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

#include <CartesianBondedEnergy.hh>

Inheritance diagram for core::scoring::methods::IdealParametersDatabase:
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Public Member Functions

 IdealParametersDatabase (Real k_len, Real k_ang, Real k_tors, Real k_tors_prot, Real k_tors_improper)
 
void init (Real k_len, Real k_ang, Real k_tors, Real k_tors_prot, Real k_tors_improper)
 
CartBondedParametersCOP lookup_torsion (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)
 Torsion Database. 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)
 
void lookup_angle_legacy (core::pose::Pose const &pose, core::conformation::Residue const &res, int atm1, int atm2, int atm3, Real &Ktheta, Real &d0)
 
void lookup_length_legacy (core::pose::Pose const &pose, core::conformation::Residue const &res, int atm1, int atm2, Real &Kd, Real &d0)
 
bool bbdep_bond_params ()
 
bool bbdep_bond_devs ()
 
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. (This may cause thread safety issues!). More...
 

Private Member Functions

void lookup_bondangle_buildideal (core::chemical::ResidueType const &restype, int atm1, int atm2, int atm3, Real &Ktheta, Real &theta0)
 
void lookup_bondlength_buildideal (core::chemical::ResidueType const &restype, int atm1, int atm2, Real &Kd, Real &d0)
 
void read_length_database (std::string infile)
 
void read_angle_database (std::string infile)
 
void read_torsion_database (std::string infile)
 
void read_bbdep_table (std::string filename, boost::unordered_map< atm_name_single, CartBondedParametersOP > &bondlengths, boost::unordered_map< atm_name_pair, CartBondedParametersOP > &bondangles, std::string res)
 
void create_parameters_for_restype (core::chemical::ResidueType const &restype, bool prepro)
 

Private Attributes

Real k_length_
 
Real k_angle_
 
Real k_torsion_
 
Real k_torsion_proton_
 
Real k_torsion_improper_
 
boost::unordered_map
< atm_name_quad,
CartBondedParametersOP > 		torsions_indep_
 
boost::unordered_map
< atm_name_triple,
CartBondedParametersOP > 		bondangles_indep_
 
boost::unordered_map
< atm_name_pair,
CartBondedParametersOP > 		bondlengths_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_
 
bool bbdep_bond_params_
 
bool bbdep_bond_devs_
 
std::map
< chemical::ResidueType const
*, ResidueCartBondedParametersOP > 		prepro_restype_data_
 
std::map
< chemical::ResidueType const
*, ResidueCartBondedParametersOP > 		nonprepro_restype_data_
 

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 
)

References init(), core::scoring::methods::K_ANGLE, core::scoring::methods::K_LENGTH, core::scoring::methods::K_TORSION, core::scoring::methods::K_TORSION_IMPROPER, and core::scoring::methods::K_TORSION_PROTON.

Member Function Documentation

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

References bbdep_bond_devs_.

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

References bbdep_bond_params_.

void core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype ( core::chemical::ResidueType const &  restype,
bool  prepro 
)
private

References core::chemical::ResidueType::aa(), core::chemical::aa_dpr, core::chemical::aa_gly, core::chemical::aa_pro, core::chemical::ResidueType::atom_being_shadowed(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(), core::chemical::ResidueType::bondangle(), core::scoring::methods::get_restag(), core::chemical::ResidueType::has(), core::chemical::is_canonical_D_aa(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), core::chemical::ResidueType::is_upper_terminus(), lookup_angle(), lookup_length(), lookup_torsion(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbrs(), nonprepro_restype_data_, core::chemical::ResidueType::num_bondangles(), core::chemical::num_canonical_aas, prepro_restype_data_, torsions_indep_, and core::chemical::ResidueType::upper_connect_id().

Referenced by parameters_for_restype().

void core::scoring::methods::IdealParametersDatabase::init ( Real  k_len,
Real  k_ang,
Real  k_tors,
Real  k_tors_prot,
Real  k_tors_improper 
)

References bbdep_bond_devs_, bbdep_bond_params_, bondangles_bbdep_def_, bondangles_bbdep_gly_, bondangles_bbdep_prepro_, bondangles_bbdep_pro_, bondangles_bbdep_valile_, bondlengths_bbdep_def_, bondlengths_bbdep_gly_, bondlengths_bbdep_prepro_, bondlengths_bbdep_pro_, bondlengths_bbdep_valile_, k_angle_, k_length_, k_torsion_, k_torsion_improper_, k_torsion_proton_, read_angle_database(), read_bbdep_table(), read_length_database(), read_torsion_database(), and core::scoring::methods::TR().

Referenced by IdealParametersDatabase().

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 
)

Angle Database build from ideal if not found

References core::chemical::ResidueType::aa(), core::chemical::aa_dil, core::chemical::aa_dpr, core::chemical::aa_dva, core::chemical::aa_gly, core::chemical::aa_ile, core::chemical::aa_pro, core::chemical::aa_val, bondangles_bbdep_def_, bondangles_bbdep_gly_, bondangles_bbdep_prepro_, bondangles_bbdep_pro_, bondangles_bbdep_valile_, bondangles_indep_, core::sequence::end, core::scoring::methods::get_restag(), lookup_bondangle_buildideal(), and core::scoring::methods::TR().

Referenced by create_parameters_for_restype().

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 
)

References core::chemical::aa_ala, core::chemical::aa_dal, core::chemical::aa_dpr, core::chemical::aa_gly, core::chemical::aa_pro, core::conformation::ResidueFactory::create_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, k_angle_, and core::conformation::Residue::type().

void core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal ( core::chemical::ResidueType const &  restype,
int  atm1,
int  atm2,
int  atm3,
Real &  Ktheta,
Real &  theta0 
)
private

References core::chemical::ResidueType::aa(), core::chemical::aa_ala, core::chemical::aa_dal, core::chemical::aa_dpr, core::chemical::aa_gly, core::chemical::aa_pro, core::chemical::ResidueType::atom_name(), core::conformation::ResidueFactory::create_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::ResidueType::has_variant_type(), and k_angle_.

Referenced by lookup_angle().

void core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal ( core::chemical::ResidueType const &  restype,
int  atm1,
int  atm2,
Real &  Kd,
Real &  d0 
)
private

References core::chemical::ResidueType::aa(), core::chemical::aa_dpr, core::chemical::aa_pro, core::chemical::ResidueType::atom_name(), core::conformation::ResidueFactory::create_residue(), and k_length_.

Referenced by lookup_length().

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 
)

BondLength Database build from ideal if not found

References core::chemical::ResidueType::aa(), core::chemical::aa_dil, core::chemical::aa_dpr, core::chemical::aa_dva, core::chemical::aa_gly, core::chemical::aa_ile, core::chemical::aa_pro, core::chemical::aa_val, bondlengths_bbdep_def_, bondlengths_bbdep_gly_, bondlengths_bbdep_prepro_, bondlengths_bbdep_pro_, bondlengths_bbdep_valile_, bondlengths_indep_, protocols::hybridization::d0, core::scoring::methods::get_restag(), lookup_bondlength_buildideal(), and core::scoring::methods::TR().

Referenced by create_parameters_for_restype().

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 
)

References core::chemical::aa_dpr, core::chemical::aa_pro, core::conformation::ResidueFactory::create_residue(), k_length_, and core::conformation::Residue::type().

CartBondedParametersCOP core::scoring::methods::IdealParametersDatabase::lookup_torsion ( 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 
)

Torsion Database.

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

Referenced by create_parameters_for_restype().

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 
)

References core::chemical::ResidueType::aa(), core::chemical::aa_arg, core::chemical::aa_cys, core::chemical::aa_dar, core::chemical::aa_dcs, core::chemical::aa_dpr, core::chemical::aa_pro, core::pose::Pose::append_residue_by_bond(), core::chemical::ResidueType::atom_name(), core::id::AtomID::atomno(), core::id::CHI, core::conformation::ResidueFactory::create_residue(), core::chemical::CUTPOINT_UPPER, core::chemical::DISULFIDE, core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_proton_chi(), k_torsion_, k_torsion_proton_, core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::ResidueType::nchi(), and core::chemical::ResidueType::proton_chi_samples().

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. (This may cause thread safety issues!).

References create_parameters_for_restype(), nonprepro_restype_data_, and prepro_restype_data_.

void core::scoring::methods::IdealParametersDatabase::read_angle_database ( std::string  infile)
private

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

Referenced by init().

void core::scoring::methods::IdealParametersDatabase::read_bbdep_table ( std::string  filename,
boost::unordered_map< atm_name_single, CartBondedParametersOP > &  bondlengths,
boost::unordered_map< atm_name_pair, CartBondedParametersOP > &  bondangles,
std::string  res 
)
private

References bbdep_bond_devs_, bondangles_indep_, and bondlengths_indep_.

Referenced by init().

void core::scoring::methods::IdealParametersDatabase::read_length_database ( std::string  infile)
private

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

Referenced by init().

void core::scoring::methods::IdealParametersDatabase::read_torsion_database ( std::string  infile)
private

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

Referenced by init().

Member Data Documentation

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

Referenced by bbdep_bond_devs(), init(), and read_bbdep_table().

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

Referenced by lookup_angle(), read_angle_database(), and read_bbdep_table().

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

Referenced by lookup_length(), read_bbdep_table(), and read_length_database().

Real core::scoring::methods::IdealParametersDatabase::k_angle_
private

Referenced by init(), lookup_angle_legacy(), and lookup_bondangle_buildideal().

Real core::scoring::methods::IdealParametersDatabase::k_length_
private

Referenced by init(), lookup_bondlength_buildideal(), and lookup_length_legacy().

Real core::scoring::methods::IdealParametersDatabase::k_torsion_
private

Referenced by init(), and lookup_torsion_legacy().

Real core::scoring::methods::IdealParametersDatabase::k_torsion_improper_
private

Referenced by init().

Real core::scoring::methods::IdealParametersDatabase::k_torsion_proton_
private

Referenced by init(), and lookup_torsion_legacy().

std::map< chemical::ResidueType const *, ResidueCartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::nonprepro_restype_data_
private

Referenced by create_parameters_for_restype(), and parameters_for_restype().

std::map< chemical::ResidueType const *, ResidueCartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::prepro_restype_data_
private

Referenced by create_parameters_for_restype(), and parameters_for_restype().

boost::unordered_map< atm_name_quad, CartBondedParametersOP > core::scoring::methods::IdealParametersDatabase::torsions_indep_
private

Referenced by create_parameters_for_restype(), lookup_torsion(), and read_torsion_database().

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