core::scoring::methods::ResidueCartBondedParameters Class Reference

#include <CartesianBondedEnergy.hh>

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

Public Member Functions
	ResidueCartBondedParameters ()
virtual	~ResidueCartBondedParameters ()
void	add_length_parameter (Size2 atom_inds, CartBondedParametersCOP)
void	add_angle_parameter (Size3 atom_inds, CartBondedParametersCOP)
void	add_torsion_parameter (Size4 atom_inds, CartBondedParametersCOP)
void	add_improper_torsion_parameter (Size4 atom_inds, CartBondedParametersCOP)
void	add_bbdep_length_parameter (Size2 atom_inds, CartBondedParametersCOP)
void	add_bbdep_angle_parameter (Size3 atom_inds, CartBondedParametersCOP)
void	add_lower_connect_angle_params (Size3 atom_inds, CartBondedParametersCOP)
void	add_upper_connect_angle_params (Size3 atom_inds, 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_torsion_params (CartBondedParametersCOP)
void	oprev_cprev_n_h_interres_torsion_params (CartBondedParametersCOP)
void	ca_nnext_c_o_interres_torsion_params (CartBondedParametersCOP)
void	pro_cd_cprev_n_ca_interres_torsion_params (CartBondedParametersCOP)
void	cprev_n_bond_length_params (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_torsion_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
CartBondedParametersCOP	ca_cprev_n_h_interres_torsion_params () const
CartBondedParametersCOP	oprev_cprev_n_h_interres_torsion_params () const
CartBondedParametersCOP	ca_nnext_c_o_interres_torsion_params () const
CartBondedParametersCOP	pro_cd_cprev_n_ca_interres_torsion_params () const
CartBondedParametersCOP	cprev_n_bond_length_params () const

Private Attributes
utility::vector1 < length_parameter >	length_params_
utility::vector1< angle_parameter >	angle_params_
utility::vector1 < torsion_parameter >	torsion_params_
utility::vector1 < torsion_parameter >	improper_torsion_params_
utility::vector1 < length_parameter >	bbdep_length_params_
utility::vector1< angle_parameter >	bbdep_angle_params_
utility::vector1< angle_parameter >	lower_connect_angle_params_
utility::vector1< angle_parameter >	upper_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_
CartBondedParametersCOP	ca_cprev_n_h_interres_torsion_params_
CartBondedParametersCOP	oprev_cprev_n_h_interres_torsion_params_
CartBondedParametersCOP	ca_nnext_c_o_interres_torsion_params_
CartBondedParametersCOP	pro_cd_cprev_n_ca_interres_torsion_params_
CartBondedParametersCOP	cprev_n_bond_length_params_

Member Typedef Documentation

typedef std::pair< Size3, CartBondedParametersCOP > core::scoring::methods::ResidueCartBondedParameters::angle_parameter

typedef std::pair< Size2, CartBondedParametersCOP > core::scoring::methods::ResidueCartBondedParameters::length_parameter

typedef utility::fixedsizearray1< Size, 2 > core::scoring::methods::ResidueCartBondedParameters::Size2

typedef utility::fixedsizearray1< Size, 3 > core::scoring::methods::ResidueCartBondedParameters::Size3

typedef utility::fixedsizearray1< Size, 4 > core::scoring::methods::ResidueCartBondedParameters::Size4

typedef std::pair< Size4, CartBondedParametersCOP > core::scoring::methods::ResidueCartBondedParameters::torsion_parameter

Constructor & Destructor Documentation

core::scoring::methods::ResidueCartBondedParameters::ResidueCartBondedParameters

(

)

core::scoring::methods::ResidueCartBondedParameters::~ResidueCartBondedParameters ( )

virtual

Member Function Documentation

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

References angle_params_.

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

References bbdep_angle_params_.

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

References bbdep_length_params_.

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

References improper_torsion_params_.

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

References length_params_.

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

References lower_connect_angle_params_.

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

References torsion_params_.

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

References upper_connect_angle_params_.

utility::vector1< angle_parameter > const& core::scoring::methods::ResidueCartBondedParameters::angle_parameters ( ) const

inline

References angle_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_singleres_angle_energies().

void core::scoring::methods::ResidueCartBondedParameters::bb_C_index

(

Size

index

)

References bb_C_index_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), and core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs().

Size core::scoring::methods::ResidueCartBondedParameters::bb_C_index ( ) const

inline

References bb_C_index_.

void core::scoring::methods::ResidueCartBondedParameters::bb_CA_index

(

Size

index

)

References bb_CA_index_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions().

Size core::scoring::methods::ResidueCartBondedParameters::bb_CA_index ( ) const

inline

References bb_CA_index_.

void core::scoring::methods::ResidueCartBondedParameters::bb_H_index

(

Size

index

)

References bb_H_index_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions().

Size core::scoring::methods::ResidueCartBondedParameters::bb_H_index ( ) const

inline

References bb_H_index_.

void core::scoring::methods::ResidueCartBondedParameters::bb_N_index

(

Size

index

)

References bb_N_index_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), and core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs().

Size core::scoring::methods::ResidueCartBondedParameters::bb_N_index ( ) const

inline

References bb_N_index_.

void core::scoring::methods::ResidueCartBondedParameters::bb_O_index

(

Size

index

)

References bb_O_index_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions().

Size core::scoring::methods::ResidueCartBondedParameters::bb_O_index ( ) const

inline

References bb_O_index_.

utility::vector1< angle_parameter > const& core::scoring::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_.

utility::vector1< length_parameter > const& core::scoring::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_.

void core::scoring::methods::ResidueCartBondedParameters::ca_cprev_n_h_interres_torsion_params

(

CartBondedParametersCOP

params

)

References ca_cprev_n_h_interres_torsion_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::ca_cprev_n_h_interres_torsion_params ( ) const

inline

References ca_cprev_n_h_interres_torsion_params_.

void core::scoring::methods::ResidueCartBondedParameters::ca_nnext_c_o_interres_torsion_params

(

CartBondedParametersCOP

params

)

References ca_nnext_c_o_interres_torsion_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::ca_nnext_c_o_interres_torsion_params ( ) const

inline

References ca_nnext_c_o_interres_torsion_params_.

void core::scoring::methods::ResidueCartBondedParameters::cprev_n_bond_length_params

(

CartBondedParametersCOP

params

)

References cprev_n_bond_length_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), and core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::cprev_n_bond_length_params ( ) const

inline

References cprev_n_bond_length_params_.

utility::vector1< torsion_parameter > const& core::scoring::methods::ResidueCartBondedParameters::improper_torsion_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_torsion_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsion_energies(), and core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsions_derivatives().

utility::vector1< length_parameter > const& core::scoring::methods::ResidueCartBondedParameters::length_parameters ( ) const

inline

References length_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_singleres_length_energies().

utility::vector1< angle_parameter > const& core::scoring::methods::ResidueCartBondedParameters::lower_connect_angle_params ( ) const

inline

References lower_connect_angle_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), and core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2().

void core::scoring::methods::ResidueCartBondedParameters::oprev_cprev_n_h_interres_torsion_params

(

CartBondedParametersCOP

params

)

References oprev_cprev_n_h_interres_torsion_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::oprev_cprev_n_h_interres_torsion_params ( ) const

inline

References oprev_cprev_n_h_interres_torsion_params_.

void core::scoring::methods::ResidueCartBondedParameters::pro_cd_cprev_n_ca_interres_torsion_params

(

CartBondedParametersCOP

params

)

References pro_cd_cprev_n_ca_interres_torsion_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::pro_cd_cprev_n_ca_interres_torsion_params ( ) const

inline

References pro_cd_cprev_n_ca_interres_torsion_params_.

void core::scoring::methods::ResidueCartBondedParameters::pro_CD_index

(

Size

index

)

References pro_CD_index_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions().

Size core::scoring::methods::ResidueCartBondedParameters::pro_CD_index ( ) const

inline

References pro_CD_index_.

utility::vector1< torsion_parameter > const& core::scoring::methods::ResidueCartBondedParameters::torsion_parameters ( ) const

inline

References torsion_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), and core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies().

utility::vector1< angle_parameter > const& core::scoring::methods::ResidueCartBondedParameters::upper_connect_angle_params ( ) const

inline

References upper_connect_angle_params_.

Referenced by core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), and core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1().

Member Data Documentation

utility::vector1< angle_parameter > core::scoring::methods::ResidueCartBondedParameters::angle_params_

private

Referenced by add_angle_parameter(), and angle_parameters().

Size core::scoring::methods::ResidueCartBondedParameters::bb_C_index_

private

Referenced by bb_C_index().

Size core::scoring::methods::ResidueCartBondedParameters::bb_CA_index_

private

Referenced by bb_CA_index().

Size core::scoring::methods::ResidueCartBondedParameters::bb_H_index_

private

Referenced by bb_H_index().

Size core::scoring::methods::ResidueCartBondedParameters::bb_N_index_

private

Referenced by bb_N_index().

Size core::scoring::methods::ResidueCartBondedParameters::bb_O_index_

private

Referenced by bb_O_index().

utility::vector1< angle_parameter > core::scoring::methods::ResidueCartBondedParameters::bbdep_angle_params_

private

Referenced by add_bbdep_angle_parameter(), and bbdep_angle_parameters().

utility::vector1< length_parameter > core::scoring::methods::ResidueCartBondedParameters::bbdep_length_params_

private

Referenced by add_bbdep_length_parameter(), and bbdep_length_parameters().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::ca_cprev_n_h_interres_torsion_params_

private

Referenced by ca_cprev_n_h_interres_torsion_params().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::ca_nnext_c_o_interres_torsion_params_

private

Referenced by ca_nnext_c_o_interres_torsion_params().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::cprev_n_bond_length_params_

private

Referenced by cprev_n_bond_length_params().

utility::vector1< torsion_parameter > core::scoring::methods::ResidueCartBondedParameters::improper_torsion_params_

private

Referenced by add_improper_torsion_parameter(), and improper_torsion_parameters().

utility::vector1< length_parameter > core::scoring::methods::ResidueCartBondedParameters::length_params_

private

Referenced by add_length_parameter(), and length_parameters().

utility::vector1< angle_parameter > core::scoring::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().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::oprev_cprev_n_h_interres_torsion_params_

private

Referenced by oprev_cprev_n_h_interres_torsion_params().

CartBondedParametersCOP core::scoring::methods::ResidueCartBondedParameters::pro_cd_cprev_n_ca_interres_torsion_params_

private

Referenced by pro_cd_cprev_n_ca_interres_torsion_params().

Size core::scoring::methods::ResidueCartBondedParameters::pro_CD_index_

private

Referenced by pro_CD_index().

utility::vector1< torsion_parameter > core::scoring::methods::ResidueCartBondedParameters::torsion_params_

private

Referenced by add_torsion_parameter(), and torsion_parameters().

utility::vector1< angle_parameter > core::scoring::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:

• src/core/scoring/methods/CartesianBondedEnergy.hh
• src/core/scoring/methods/CartesianBondedEnergy.cc