core::scoring::disulfides::DisulfideAtomIndices Class Reference

This class is used by the *DisulfideEnergyContainer and the *DisulfidePotential classes to rapidly index into a residue that's known to form a disulfide. For the sake of computing derivatives, there are only three atoms that need to be readily available: CA, CB, and the atom which makes the disulfide bond, either SG or CEN. The DisulfideEnergyContainer is responsible for keeping the indices in one of these objects up-to-date with the residue it is meant to shadow. More...

#include <DisulfideAtomIndices.hh>

Public Member Functions
	DisulfideAtomIndices (conformation::Residue const &res)
bool	atom_gets_derivatives (Size atom_index) const
DisulfideDerivativeAtom	derivative_atom (Size atom_index) const
Size	c_alpha_index () const
Size	c_beta_index () const
Size	disulf_atom_index () const
	The atom which participates in the disulfide bond SG for fullatom or CEN for centroid. More...

Private Attributes
Size	c_alpha_index_
Size	c_beta_index_
Size	disulf_atom_index_
utility::vector1< DisulfideDerivativeAtom >	derivative_atom_types_

Detailed Description

This class is used by the *DisulfideEnergyContainer and the *DisulfidePotential classes to rapidly index into a residue that's known to form a disulfide. For the sake of computing derivatives, there are only three atoms that need to be readily available: CA, CB, and the atom which makes the disulfide bond, either SG or CEN. The DisulfideEnergyContainer is responsible for keeping the indices in one of these objects up-to-date with the residue it is meant to shadow.

Constructor & Destructor Documentation

DisulfideAtomIndices()

core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices

(

conformation::Residue const &

res

)

References core::chemical::ResidueType::atom_base(), core::conformation::Residue::atom_index(), c_alpha_index_, c_beta_index_, core::scoring::disulfides::CYS_C_ALPHA, core::scoring::disulfides::CYS_C_BETA, core::scoring::disulfides::CYS_CEN, core::scoring::disulfides::CYS_S_GAMMA, derivative_atom_types_, disulf_atom_index_, core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::chemical::ResidueType::has(), core::scoring::disulfides::TR(), and core::conformation::Residue::type().

Member Function Documentation

atom_gets_derivatives()

bool core::scoring::disulfides::DisulfideAtomIndices::atom_gets_derivatives

(

Size

atom_index

)

const

References derivative_atom_types_, and core::scoring::disulfides::NO_DERIVATIVES_FOR_ATOM.

c_alpha_index()

Size core::scoring::disulfides::DisulfideAtomIndices::c_alpha_index ( ) const

inline

References c_alpha_index_.

Referenced by core::energy_methods::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), and core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params().

c_beta_index()

Size core::scoring::disulfides::DisulfideAtomIndices::c_beta_index ( ) const

inline

References c_beta_index_.

Referenced by core::energy_methods::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), and core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params().

derivative_atom()

DisulfideDerivativeAtom core::scoring::disulfides::DisulfideAtomIndices::derivative_atom

(

Size

atom_index

)

const

References derivative_atom_types_.

Referenced by core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old().

disulf_atom_index()

Size core::scoring::disulfides::DisulfideAtomIndices::disulf_atom_index ( ) const

inline

The atom which participates in the disulfide bond SG for fullatom or CEN for centroid.

References disulf_atom_index_.

Referenced by core::energy_methods::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old(), and core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params().

Member Data Documentation

c_alpha_index_

Size core::scoring::disulfides::DisulfideAtomIndices::c_alpha_index_

private

Referenced by c_alpha_index(), and DisulfideAtomIndices().

c_beta_index_

Size core::scoring::disulfides::DisulfideAtomIndices::c_beta_index_

private

Referenced by c_beta_index(), and DisulfideAtomIndices().

derivative_atom_types_

utility::vector1< DisulfideDerivativeAtom > core::scoring::disulfides::DisulfideAtomIndices::derivative_atom_types_

private

Referenced by atom_gets_derivatives(), derivative_atom(), and DisulfideAtomIndices().

disulf_atom_index_

Size core::scoring::disulfides::DisulfideAtomIndices::disulf_atom_index_

private

Referenced by disulf_atom_index(), and DisulfideAtomIndices().

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

• src/core/scoring/disulfides/DisulfideAtomIndices.hh
• src/core/scoring/disulfides/DisulfideAtomIndices.cc