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core::scoring::Ramachandran Class Reference

#include <Ramachandran.hh>

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Public Types

typedef pose::Pose Pose
 
typedef chemical::AA AA
 

Public Member Functions

 Ramachandran ()
 
 Ramachandran (std::string const &rama_map_filename, bool use_bicubic_interpolation)
 
virtual ~Ramachandran ()
 
Real eval_rama_score_residue (AA const res_aa, Real const phi, Real const psi) const
 
void eval_rama_score_residue (conformation::Residue const &res, Real &rama, Real &drama_dphi, Real &drama_dpsi) const
 
void eval_rama_score_residue (AA const res_aa, Real const phi, Real const psi, Real &rama, Real &drama_dphi, Real &drama_dpsi) const
 
void eval_rama_score_residue (bool use_bicubic_interpolation, bool rama_not_squared, AA const res_aa, Real const phi, Real const psi, Real &rama, Real &drama_dphi, Real &drama_dpsi) const
 
void random_phipsi_from_rama (AA const res_aa, Real &phi, Real &psi) const
 
void random_phipsi_from_rama_by_torsion_bin (AA const res_aa, Real &phi, Real &psi, char const torsion_bin) const
 functions for torsion-bin specific but otherwise random phi/psi angles More...
 
core::Size get_torsion_bin_index (char torsion_bin) const
 
void init_rama_sampling_tables_by_torsion_bin ()
 
void get_entries_per_torsion_bin (AA const res_aa, std::map< char, core::Size > &tb_frequencies) const
 
void eval_rama_score_all (Pose &pose, ScoreFunction const &scorefxn) const
 evaluate rama score for each (protein) residue and store that score in the pose.energies() object More...
 
void write_rama_score_all (Pose const &pose) const
 
void eval_procheck_rama (Pose const &a_pose, Real &favorable, Real &allowed, Real &generous) const
 

Private Member Functions

void read_rama (std::string const &rama_map_filename, bool use_bicubic_interpolation)
 
void init_rama_sampling_table (char const torsion_bin)
 

Private Attributes

utility::vector1
< numeric::interpolation::spline::BicubicSpline > 		rama_energy_splines_
 
utility::vector1
< utility::vector1
< utility::vector1< Real > > > 		rama_sampling_table_
 
utility::vector1
< utility::vector1
< utility::vector1
< utility::vector1< Real > > > > 		rama_sampling_table_by_torsion_bin_
 

Static Private Attributes

static bool rama_initialized_
 
static ObjexxFCL::FArray4D< Real > ram_probabil_
 
static ObjexxFCL::FArray4D_int ram_counts_
 
static ObjexxFCL::FArray4D< Real > ram_energ_
 
static int const n_phi_ = 36
 
static int const n_psi_ = 36
 
static Real const binw_
 
static Real const rama_sampling_thold_
 
static Real const rama_sampling_factor_
 
static int const n_aa_ = 20
 
static ObjexxFCL::FArray2D< Real > ram_entropy_
 

Detailed Description

Definition at line 52 of file Ramachandran.hh.

Member Typedef Documentation

typedef chemical::AA core::scoring::Ramachandran::AA

Definition at line 56 of file Ramachandran.hh.

typedef pose::Pose core::scoring::Ramachandran::Pose

Definition at line 55 of file Ramachandran.hh.

Constructor & Destructor Documentation

core::scoring::Ramachandran::Ramachandran ( )

Definition at line 78 of file Ramachandran.cc.

core::scoring::Ramachandran::Ramachandran ( std::string const &  rama_map_filename,
bool  use_bicubic_interpolation 
)

Definition at line 87 of file Ramachandran.cc.

core::scoring::Ramachandran::~Ramachandran ( )
virtual

Definition at line 65 of file Ramachandran.cc.

Member Function Documentation

void core::scoring::Ramachandran::eval_procheck_rama ( Pose const &  a_pose,
Real &  favorable,
Real &  allowed,
Real &  generous 
) const

Definition at line 588 of file Ramachandran.cc.

void core::scoring::Ramachandran::eval_rama_score_all ( pose::Pose &  pose,
ScoreFunction const &  scorefxn 
) const

evaluate rama score for each (protein) residue and store that score in the pose.energies() object

Definition at line 100 of file Ramachandran.cc.

References core::pose::Pose::energies(), core::scoring::ScoreFunction::has_zero_weight(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::scoring::Energies::onebody_energies(), core::scoring::rama, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), and core::optimization::symmetry::SymAtomTreeMultifunc::dump().

Real core::scoring::Ramachandran::eval_rama_score_residue ( AA const  res_aa,
Real const  phi,
Real const  psi 
) const

Definition at line 465 of file Ramachandran.cc.

References core::scoring::rama.

Referenced by core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_c_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_full(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_full(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_n_terminus(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_phi_only(), protocols::swa::StepWiseScreener::get_main_chain_torsion_set_list_sample_psi_only(), protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_psi_only(), protocols::simple_moves::SmallMover::make_move(), protocols::simple_moves::ShearMover::make_move(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_rama_check(), and core::scoring::methods::RamachandranEnergy::residue_energy().

void core::scoring::Ramachandran::eval_rama_score_residue ( conformation::Residue const &  res,
Real &  rama,
Real &  drama_dphi,
Real &  drama_dpsi 
) const

Definition at line 434 of file Ramachandran.cc.

References core::conformation::Residue::aa(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::mainchain_torsion(), protocols::swa::phi(), protocols::swa::psi(), and core::scoring::rama.

void core::scoring::Ramachandran::eval_rama_score_residue ( AA const  res_aa,
Real const  phi,
Real const  psi,
Real &  rama,
Real &  drama_dphi,
Real &  drama_dpsi 
) const

Definition at line 478 of file Ramachandran.cc.

void core::scoring::Ramachandran::eval_rama_score_residue ( bool  use_bicubic_interpolation,
bool  rama_not_squared,
AA const  res_aa,
Real const  phi,
Real const  psi,
Real &  rama,
Real &  drama_dphi,
Real &  drama_dpsi 
) const

Definition at line 496 of file Ramachandran.cc.

References core::scoring::rama.

void core::scoring::Ramachandran::get_entries_per_torsion_bin ( AA const  res_aa,
std::map< char, core::Size > &  tb_frequencies 
) const

Definition at line 419 of file Ramachandran.cc.

References init_rama_sampling_tables_by_torsion_bin().

Referenced by protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::refill_torsion_string_vector().

core::Size core::scoring::Ramachandran::get_torsion_bin_index ( char  torsion_bin) const

Definition at line 401 of file Ramachandran.cc.

void core::scoring::Ramachandran::init_rama_sampling_table ( char const  torsion_bin)
private

Initialize the table holding the sample-able torsion space for each residue with each torsion given indices proportionate to its probability

Definition at line 165 of file Ramachandran.cc.

References core::conformation::get_torsion_bin(), and core::io::serialization::size().

void core::scoring::Ramachandran::init_rama_sampling_tables_by_torsion_bin ( )

Definition at line 409 of file Ramachandran.cc.

Referenced by get_entries_per_torsion_bin().

void core::scoring::Ramachandran::random_phipsi_from_rama ( AA const  res_aa,
Real &  phi,
Real &  psi 
) const

Sample phi/psi torsions with probabilities proportionate to their Ramachandran probabilities Note – this function had previously required that the option loops::nonpivot_torsion_sampling be active. This function now performs a just-in-time check to initialize these tables the first time they are requested – To properly multi-thread this code, the function should nab a mutex so that no two threads try to execute the code at once.

Definition at line 292 of file Ramachandran.cc.

Referenced by protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain().

void core::scoring::Ramachandran::random_phipsi_from_rama_by_torsion_bin ( AA const  res_aa,
Real &  phi,
Real &  psi,
char const  torsion_bin 
) const

functions for torsion-bin specific but otherwise random phi/psi angles

Author
Amelie Stein

Sample phi/psi torsions with probabilities proportionate to their Ramachandran probabilities – this version performs lookup restricted to specified torsion bins based on random_phipsi_from_rama and has the same issue for parallel running

Author
Amelie Stein (ameli.nosp@m.e.st.nosp@m.ein@u.nosp@m.csf..nosp@m.edu)
Date
Fri May 11 15:52:01 PDT 2012

returns a random phi/psi combination within the given torsion bin – WARNING: this will only work for the torsion bins that are currently implemented

Definition at line 339 of file Ramachandran.cc.

Referenced by protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber::perturb_chain(), and protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber::perturb_chain().

void core::scoring::Ramachandran::read_rama ( std::string const &  rama_map_filename,
bool  use_bicubic_interpolation 
)
private

Definition at line 597 of file Ramachandran.cc.

References core::chemical::num_canonical_aas.

void core::scoring::Ramachandran::write_rama_score_all ( Pose const &  pose) const

Definition at line 158 of file Ramachandran.cc.

Member Data Documentation

Real const core::scoring::R::binw_
staticprivate

Definition at line 176 of file Ramachandran.hh.

int const core::scoring::Ramachandran::n_aa_ = 20
staticprivate

Definition at line 179 of file Ramachandran.hh.

int const core::scoring::Ramachandran::n_phi_ = 36
staticprivate

Definition at line 174 of file Ramachandran.hh.

int const core::scoring::Ramachandran::n_psi_ = 36
staticprivate

Definition at line 175 of file Ramachandran.hh.

ObjexxFCL::FArray4D_int core::scoring::R::ram_counts_
staticprivate

Definition at line 169 of file Ramachandran.hh.

ObjexxFCL::FArray4D< Real > core::scoring::R::ram_energ_
staticprivate

Definition at line 171 of file Ramachandran.hh.

ObjexxFCL::FArray2D< Real > core::scoring::R::ram_entropy_
staticprivate

Definition at line 180 of file Ramachandran.hh.

ObjexxFCL::FArray4D< Real > core::scoring::R::ram_probabil_
staticprivate

Definition at line 167 of file Ramachandran.hh.

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::Ramachandran::rama_energy_splines_
private

Definition at line 172 of file Ramachandran.hh.

bool core::scoring::R::rama_initialized_
staticprivate

Definition at line 165 of file Ramachandran.hh.

Real const core::scoring::R::rama_sampling_factor_
staticprivate

Definition at line 178 of file Ramachandran.hh.

utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::Ramachandran::rama_sampling_table_
private

Definition at line 181 of file Ramachandran.hh.

utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > core::scoring::Ramachandran::rama_sampling_table_by_torsion_bin_
private

Definition at line 182 of file Ramachandran.hh.

Real const core::scoring::R::rama_sampling_thold_
staticprivate

Definition at line 177 of file Ramachandran.hh.

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