameters::ca_cprev_n_h_interres_improper_params ( core::scoring::methods::CartBondedParametersCOP  params)
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::ca_cprev_n_h_interres_improper_params ( ) const
inline
void core::energy_methods::ResidueCartBondedParameters::ca_nnext_c_o_interres_improper_params ( core::scoring::methods::CartBondedParametersCOP  params)
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::ca_nnext_c_o_interres_improper_params ( ) const
inline
void core::energy_methods::ResidueCartBondedParameters::cprev_n_bond_length_params ( core::scoring::methods::CartBondedParametersCOP  params)
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::cprev_n_bond_length_params ( ) const
inline
utility::vector1< torsion_parameter > const& core::energy_methods::ResidueCartBondedParameters::improper_parameters ( ) const
inline

Exactly the same as proper torsion parameters, but parceled out into their own section so that debugging information can be given for these torsions in particular.

References improper_params_.

Referenced by core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), and core::energy_methods::CartesianBondedEnergy::eval_singleres_improper_energies().

utility::vector1< length_parameter > const& core::energy_methods::ResidueCartBondedParameters::length_parameters ( ) const
inline
utility::vector1< angle_parameter > const& core::energy_methods::ResidueCartBondedParameters::lower_connect_angle_params ( ) const
inline
void core::energy_methods::ResidueCartBondedParameters::oprev_cprev_n_h_interres_improper_params ( core::scoring::methods::CartBondedParametersCOP  params)
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::oprev_cprev_n_h_interres_improper_params ( ) const
inline
void core::energy_methods::ResidueCartBondedParameters::pro_cd_cprev_n_ca_interres_improper_params ( core::scoring::methods::CartBondedParametersCOP  params)
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::pro_cd_cprev_n_ca_interres_improper_params ( ) const
inline
void core::energy_methods::ResidueCartBondedParameters::pro_CD_index ( Size  index)
Size core::energy_methods::ResidueCartBondedParameters::pro_CD_index ( ) const
inline

References pro_CD_index_.

utility::vector1< torsion_parameter > const& core::energy_methods::ResidueCartBondedParameters::torsion_parameters ( ) const
inline
utility::vector1< angle_parameter > const& core::energy_methods::ResidueCartBondedParameters::upper_connect_angle_params ( ) const
inline

Member Data Documentation

utility::vector1< angle_parameter > core::energy_methods::ResidueCartBondedParameters::angle_params_
private
Size core::energy_methods::ResidueCartBondedParameters::bb_C_index_
private

Referenced by bb_C_index().

Size core::energy_methods::ResidueCartBondedParameters::bb_CA_index_
private

Referenced by bb_CA_index().

Size core::energy_methods::ResidueCartBondedParameters::bb_H_index_
private

Referenced by bb_H_index().

Size core::energy_methods::ResidueCartBondedParameters::bb_N_index_
private

Referenced by bb_N_index().

Size core::energy_methods::ResidueCartBondedParameters::bb_O_index_
private

Referenced by bb_O_index().

utility::vector1< angle_parameter > core::energy_methods::ResidueCartBondedParameters::bbdep_angle_params_
private
utility::vector1< length_parameter > core::energy_methods::ResidueCartBondedParameters::bbdep_length_params_
private
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::ca_cprev_n_h_interres_improper_params_
private
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::ca_nnext_c_o_interres_improper_params_
private
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::cprev_n_bond_length_params_
private
utility::vector1< torsion_parameter > core::energy_methods::ResidueCartBondedParameters::improper_params_
private
utility::vector1< length_parameter > core::energy_methods::ResidueCartBondedParameters::length_params_
private
utility::vector1< angle_parameter > core::energy_methods::ResidueCartBondedParameters::lower_connect_angle_params_
private

For amino acids only: if they have a lower connection, then what are the angle parameters for Cprev-at1-at2 for all atoms at2 bonded to lower-connect-atom at1?

Referenced by add_lower_connect_angle_params(), and lower_connect_angle_params().

core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::oprev_cprev_n_h_interres_improper_params_
private
core::scoring::methods::CartBondedParametersCOP core::energy_methods::ResidueCartBondedParameters::pro_cd_cprev_n_ca_interres_improper_params_
private
Size core::energy_methods::ResidueCartBondedParameters::pro_CD_index_
private

Referenced by pro_CD_index().

utility::vector1< torsion_parameter > core::energy_methods::ResidueCartBondedParameters::torsion_params_
private
utility::vector1< angle_parameter > core::energy_methods::ResidueCartBondedParameters::upper_connect_angle_params_
private

For amino acids only: if they have an upper connection, then what are the angle parameters for Nnext-at1-at2 for all atoms at2 bonded to upper-connect-atom at1?

Referenced by add_upper_connect_angle_params(), and upper_connect_angle_params().


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