#include <FullatomDisulfidePotential.hh>

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

Collaboration diagram for core::scoring::disulfides::FullatomDisulfidePotential:

Public Types
typedef utility::pointer::ReferenceCount	parent

Public Member Functions
	FullatomDisulfidePotential ()

virtual	~FullatomDisulfidePotential ()

void	print_score_functions () const

void	score_this_disulfide (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 (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

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_

Detailed Description

Definition at line 46 of file FullatomDisulfidePotential.hh.

Member Typedef Documentation

typedef utility::pointer::ReferenceCount core::scoring::disulfides::FullatomDisulfidePotential::parent

Definition at line 49 of file FullatomDisulfidePotential.hh.

Constructor & Destructor Documentation

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

Definition at line 145 of file FullatomDisulfidePotential.cc.

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

virtual

Definition at line 154 of file FullatomDisulfidePotential.cc.

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,
		Size const	at1,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

Definition at line 271 of file FullatomDisulfidePotential.cc.

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::scoring::constraints::DihedralConstraint::fill_f1_f2(), core::scoring::constraints::AngleConstraint::fill_f1_f2(), core::scoring::constraints::AtomPairConstraint::fill_f1_f2(), core::conformation::Residue::seqpos(), sg_dist_func_, and sgsg_dihedral_func_.

Referenced by core::scoring::disulfides::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), and core::scoring::disulfides::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

Definition at line 422 of file FullatomDisulfidePotential.cc.

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 score_this_disulfide().

void core::scoring::disulfides::FullatomDisulfidePotential::print_score_functions ( ) const

Definition at line 157 of file FullatomDisulfidePotential.cc.

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 &	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

Definition at line 191 of file FullatomDisulfidePotential.cc.

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

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