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

#include <FullatomDisulfidePotential.hh>

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

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

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]res1The lower residue of the disulfide
[in]res2The upper residue of the disulfide. Assumed to be bonded to res1
[out]distance_score_this_disulfideA score based on S-S distance
[out]csangles_score_this_disulfideA score based on the Cb-S angles
[out]dihedral_score_this_disulfideA score based on the S-S dihedral
[out]ca_dihedral_sc_this_disulfA score based on the Cb-S dihedrals
[out]truefalse_fa_disulfTrue 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::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), and core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext().

Member Data Documentation

CB_Angle_FuncOP core::scoring::disulfides::FullatomDisulfidePotential::cb_angle_func_
private
CBSG_Dihedral_FuncOP core::scoring::disulfides::FullatomDisulfidePotential::cbsg_dihedral_func_
private
Real const core::scoring::disulfides::FullatomDisulfidePotential::disulf_ssdist_cutoff_
private
Real core::scoring::disulfides::FullatomDisulfidePotential::mest_
private
FullatomDisulfideParams13 core::scoring::disulfides::FullatomDisulfidePotential::params_
private
SG_Dist_FuncOP core::scoring::disulfides::FullatomDisulfidePotential::sg_dist_func_
private
SGSG_Dihedral_FuncOP core::scoring::disulfides::FullatomDisulfidePotential::sgsg_dihedral_func_
private
Real core::scoring::disulfides::FullatomDisulfidePotential::shift_
private

Referenced by score_this_disulfide().

Real core::scoring::disulfides::FullatomDisulfidePotential::wt_ang_
private
Real core::scoring::disulfides::FullatomDisulfidePotential::wt_dihCS_
private
Real core::scoring::disulfides::FullatomDisulfidePotential::wt_dihSS_
private
Real core::scoring::disulfides::FullatomDisulfidePotential::wt_len_
private

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