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core::scoring::Ramachandran2B Class Reference

#include <Ramachandran2B.hh>

Inheritance diagram for core::scoring::Ramachandran2B:
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Public Types

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

Public Member Functions

 Ramachandran2B ()
 
virtual ~Ramachandran2B ()
 
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, chemical::AA const left_aa, chemical::AA const right_aa, Real &rama, Real &drama_dphi, Real &drama_dpsi) const
 
Real RamaE_Lower (conformation::Residue const &rsd, chemical::AA const &neighbor, Real &drama_dphi, Real &drama_dpsi) const
 
Real RamaE_Lower (conformation::Residue const &rsd, chemical::AA const &neighbor) const
 
Real RamaE_Upper (conformation::Residue const &rsd, chemical::AA const &neighbor, Real &drama_dphi, Real &drama_dpsi) const
 
Real RamaE_Upper (conformation::Residue const &rsd, chemical::AA const &neighbor) const
 
Real RamaE (conformation::Residue const &rsd, Real &drama_dphi, Real &drama_dpsi) const
 
Real RamaE (conformation::Residue const &rsd) 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 IdealizeRamaEnergy (Real const phi, Real const psi, Real &rama, Real &drama_dphi, Real &drama_dpsi, Real const entropy, ObjexxFCL::FArray2A< Real > const &rama_for_res) const
 
void random_phipsi_from_rama_left (AA const left_aa, AA const pos_aa, Real &phi, Real &psi) const
 
void random_phipsi_from_rama_right (AA const pos_aa, AA const right_aa, Real &phi, Real &psi) const
 
void random_phipsi_from_rama_by_torsion_bin_left (AA const left_aa, AA const pos_aa, Real &phi, Real &psi, char const torsion_bin) const
 function for torsion-bin specific but otherwise random phi/psi angles More...
 
void random_phipsi_from_rama_by_torsion_bin_right (AA const pos_aa, AA const right_aa, Real &phi, Real &psi, char const torsion_bin) const
 
core::Size get_torsion_bin_index (char torsion_bin) const
 
void init_rama_sampling_tables_by_torsion_bin ()
 
void get_entries_per_torsion_bin_left (AA const left_aa, AA const pos_aa, std::map< char, core::Size > &tb_frequencies) const
 
void get_entries_per_torsion_bin_right (AA const pos_aa, AA const right_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
 

Private Member Functions

void read_rama ()
 
void init_rama_sampling_table_left (const char torsion_bin)
 based on the corresponding function for the Ramachandran class, but with adapted dimensions to accommodate the two neighbors More...
 
void init_rama_sampling_table_right (const char torsion_bin)
 based on the corresponding function for the Ramachandran class, but with adapted dimensions to accommodate the two neighbors More...
 

Private Attributes

ObjexxFCL::FArray3D< Realram_energ_
 
ObjexxFCL::FArray1D< Realram_entropy_
 
ObjexxFCL::FArray4D< Realram_energ_left_
 
ObjexxFCL::FArray2D< Realram_entropy_left_
 
ObjexxFCL::FArray4D< Realram_energ_right_
 
ObjexxFCL::FArray2D< Realram_entropy_right_
 
Real const rama_score_limit_
 
utility::vector1
< utility::vector1
< utility::vector1
< utility::vector1< Real > > > > 
left_rama_sampling_table_
 
utility::vector1
< utility::vector1
< utility::vector1
< utility::vector1
< utility::vector1< Real > > > > > 
left_rama_sampling_table_by_torsion_bin_
 
utility::vector1
< utility::vector1
< utility::vector1
< utility::vector1< Real > > > > 
right_rama_sampling_table_
 
utility::vector1
< utility::vector1
< utility::vector1
< utility::vector1
< utility::vector1< Real > > > > > 
right_rama_sampling_table_by_torsion_bin_
 

Static Private Attributes

static int const n_phi_ = 36
 
static int const n_psi_ = 36
 
static Real const binw_
 
static int const n_aa_ = 20
 
static int const nullaa = 21
 
static ObjexxFCL::FArray4D< Realleft_ram_probabil_
 
static ObjexxFCL::FArray4D< Realright_ram_probabil_
 
static Real const rama_sampling_thold_
 
static Real const rama_sampling_factor_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::Ramachandran2B::Ramachandran2B ( )

References read_rama().

core::scoring::Ramachandran2B::~Ramachandran2B ( )
virtual

Member Function Documentation

void core::scoring::Ramachandran2B::eval_rama_score_all ( pose::Pose pose,
ScoreFunction const &  scorefxn 
) const
Real core::scoring::Ramachandran2B::eval_rama_score_residue ( AA const  res_aa,
Real const  phi,
Real const  psi 
) const
void core::scoring::Ramachandran2B::eval_rama_score_residue ( conformation::Residue const &  res,
chemical::AA const  left_aa,
chemical::AA const  right_aa,
Real rama,
Real drama_dphi,
Real drama_dpsi 
) const
void core::scoring::Ramachandran2B::eval_rama_score_residue ( conformation::Residue const &  res,
Real rama,
Real drama_dphi,
Real drama_dpsi 
) const
void core::scoring::Ramachandran2B::eval_rama_score_residue ( AA const  res_aa,
Real const  phi,
Real const  psi,
Real rama,
Real drama_dphi,
Real drama_dpsi 
) const
void core::scoring::Ramachandran2B::get_entries_per_torsion_bin_left ( AA const  left_aa,
AA const  pos_aa,
std::map< char, core::Size > &  tb_frequencies 
) const
void core::scoring::Ramachandran2B::get_entries_per_torsion_bin_right ( AA const  pos_aa,
AA const  right_aa,
std::map< char, core::Size > &  tb_frequencies 
) const
core::Size core::scoring::Ramachandran2B::get_torsion_bin_index ( char  torsion_bin) const
void core::scoring::Ramachandran2B::IdealizeRamaEnergy ( Real const  phi,
Real const  psi,
Real rama,
Real drama_dphi,
Real drama_dpsi,
Real const  entropy,
ObjexxFCL::FArray2A< Real > const &  rama_for_res 
) const
void core::scoring::Ramachandran2B::init_rama_sampling_table_left ( const char  torsion_bin)
private

based on the corresponding function for the Ramachandran class, but with adapted dimensions to accommodate the two neighbors

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

Author
Amelie Stein ameli.nosp@m.e.st.nosp@m.ein@u.nosp@m.csf..nosp@m.edu

References binw_, core::conformation::get_torsion_bin(), get_torsion_bin_index(), left_ram_probabil_, left_rama_sampling_table_, left_rama_sampling_table_by_torsion_bin_, n_aa_, n_phi_, n_psi_, rama_sampling_factor_, rama_sampling_thold_, and core::io::serialization::size().

Referenced by init_rama_sampling_tables_by_torsion_bin(), and random_phipsi_from_rama_left().

void core::scoring::Ramachandran2B::init_rama_sampling_table_right ( const char  torsion_bin)
private

based on the corresponding function for the Ramachandran class, but with adapted dimensions to accommodate the two neighbors

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

Author
Amelie Stein ameli.nosp@m.e.st.nosp@m.ein@u.nosp@m.csf..nosp@m.edu

References binw_, core::conformation::get_torsion_bin(), get_torsion_bin_index(), n_aa_, n_phi_, n_psi_, rama_sampling_factor_, rama_sampling_thold_, right_ram_probabil_, right_rama_sampling_table_, right_rama_sampling_table_by_torsion_bin_, and core::io::serialization::size().

Referenced by init_rama_sampling_tables_by_torsion_bin(), and random_phipsi_from_rama_right().

void core::scoring::Ramachandran2B::init_rama_sampling_tables_by_torsion_bin ( )
Real core::scoring::Ramachandran2B::RamaE ( conformation::Residue const &  rsd,
Real drama_dphi,
Real drama_dpsi 
) const
Real core::scoring::Ramachandran2B::RamaE ( conformation::Residue const &  rsd) const

References RamaE().

Real core::scoring::Ramachandran2B::RamaE_Lower ( conformation::Residue const &  rsd,
chemical::AA const &  neighbor,
Real drama_dphi,
Real drama_dpsi 
) const
Real core::scoring::Ramachandran2B::RamaE_Lower ( conformation::Residue const &  rsd,
chemical::AA const &  neighbor 
) const

References RamaE_Lower().

Real core::scoring::Ramachandran2B::RamaE_Upper ( conformation::Residue const &  rsd,
chemical::AA const &  neighbor,
Real drama_dphi,
Real drama_dpsi 
) const
Real core::scoring::Ramachandran2B::RamaE_Upper ( conformation::Residue const &  rsd,
chemical::AA const &  neighbor 
) const

References RamaE_Upper().

void core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_left ( AA const  left_aa,
AA const  pos_aa,
Real phi,
Real psi,
char const  torsion_bin 
) const

function 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

References binw_, get_torsion_bin_index(), init_rama_sampling_tables_by_torsion_bin(), and left_rama_sampling_table_by_torsion_bin_.

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

void core::scoring::Ramachandran2B::random_phipsi_from_rama_by_torsion_bin_right ( AA const  pos_aa,
AA const  right_aa,
Real phi,
Real psi,
char const  torsion_bin 
) const
void core::scoring::Ramachandran2B::random_phipsi_from_rama_left ( AA const  left_aa,
AA const  pos_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.

References binw_, init_rama_sampling_table_left(), and left_rama_sampling_table_.

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

void core::scoring::Ramachandran2B::random_phipsi_from_rama_right ( AA const  pos_aa,
AA const  right_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.

References binw_, init_rama_sampling_table_right(), and right_rama_sampling_table_.

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

void core::scoring::Ramachandran2B::read_rama ( )
private
void core::scoring::Ramachandran2B::write_rama_score_all ( Pose const &  pose) const

Member Data Documentation

Real const core::scoring::Ramachandran2B::binw_
staticprivate
ObjexxFCL::FArray4D< Real > core::scoring::Ramachandran2B::left_ram_probabil_
staticprivate
utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > core::scoring::Ramachandran2B::left_rama_sampling_table_
private
utility::vector1< utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > > core::scoring::Ramachandran2B::left_rama_sampling_table_by_torsion_bin_
private
int const core::scoring::Ramachandran2B::n_aa_ = 20
staticprivate
int const core::scoring::Ramachandran2B::n_phi_ = 36
staticprivate
int const core::scoring::Ramachandran2B::n_psi_ = 36
staticprivate
int const core::scoring::Ramachandran2B::nullaa = 21
staticprivate

Referenced by read_rama().

ObjexxFCL::FArray3D< Real > core::scoring::Ramachandran2B::ram_energ_
private
ObjexxFCL::FArray4D< Real > core::scoring::Ramachandran2B::ram_energ_left_
private

Referenced by RamaE_Lower(), and read_rama().

ObjexxFCL::FArray4D< Real > core::scoring::Ramachandran2B::ram_energ_right_
private

Referenced by RamaE_Upper(), and read_rama().

ObjexxFCL::FArray1D< Real > core::scoring::Ramachandran2B::ram_entropy_
private
ObjexxFCL::FArray2D< Real > core::scoring::Ramachandran2B::ram_entropy_left_
private

Referenced by RamaE_Lower(), and read_rama().

ObjexxFCL::FArray2D< Real > core::scoring::Ramachandran2B::ram_entropy_right_
private

Referenced by RamaE_Upper(), and read_rama().

Real const core::scoring::Ramachandran2B::rama_sampling_factor_
staticprivate
Real const core::scoring::Ramachandran2B::rama_sampling_thold_
staticprivate
Real const core::scoring::Ramachandran2B::rama_score_limit_
private

Referenced by IdealizeRamaEnergy().

ObjexxFCL::FArray4D< Real > core::scoring::Ramachandran2B::right_ram_probabil_
staticprivate
utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > core::scoring::Ramachandran2B::right_rama_sampling_table_
private
utility::vector1< utility::vector1< utility::vector1< utility::vector1< utility::vector1< Real > > > > > core::scoring::Ramachandran2B::right_rama_sampling_table_by_torsion_bin_
private

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