Rosetta
|
secondary structure scoring cut from classic rosetta structure.h/structure.cc More...
#include <SSPairPotential.hh>
Public Types | |
typedef std::string | String |
typedef core::Size | Size |
typedef core::Real | Real |
typedef core::Vector | Vector |
typedef core::pose::Pose | Pose |
typedef core::scoring::EnergyGraph | EnergyGraph |
typedef protocols::fldsgn::topology::DimerPairing | DimerPairing |
typedef protocols::fldsgn::topology::BB_Pos | BB_Pos |
typedef protocols::fldsgn::topology::SS_Info2 | SS_Info2 |
typedef protocols::fldsgn::topology::DimerPairings | DimerPairings |
typedef ObjexxFCL::FArray1D< int > | FArray1D_int |
typedef ObjexxFCL::FArray1D< Real > | FArray1D_real |
typedef ObjexxFCL::FArray4D< Real > | FArray4D_real |
Public Member Functions | |
SSPairPotential () | |
default constructor More... | |
~SSPairPotential () override | |
default destructor More... | |
void | score (Pose const &pose, SS_Info2 const &ss_info, DimerPairings &dimer_pairs, Real &ss_score) const |
score secondary structure More... | |
Private Member Functions | |
void | pair_dp (core::Size const &ss1, core::Size const &ss2, BB_Pos const &bb_pos, Real &dp, Vector const &mid_vector, core::Size &sign1, core::Size &sign2) const |
calculate sum of dot product of the co vectors of strand dimers ss1 and ss2 More... | |
Real | calc_phithetascore (core::Size const strand_seqsep, Real const phi, Real const theta) const |
return score of phitheta More... | |
Real | calc_dotscore (Real const dpall) const |
return dot score More... | |
Real | calc_rsigmascore (Real sig, Real dist, core::Size const sign1, core::Size const sign2) const |
return rsigma score More... | |
void | load_phi_theta_bins (String const &ss_filename="scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth") |
load phi/theta bins for use in secondary structure scoring More... | |
void | load_dotscore_bins () |
Static Private Member Functions | |
static void | rsigma_dot_initializer (FArray4D_real &rsigma_dot) |
Private Attributes | |
Real | strand_dist_cutoff_ |
core::Size | dimer_seqsep_cutoff_ |
core::Size | lowstrand_ |
FArray4D_real | phithetascore_ |
FArray1D_real | dotscore_ |
FArray4D_real | rsigma_dot_ |
secondary structure scoring cut from classic rosetta structure.h/structure.cc
typedef protocols::fldsgn::topology::BB_Pos protocols::fldsgn::potentials::sspot::SSPairPotential::BB_Pos |
typedef protocols::fldsgn::topology::DimerPairing protocols::fldsgn::potentials::sspot::SSPairPotential::DimerPairing |
typedef protocols::fldsgn::topology::DimerPairings protocols::fldsgn::potentials::sspot::SSPairPotential::DimerPairings |
typedef core::scoring::EnergyGraph protocols::fldsgn::potentials::sspot::SSPairPotential::EnergyGraph |
typedef ObjexxFCL::FArray1D< int > protocols::fldsgn::potentials::sspot::SSPairPotential::FArray1D_int |
typedef ObjexxFCL::FArray1D< Real > protocols::fldsgn::potentials::sspot::SSPairPotential::FArray1D_real |
typedef ObjexxFCL::FArray4D< Real > protocols::fldsgn::potentials::sspot::SSPairPotential::FArray4D_real |
typedef protocols::fldsgn::topology::SS_Info2 protocols::fldsgn::potentials::sspot::SSPairPotential::SS_Info2 |
typedef std::string protocols::fldsgn::potentials::sspot::SSPairPotential::String |
protocols::fldsgn::potentials::sspot::SSPairPotential::SSPairPotential | ( | ) |
default constructor
References load_dotscore_bins(), and load_phi_theta_bins().
|
overridedefault |
default destructor
destructor
|
private |
|
private |
|
private |
|
private |
References dotscore_.
Referenced by SSPairPotential().
|
private |
load phi/theta bins for use in secondary structure scoring
References phithetascore_.
Referenced by SSPairPotential().
|
private |
calculate sum of dot product of the co vectors of strand dimers ss1 and ss2
with the vector connecting the midpoints of the dimer vectors (vdist)
also determine return the sign of the dot products for each dimer
to determine which direction the CO groups point
References protocols::fldsgn::topology::BB_Pos::C(), and protocols::fldsgn::topology::BB_Pos::O().
Referenced by score().
|
staticprivate |
void protocols::fldsgn::potentials::sspot::SSPairPotential::score | ( | Pose const & | pose, |
SS_Info2 const & | ss_info, | ||
DimerPairings & | dimer_pairs, | ||
Real & | ss_score | ||
) | const |
score secondary structure
References protocols::fldsgn::topology::SS_Info2::bb_pos(), protocols::fldsgn::topology::BB_Pos::C(), calc_dotscore(), calc_phithetascore(), calc_rsigmascore(), dimer_seqsep_cutoff_, core::sequence::end, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::fldsgn::topology::DimerPairings::finalize(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::chemical::ResidueType::is_upper_terminus(), lowstrand_, protocols::fldsgn::topology::BB_Pos::N(), pair_dp(), protocols::fldsgn::topology::DimerPairing::res1(), protocols::fldsgn::topology::DimerPairing::res2(), core::pose::Pose::residue_type(), protocols::fldsgn::topology::DimerPairing::score(), protocols::fldsgn::potentials::sspot::spherical(), protocols::loops::loop_closure::ccd::strand, strand_dist_cutoff_, protocols::fldsgn::topology::SS_Info2::strand_id(), protocols::fldsgn::topology::SS_Info2::strands(), and protocols::fldsgn::topology::DimerPairing::valid().
|
private |
Referenced by score().
|
private |
Referenced by calc_dotscore(), and load_dotscore_bins().
|
private |
Referenced by score().
|
private |
Referenced by calc_phithetascore(), and load_phi_theta_bins().
|
private |
Referenced by calc_rsigmascore().
|
private |
Referenced by score().