core::scoring::disulfides::FullatomDisulfidePotential Class Reference

#include <FullatomDisulfidePotential.hh>

Inheritance diagram for core::scoring::disulfides::FullatomDisulfidePotential:

Public Types
typedef utility::VirtualBase	parent

Public Member Functions
	FullatomDisulfidePotential ()
	~FullatomDisulfidePotential () override
void	print_score_functions () const
void	score_this_disulfide_old (conformation::Residue const &res1, conformation::Residue const &res2, DisulfideAtomIndices const &res1_atom_indices, DisulfideAtomIndices const &res2_atom_indices, Energy &distance_score_this_disulfide, Energy &csangles_score_this_disulfide, Energy &dihedral_score_this_disulfide, Energy &ca_dihedral_sc_this_disulf, bool &truefalse_fa_disulf) const
	Calculated scores for a disulfide bond between two residues. More...
void	get_disulfide_derivatives_old (conformation::Residue const &res1, conformation::Residue const &res2, DisulfideAtomIndices const &res1_atom_indices, DisulfideAtomIndices const &res2_atom_indices, Size const at1, EnergyMap const &weights, Vector &F1, Vector &F2) const
void	score_this_disulfide (conformation::Residue const &res1, conformation::Residue const &res2, DisulfideAtomIndices const &res1_atom_indices, DisulfideAtomIndices const &res2_atom_indices, Energy &score) const
void	get_disulfide_derivatives (conformation::Residue const &res1, conformation::Residue const &res2, DisulfideAtomIndices const &res1_atom_indices, DisulfideAtomIndices const &res2_atom_indices, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const

Private Member Functions
void	get_disulfide_params (conformation::Residue const &res1, conformation::Residue const &res2, DisulfideAtomIndices const &res1_atom_indices, DisulfideAtomIndices const &res2_atom_indices, Distance &dist_between_sulfurs, Real &cs_bond_angle_1, Real &cs_bond_angle_2, Real &disulf_dihedral_angle, Real &disulf_ca_dihedral_angle_1, Real &disulf_ca_dihedral_angle_2) const
	Private: Methods, Data Initializers ///. More...

Private Attributes
Real const	disulf_ssdist_cutoff_
CBSG_Dihedral_FuncOP	cbsg_dihedral_func_
SGSG_Dihedral_FuncOP	sgsg_dihedral_func_
CB_Angle_FuncOP	cb_angle_func_
SG_Dist_FuncOP	sg_dist_func_
Real	wt_dihSS_
Real	wt_dihCS_
Real	wt_ang_
Real	wt_len_
Real	shift_
Real	mest_
FullatomDisulfideParams13	params_

Member Typedef Documentation

typedef utility::VirtualBase core::scoring::disulfides::FullatomDisulfidePotential::parent

Constructor & Destructor Documentation

core::scoring::disulfides::FullatomDisulfidePotential::FullatomDisulfidePotential

(

)

References mest_.

core::scoring::disulfides::FullatomDisulfidePotential::~FullatomDisulfidePotential ( )

overridedefault

Member Function Documentation

void core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		DisulfideAtomIndices const &	res1_atom_indices,
		DisulfideAtomIndices const &	res2_atom_indices,
		EnergyMap const &	weights,
		utility::vector1< DerivVectorPair > &	r1_atom_derivs,
		utility::vector1< DerivVectorPair > &	r2_atom_derivs
	)		const

References core::scoring::disulfides::FullatomDisulfideParams13::a_kappa, core::scoring::disulfides::FullatomDisulfideParams13::a_mu, core::scoring::disulfides::DisulfideAtomIndices::c_alpha_index(), core::scoring::disulfides::DisulfideAtomIndices::c_beta_index(), core::scoring::disulfides::FullatomDisulfideParams13::d_location, core::scoring::disulfides::FullatomDisulfideParams13::d_scale, core::scoring::disulfides::FullatomDisulfideParams13::d_shape, core::scoring::disulfides::FullatomDisulfideParams13::dcs_kappa1, core::scoring::disulfides::FullatomDisulfideParams13::dcs_kappa2, core::scoring::disulfides::FullatomDisulfideParams13::dcs_kappa3, core::scoring::disulfides::FullatomDisulfideParams13::dcs_logA1, core::scoring::disulfides::FullatomDisulfideParams13::dcs_logA2, core::scoring::disulfides::FullatomDisulfideParams13::dcs_logA3, core::scoring::disulfides::FullatomDisulfideParams13::dcs_mu1, core::scoring::disulfides::FullatomDisulfideParams13::dcs_mu2, core::scoring::disulfides::FullatomDisulfideParams13::dcs_mu3, core::scoring::disulfides::DisulfideAtomIndices::disulf_atom_index(), core::scoring::dslf_fa13, core::scoring::disulfides::FullatomDisulfideParams13::dss_kappa1, core::scoring::disulfides::FullatomDisulfideParams13::dss_kappa2, core::scoring::disulfides::FullatomDisulfideParams13::dss_logA1, core::scoring::disulfides::FullatomDisulfideParams13::dss_logA2, core::scoring::disulfides::FullatomDisulfideParams13::dss_mu1, core::scoring::disulfides::FullatomDisulfideParams13::dss_mu2, get_disulfide_params(), core::chemical::ResidueTypeBase::is_d_aa(), mest_, params_, core::conformation::Residue::type(), wt_ang_, wt_dihCS_, wt_dihSS_, wt_len_, and core::conformation::Residue::xyz().

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), and core::energy_methods::FullatomDisulfideEnergy::eval_residue_pair_derivatives().

void core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_derivatives_old	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		DisulfideAtomIndices const &	res1_atom_indices,
		DisulfideAtomIndices const &	res2_atom_indices,
		Size const	at1,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

References core::conformation::Residue::atom_index(), core::scoring::disulfides::DisulfideAtomIndices::c_alpha_index(), core::scoring::disulfides::DisulfideAtomIndices::c_beta_index(), cb_angle_func_, cbsg_dihedral_func_, core::scoring::disulfides::CYS_C_ALPHA, core::scoring::disulfides::CYS_C_BETA, core::scoring::disulfides::CYS_S_GAMMA, core::scoring::disulfides::DisulfideAtomIndices::derivative_atom(), core::scoring::disulfides::DisulfideAtomIndices::disulf_atom_index(), core::scoring::dslf_ca_dih, core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dih, core::scoring::dslf_ss_dst, core::conformation::Residue::seqpos(), sg_dist_func_, and sgsg_dihedral_func_.

Referenced by core::energy_methods::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), and core::energy_methods::FullatomDisulfideEnergy::old_eval_atom_derivative().

void core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params ( conformation::Residue const &  res1, conformation::Residue const &  res2, DisulfideAtomIndices const &  res1_atom_indices, DisulfideAtomIndices const &  res2_atom_indices, Distance &  dist_between_sulfurs, Real &  cs_bond_angle_1, Real &  cs_bond_angle_2, Real &  disulf_dihedral_angle, Real &  disulf_ca_dihedral_angle_1, Real &  disulf_ca_dihedral_angle_2  ) const

private

Private: Methods, Data Initializers ///.

Calculates several geometrical parameters of a fullatom disulfide bond

given residue num for 2 cys involved in disulfide bond, returns four quantities: sulf-sulf dist, 2 carb-sulf bond angles, and a 4-atom dihedral angle. Angles are returned in degrees.

Parameters

[in]	coord1	- in - fullatom coords of cys 1
[in]	coord2	- in - fullatom coords of cys 2
[out]	dist_between_sulfurs	- out - s1-s2 distance
[out]	cs_bond_angle_1	- out - cb1-s1-s2 bond angle
[out]	cs_bond_angle_2	- out - cb2-s1-s2 bond angle
[out]	disulf_dihedral_angle	- out - cb1-s1-s2-cb2 dihedral
[out]	disulf_ca_dihedral_angle_1	- out - ca1-cb1-s1-s2 dihedral
[out]	disulf_ca_dihedral_angle_2	- out - ca2-cb2-s2-s1 dihedral

Author

Bill Schief

References core::conformation::Residue::atom(), core::scoring::disulfides::DisulfideAtomIndices::c_alpha_index(), core::scoring::disulfides::DisulfideAtomIndices::c_beta_index(), core::scoring::disulfides::DisulfideAtomIndices::disulf_atom_index(), and protocols::kinmatch::xyz().

Referenced by get_disulfide_derivatives(), score_this_disulfide(), and score_this_disulfide_old().

void core::scoring::disulfides::FullatomDisulfidePotential::print_score_functions

(

)

const

References cb_angle_func_, cbsg_dihedral_func_, core::kinematics::distance(), sg_dist_func_, and sgsg_dihedral_func_.

void core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		DisulfideAtomIndices const &	res1_atom_indices,
		DisulfideAtomIndices const &	res2_atom_indices,
		Energy &	score
	)		const

References core::scoring::disulfides::FullatomDisulfideParams13::a_kappa, core::scoring::disulfides::FullatomDisulfideParams13::a_logA, core::scoring::disulfides::FullatomDisulfideParams13::a_mu, core::scoring::disulfides::FullatomDisulfideParams13::d_location, core::scoring::disulfides::FullatomDisulfideParams13::d_scale, core::scoring::disulfides::FullatomDisulfideParams13::d_shape, core::scoring::disulfides::FullatomDisulfideParams13::dcs_kappa1, core::scoring::disulfides::FullatomDisulfideParams13::dcs_kappa2, core::scoring::disulfides::FullatomDisulfideParams13::dcs_kappa3, core::scoring::disulfides::FullatomDisulfideParams13::dcs_logA1, core::scoring::disulfides::FullatomDisulfideParams13::dcs_logA2, core::scoring::disulfides::FullatomDisulfideParams13::dcs_logA3, core::scoring::disulfides::FullatomDisulfideParams13::dcs_mu1, core::scoring::disulfides::FullatomDisulfideParams13::dcs_mu2, core::scoring::disulfides::FullatomDisulfideParams13::dcs_mu3, core::scoring::disulfides::FullatomDisulfideParams13::dss_kappa1, core::scoring::disulfides::FullatomDisulfideParams13::dss_kappa2, core::scoring::disulfides::FullatomDisulfideParams13::dss_logA1, core::scoring::disulfides::FullatomDisulfideParams13::dss_logA2, core::scoring::disulfides::FullatomDisulfideParams13::dss_mixed_kappa1, core::scoring::disulfides::FullatomDisulfideParams13::dss_mixed_kappa2, core::scoring::disulfides::FullatomDisulfideParams13::dss_mixed_logA1, core::scoring::disulfides::FullatomDisulfideParams13::dss_mixed_logA2, core::scoring::disulfides::FullatomDisulfideParams13::dss_mixed_mu1, core::scoring::disulfides::FullatomDisulfideParams13::dss_mixed_mu2, core::scoring::disulfides::FullatomDisulfideParams13::dss_mu1, core::scoring::disulfides::FullatomDisulfideParams13::dss_mu2, get_disulfide_params(), core::chemical::ResidueTypeBase::is_d_aa(), mest_, params_, shift_, core::conformation::Residue::type(), wt_ang_, wt_dihCS_, wt_dihSS_, and wt_len_.

Referenced by core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy(), core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy_ext(), and protocols::ligand_docking::ga_ligand_dock::GridScorer::score().

void core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide_old	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2,
		DisulfideAtomIndices const &	res1_atom_indices,
		DisulfideAtomIndices const &	res2_atom_indices,
		Energy &	distance_score_this_disulfide,
		Energy &	csangles_score_this_disulfide,
		Energy &	dihedral_score_this_disulfide,
		Energy &	ca_dihedral_sc_this_disulf,
		bool &	truefalse_fa_disulf
	)		const

Calculated scores for a disulfide bond between two residues.

Parameters

[in]	res1	The lower residue of the disulfide
[in]	res2	The upper residue of the disulfide. Assumed to be bonded to res1
[out]	distance_score_this_disulfide	A score based on S-S distance
[out]	csangles_score_this_disulfide	A score based on the Cb-S angles
[out]	dihedral_score_this_disulfide	A score based on the S-S dihedral
[out]	ca_dihedral_sc_this_disulf	A score based on the Cb-S dihedrals
[out]	truefalse_fa_disulf	True if these residues should be disulfide bonded

Scores are interpolated from the histograms created by the farlx_*_initializer methods. The distance score has such a histogram as its core with two linear functions at either side so that the score increases to infinity

References cb_angle_func_, cbsg_dihedral_func_, disulf_ssdist_cutoff_, get_disulfide_params(), sg_dist_func_, and sgsg_dihedral_func_.

Referenced by core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy(), and core::energy_methods::FullatomDisulfideEnergy::residue_pair_energy_ext().

Member Data Documentation

CB_Angle_FuncOP core::scoring::disulfides::FullatomDisulfidePotential::cb_angle_func_

private

Referenced by get_disulfide_derivatives_old(), print_score_functions(), and score_this_disulfide_old().

CBSG_Dihedral_FuncOP core::scoring::disulfides::FullatomDisulfidePotential::cbsg_dihedral_func_

private

Referenced by get_disulfide_derivatives_old(), print_score_functions(), and score_this_disulfide_old().

Real const core::scoring::disulfides::FullatomDisulfidePotential::disulf_ssdist_cutoff_

private

Referenced by score_this_disulfide_old().

Real core::scoring::disulfides::FullatomDisulfidePotential::mest_

private

Referenced by FullatomDisulfidePotential(), get_disulfide_derivatives(), and score_this_disulfide().

FullatomDisulfideParams13 core::scoring::disulfides::FullatomDisulfidePotential::params_

private

Referenced by get_disulfide_derivatives(), and score_this_disulfide().

SG_Dist_FuncOP core::scoring::disulfides::FullatomDisulfidePotential::sg_dist_func_

private

Referenced by get_disulfide_derivatives_old(), print_score_functions(), and score_this_disulfide_old().

SGSG_Dihedral_FuncOP core::scoring::disulfides::FullatomDisulfidePotential::sgsg_dihedral_func_

private

Referenced by get_disulfide_derivatives_old(), print_score_functions(), and score_this_disulfide_old().

Real core::scoring::disulfides::FullatomDisulfidePotential::shift_

private

Referenced by score_this_disulfide().

Real core::scoring::disulfides::FullatomDisulfidePotential::wt_ang_

private

Referenced by get_disulfide_derivatives(), and score_this_disulfide().

Real core::scoring::disulfides::FullatomDisulfidePotential::wt_dihCS_

private

Referenced by get_disulfide_derivatives(), and score_this_disulfide().

Real core::scoring::disulfides::FullatomDisulfidePotential::wt_dihSS_

private

Referenced by get_disulfide_derivatives(), and score_this_disulfide().

Real core::scoring::disulfides::FullatomDisulfidePotential::wt_len_

private

Referenced by get_disulfide_derivatives(), and score_this_disulfide().

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

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