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Rosetta
2021.07
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#include <CartesianBondedEnergy.hh>
Public Types | |
typedef boost::unordered_map < atm_name_quad, core::scoring::methods::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 | |
IdealParametersDatabase & | operator= (IdealParametersDatabase const &)=delete |
~IdealParametersDatabase () override | |
core::scoring::methods::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... | |
core::scoring::methods::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) |
core::scoring::methods::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, core::scoring::methods::CartBondedParametersOP > &bondlengths, boost::unordered_map< atm_name_pair, core::scoring::methods::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... | |
typedef boost::unordered_map< atm_name_quad, core::scoring::methods::CartBondedParametersOP > core::energy_methods::IdealParametersDatabase::TorsionsIndepSubmap |
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References nonprepro_restype_data_, prepro_restype_data_, and restype_destruction_observer().
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References impropers_indep_.
Referenced by read_improper_database().
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References bbdep_bond_devs_.
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References bbdep_bond_params_.
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Generate cached parameters for the given ResidueType.
References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_dpr, 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(), generate_impropers_map_res(), core::energy_methods::get_restag(), core::chemical::ResidueType::has(), impropers_indep_, core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::ResidueType::is_upper_terminus(), lookup_angle(), lookup_improper(), lookup_length(), core::chemical::ResidueType::lower_connect_id(), protocols::mean_field::max(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbrs(), core::chemical::ResidueType::num_bondangles(), protocols::sic_dock::range(), torsions_indep_, and core::chemical::ResidueType::upper_connect_id().
Referenced by parameters_for_restype().
IdealParametersDatabase::TorsionsIndepSubmap core::energy_methods::IdealParametersDatabase::generate_impropers_map_res | ( | core::chemical::ResidueType const & | restype | ) |
Get the improper torsion constraints for the particular residue.
References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_gly, core::chemical::AromaticBond, core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::bond_type(), core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::bonds(), core::chemical::element::C, core::chemical::DoubleBond, core::chemical::ResidueType::element_type(), core::energy_methods::get_restag(), core::chemical::element::K, k_torsion_, core::chemical::ResidueTypeBase::name(), and core::energy_methods::TR().
Referenced by create_parameters_for_restype().
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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_improper_database(), read_length_database(), read_torsion_database(), and core::energy_methods::TR().
Referenced by IdealParametersDatabase().
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References k_torsion_.
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References k_torsion_improper_.
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References k_torsion_proton_.
core::scoring::methods::CartBondedParametersCOP core::energy_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::ResidueTypeBase::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::energy_methods::get_restag(), lookup_bondangle_buildideal(), and core::energy_methods::TR().
Referenced by create_parameters_for_restype().
void core::energy_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 |
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References core::chemical::ResidueTypeBase::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::ResidueTypeBase::has_variant_type(), and k_angle_.
Referenced by lookup_angle().
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core::scoring::methods::CartBondedParametersCOP core::energy_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 | ||
) |
References core::energy_methods::get_restag(), and impropers_indep_.
Referenced by create_parameters_for_restype().
core::scoring::methods::CartBondedParametersCOP core::energy_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::ResidueTypeBase::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::energy_methods::get_restag(), lookup_bondlength_buildideal(), and core::energy_methods::TR().
Referenced by create_parameters_for_restype().
void core::energy_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::energy_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 |
References core::chemical::ResidueTypeBase::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::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::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().
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ResidueCartBondedParameters const & core::energy_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().
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References bondangles_indep_, core::chemical::element::K, and core::energy_methods::TR().
Referenced by init().
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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().
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References add_impropers_from_stream(), impropers_indep_, and core::energy_methods::TR().
Referenced by init().
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References bondlengths_indep_, and core::energy_methods::TR().
Referenced by init().
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References torsions_indep_, and core::energy_methods::TR().
Referenced by init().
void core::energy_methods::IdealParametersDatabase::restype_destruction_observer | ( | core::chemical::RestypeDestructionEvent const & | event | ) |
References nonprepro_restype_data_, prepro_restype_data_, and core::chemical::RestypeDestructionEvent::restype.
Referenced by parameters_for_restype(), and ~IdealParametersDatabase().
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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).
References core::energy_methods::TR().
Referenced by read_bbdep_table().
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Referenced by bbdep_bond_devs(), init(), and read_bbdep_table().
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Referenced by bbdep_bond_params(), and init().
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Referenced by init(), and lookup_angle().
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Referenced by init(), and lookup_angle().
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Referenced by init(), and lookup_angle().
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Referenced by init(), and lookup_angle().
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Referenced by init(), and lookup_angle().
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Referenced by lookup_angle(), read_angle_database(), and read_bbdep_table().
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Referenced by init(), and lookup_length().
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Referenced by init(), and lookup_length().
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Referenced by init(), and lookup_length().
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Referenced by init(), and lookup_length().
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Referenced by init(), and lookup_length().
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Referenced by lookup_length(), read_bbdep_table(), and read_length_database().
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Referenced by add_impropers_from_stream(), create_parameters_for_restype(), lookup_improper(), and read_improper_database().
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Referenced by init(), k_angle(), lookup_angle_legacy(), and lookup_bondangle_buildideal().
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Referenced by init(), k_length(), lookup_bondlength_buildideal(), and lookup_length_legacy().
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Referenced by generate_impropers_map_res(), init(), k_torsion(), and lookup_torsion_legacy().
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Referenced by init(), and k_torsion_improper().
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Referenced by init(), k_torsion_proton(), and lookup_torsion_legacy().
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Referenced by parameters_for_restype(), restype_destruction_observer(), and ~IdealParametersDatabase().
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Referenced by parameters_for_restype(), restype_destruction_observer(), and ~IdealParametersDatabase().
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Referenced by create_parameters_for_restype(), and read_torsion_database().