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core::scoring::methods::IdealParametersDatabase Class Reference

#include <CartesianBondedEnergy.hh>

Inheritance diagram for core::scoring::methods::IdealParametersDatabase:
Inheritance graph
[legend]

Public Types

typedef boost::unordered_map
< atm_name_quad,
CartBondedParametersOP
TorsionsIndepSubmap
 

Public Member Functions

 IdealParametersDatabase (Real k_len, Real k_ang, Real k_tors, Real k_tors_prot, Real k_tors_improper)
 
 IdealParametersDatabase (IdealParametersDatabase const &)=delete
 
IdealParametersDatabaseoperator= (IdealParametersDatabase const &)=delete
 
 ~IdealParametersDatabase () override
 
CartBondedParametersCOP lookup_improper (core::chemical::ResidueType const &rsd_type, std::string const &atm1_name, std::string const &atm2_name, std::string const &atm3_name, std::string const &atm4_name)
 
TorsionsIndepSubmap generate_impropers_map_res (core::chemical::ResidueType const &restype)
 Get the improper torsion constraints for the particular residue. More...
 
CartBondedParametersCOP lookup_angle (core::chemical::ResidueType const &rsd_type, bool pre_proline, std::string const &atm1_name, std::string const &atm2_name, std::string const &atm3_name, int atm1idx, int atm2idx, int atm3idx)
 
CartBondedParametersCOP lookup_length (core::chemical::ResidueType const &rsd_type, bool pre_proline, std::string const &atm1_name, std::string const &atm2_name, int atm1idx, int atm2idx)
 
void lookup_torsion_legacy (core::chemical::ResidueType const &restype, int atm1, int atm2, int atm3, int atm4, Real &Kphi, Real &phi0, Real &phi_step) const
 
void lookup_angle_legacy (core::pose::Pose const &pose, core::conformation::Residue const &res, int atm1, int atm2, int atm3, Real &Ktheta, Real &d0) const
 
void lookup_length_legacy (core::pose::Pose const &pose, core::conformation::Residue const &res, int atm1, int atm2, Real &Kd, Real &d0) const
 
bool bbdep_bond_params () const
 
bool bbdep_bond_devs () const
 
ResidueCartBondedParameters const & parameters_for_restype (core::chemical::ResidueType const &restype, bool prepro)
 Return a list of all the bond lengths, bond angles, and bond torsions for a single residue type. This list is constructed lazily as required. More...
 
Real k_length () const
 
Real k_angle () const
 
Real k_torsion () const
 
Real k_torsion_proton () const
 
Real k_torsion_improper () const
 
void restype_destruction_observer (core::chemical::RestypeDestructionEvent const &event)
 

Private Member Functions

void init (Real k_len, Real k_ang, Real k_tors, Real k_tors_prot, Real k_tors_improper)
 
void lookup_bondangle_buildideal (core::chemical::ResidueType const &restype, int atm1, int atm2, int atm3, Real &Ktheta, Real &theta0) const
 
void lookup_bondlength_buildideal (core::chemical::ResidueType const &restype, int atm1, int atm2, Real &Kd, Real &d0) const
 
void read_length_database (std::string const &infile, bool const symmetrize_gly)
 
void read_angle_database (std::string const &infile, bool const symmetrize_gly)
 
void read_torsion_database (std::string const &infile, bool const symmetrize_gly)
 
void read_improper_database (std::string const &infile, bool const symmetrize_gly)
 
void add_impropers_from_stream (std::istream &instream)
 
void read_bbdep_table (std::string const &filename, boost::unordered_map< atm_name_single, CartBondedParametersOP > &bondlengths, boost::unordered_map< atm_name_pair, CartBondedParametersOP > &bondangles, std::string const &res, bool const symmetrize_table)
 Read bb-dependent tables. More...
 
ResidueCartBondedParametersCOP create_parameters_for_restype (core::chemical::ResidueType const &restype, bool prepro)
 Generate cached parameters for the given ResidueType. More...
 
void symmetrize_tables (ObjexxFCL::FArray2D< core::Real > &table) const
 Symmetrize the glycine backbone-dependent table. More...
 

Private Attributes

Real k_length_
 
Real k_angle_
 
Real k_torsion_
 
Real k_torsion_proton_
 
Real k_torsion_improper_
 
bool bbdep_bond_params_
 
bool bbdep_bond_devs_
 
boost::unordered_map
< atm_name_pair,
CartBondedParametersOP
bondlengths_indep_
 
boost::unordered_map
< atm_name_triple,
CartBondedParametersOP
bondangles_indep_
 
boost::unordered_multimap
< atm_name_quad,
CartBondedParametersOP
torsions_indep_
 
boost::unordered_map
< atm_name_quad,
CartBondedParametersOP
impropers_indep_
 
boost::unordered_map
< atm_name_pair,
CartBondedParametersOP
bondangles_bbdep_def_
 
boost::unordered_map
< atm_name_pair,
CartBondedParametersOP
bondangles_bbdep_pro_
 
boost::unordered_map
< atm_name_pair,
CartBondedParametersOP
bondangles_bbdep_valile_
 
boost::unordered_map
< atm_name_pair,
CartBondedParametersOP
bondangles_bbdep_prepro_
 
boost::unordered_map
< atm_name_pair,
CartBondedParametersOP
bondangles_bbdep_gly_
 
boost::unordered_map
< atm_name_single,
CartBondedParametersOP
bondlengths_bbdep_def_
 
boost::unordered_map
< atm_name_single,
CartBondedParametersOP
bondlengths_bbdep_pro_
 
boost::unordered_map
< atm_name_single,
CartBondedParametersOP
bondlengths_bbdep_valile_
 
boost::unordered_map
< atm_name_single,
CartBondedParametersOP
bondlengths_bbdep_prepro_
 
boost::unordered_map
< atm_name_single,
CartBondedParametersOP
bondlengths_bbdep_gly_
 
std::map
< chemical::ResidueType const
*, ResidueCartBondedParametersCOP
prepro_restype_data_
 
std::map
< chemical::ResidueType const
*, ResidueCartBondedParametersCOP
nonprepro_restype_data_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::methods::IdealParametersDatabase::IdealParametersDatabase ( Real  k_len,
Real  k_ang,
Real  k_tors,
Real  k_tors_prot,
Real  k_tors_improper 
)
core::scoring::methods::IdealParametersDatabase::IdealParametersDatabase ( IdealParametersDatabase const &  )
delete
core::scoring::methods::IdealParametersDatabase::~IdealParametersDatabase ( )
override

Member Function Documentation

void core::scoring::methods::IdealParametersDatabase::add_impropers_from_stream ( std::istream &  instream)
private

References impropers_indep_.

Referenced by read_improper_database().

bool core::scoring::methods::IdealParametersDatabase::bbdep_bond_devs ( ) const
inline

References bbdep_bond_devs_.

bool core::scoring::methods::IdealParametersDatabase::bbdep_bond_params ( ) const
inline

References bbdep_bond_params_.

ResidueCartBondedParametersCOP core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype ( core::chemical::ResidueType const &  restype,
bool  prepro 
)
private
IdealParametersDatabase::TorsionsIndepSubmap core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res ( core::chemical::ResidueType const &  restype)
void core::scoring::methods::IdealParametersDatabase::init ( Real  k_len,
Real  k_ang,
Real  k_tors,
Real  k_tors_prot,
Real  k_tors_improper 
)
private
Real core::scoring::methods::IdealParametersDatabase::k_angle ( ) const
inline

References k_angle_.

Real core::scoring::methods::IdealParametersDatabase::k_length ( ) const
inline

References k_length_.

Real core::scoring::methods::IdealParametersDatabase::k_torsion ( ) const
inline

References k_torsion_.

Real core::scoring::methods::IdealParametersDatabase::k_torsion_improper ( ) const
inline

References k_torsion_improper_.

Real core::scoring::methods::IdealParametersDatabase::k_torsion_proton ( ) const
inline

References k_torsion_proton_.

CartBondedParametersCOP core::scoring::methods::IdealParametersDatabase::lookup_angle ( core::chemical::ResidueType const &  restype,
bool  pre_proline,
std::string const &  atm1_name,
std::string const &  atm2_name,
std::string const &  atm3_name,
int  atm1idx,
int  atm2idx,
int  atm3idx 
)
void core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy ( core::pose::Pose const &  pose,
core::conformation::Residue const &  res,
int  atm1,
int  atm2,
int  atm3,
Real Ktheta,
Real d0 
) const
void core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal ( core::chemical::ResidueType const &  restype,
int  atm1,
int  atm2,
int  atm3,
Real Ktheta,
Real theta0 
) const
private
void core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal ( core::chemical::ResidueType const &  restype,
int  atm1,
int  atm2,
Real Kd,
Real d0 
) const
private
CartBondedParametersCOP core::scoring::methods::IdealParametersDatabase::lookup_improper ( core::chemical::ResidueType const &  rsd_type,
std::string const &  atm1_name,
std::string const &  atm2_name,
std::string const &  atm3_name,
std::string const &  atm4_name 
)
CartBondedParametersCOP core::scoring::methods::IdealParametersDatabase::lookup_length ( core::chemical::ResidueType const &  rsd_type,
bool  pre_proline,
std::string const &  atm1_name,
std::string const &  atm2_name,
int  atm1idx,
int  atm2idx 
)
void core::scoring::methods::IdealParametersDatabase::lookup_length_legacy ( core::pose::Pose const &  pose,
core::conformation::Residue const &  res,
int  atm1,
int  atm2,
Real Kd,
Real d0 
) const
void core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy ( core::chemical::ResidueType const &  restype,
int  atm1,
int  atm2,
int  atm3,
int  atm4,
Real Kphi,
Real phi0,
Real phi_step 
) const
IdealParametersDatabase& core::scoring::methods::IdealParametersDatabase::operator= ( IdealParametersDatabase const &  )
delete
ResidueCartBondedParameters const & core::scoring::methods::IdealParametersDatabase::parameters_for_restype ( core::chemical::ResidueType const &  restype,
bool  prepro 
)

Return a list of all the bond lengths, bond angles, and bond torsions for a single residue type. This list is constructed lazily as required.

References core::chemical::ResidueType::attach_destruction_obs(), create_parameters_for_restype(), nonprepro_restype_data_, prepro_restype_data_, and restype_destruction_observer().

void core::scoring::methods::IdealParametersDatabase::read_angle_database ( std::string const &  infile,
bool const  symmetrize_gly 
)
private
void core::scoring::methods::IdealParametersDatabase::read_bbdep_table ( std::string const &  filename,
boost::unordered_map< atm_name_single, CartBondedParametersOP > &  bondlengths,
boost::unordered_map< atm_name_pair, CartBondedParametersOP > &  bondangles,
std::string const &  resbase,
bool const  symmetrize_table 
)
private

Read bb-dependent tables.

Smooth using bbdep data corresponding to residue 'resbase'

References bbdep_bond_devs_, bondangles_indep_, bondlengths_indep_, and symmetrize_tables().

Referenced by init().

void core::scoring::methods::IdealParametersDatabase::read_improper_database ( std::string const &  infile,
bool const  symmetrize_gly 
)
private
void core::scoring::methods::IdealParametersDatabase::read_length_database ( std::string const &  infile,
bool const  symmetrize_gly 
)
private

References bondlengths_indep_, and core::scoring::methods::TR().

Referenced by init().

void core::scoring::methods::IdealParametersDatabase::read_torsion_database ( std::string const &  infile,
bool const  symmetrize_gly 
)
private

References torsions_indep_, and core::scoring::methods::TR().

Referenced by init().

void core::scoring::methods::IdealParametersDatabase::restype_destruction_observer ( core::chemical::RestypeDestructionEvent const &  event)
void core::scoring::methods::IdealParametersDatabase::symmetrize_tables ( ObjexxFCL::FArray2D< core::Real > &  table) const
private

Symmetrize the glycine backbone-dependent table.

Only called if the score::symmetric_gly_tables option is used. Intended for design with glyceine in a mixed D/L context (in which there should be no preference for a left-handed conformation over a right).

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::scoring::methods::TR().

Referenced by read_bbdep_table().

Member Data Documentation

bool core::scoring::methods::IdealParametersDatabase::bbdep_bond_devs_
private
bool core::scoring::methods::IdealParametersDatabase::bbdep_bond_params_
private

Referenced by bbdep_bond_params(), and init().

boost::unordered_map< atm_name_pair, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondangles_bbdep_def_
private

Referenced by init(), and lookup_angle().

boost::unordered_map< atm_name_pair, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondangles_bbdep_gly_
private

Referenced by init(), and lookup_angle().

boost::unordered_map< atm_name_pair, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondangles_bbdep_prepro_
private

Referenced by init(), and lookup_angle().

boost::unordered_map< atm_name_pair, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondangles_bbdep_pro_
private

Referenced by init(), and lookup_angle().

boost::unordered_map< atm_name_pair, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondangles_bbdep_valile_
private

Referenced by init(), and lookup_angle().

boost::unordered_map< atm_name_triple, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondangles_indep_
private
boost::unordered_map< atm_name_single, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondlengths_bbdep_def_
private

Referenced by init(), and lookup_length().

boost::unordered_map< atm_name_single, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondlengths_bbdep_gly_
private

Referenced by init(), and lookup_length().

boost::unordered_map< atm_name_single, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondlengths_bbdep_prepro_
private

Referenced by init(), and lookup_length().

boost::unordered_map< atm_name_single, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondlengths_bbdep_pro_
private

Referenced by init(), and lookup_length().

boost::unordered_map< atm_name_single, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondlengths_bbdep_valile_
private

Referenced by init(), and lookup_length().

boost::unordered_map< atm_name_pair, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::bondlengths_indep_
private
boost::unordered_map< atm_name_quad, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::impropers_indep_
private
Real core::scoring::methods::IdealParametersDatabase::k_angle_
private
Real core::scoring::methods::IdealParametersDatabase::k_length_
private
Real core::scoring::methods::IdealParametersDatabase::k_torsion_
private
Real core::scoring::methods::IdealParametersDatabase::k_torsion_improper_
private

Referenced by init(), and k_torsion_improper().

Real core::scoring::methods::IdealParametersDatabase::k_torsion_proton_
private
std::map< chemical::ResidueType const *, ResidueCartBondedParametersCOP > core::scoring::methods::IdealParametersDatabase::nonprepro_restype_data_
private
std::map< chemical::ResidueType const *, ResidueCartBondedParametersCOP > core::scoring::methods::IdealParametersDatabase::prepro_restype_data_
private
boost::unordered_multimap< atm_name_quad, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::torsions_indep_
private

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