core::energy_methods::IdealParametersDatabase Class Reference

#include <CartesianBondedEnergy.hh>

Inheritance diagram for core::energy_methods::IdealParametersDatabase:

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...

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, core::scoring::methods::CartBondedParametersOP >	bondlengths_indep_
boost::unordered_map < atm_name_triple, core::scoring::methods::CartBondedParametersOP >	bondangles_indep_
boost::unordered_multimap < atm_name_quad, core::scoring::methods::CartBondedParametersOP >	torsions_indep_
boost::unordered_map < atm_name_quad, core::scoring::methods::CartBondedParametersOP >	impropers_indep_
boost::unordered_map < atm_name_pair, core::scoring::methods::CartBondedParametersOP >	bondangles_bbdep_def_
boost::unordered_map < atm_name_pair, core::scoring::methods::CartBondedParametersOP >	bondangles_bbdep_pro_
boost::unordered_map < atm_name_pair, core::scoring::methods::CartBondedParametersOP >	bondangles_bbdep_valile_
boost::unordered_map < atm_name_pair, core::scoring::methods::CartBondedParametersOP >	bondangles_bbdep_prepro_
boost::unordered_map < atm_name_pair, core::scoring::methods::CartBondedParametersOP >	bondangles_bbdep_gly_
boost::unordered_map < atm_name_single, core::scoring::methods::CartBondedParametersOP >	bondlengths_bbdep_def_
boost::unordered_map < atm_name_single, core::scoring::methods::CartBondedParametersOP >	bondlengths_bbdep_pro_
boost::unordered_map < atm_name_single, core::scoring::methods::CartBondedParametersOP >	bondlengths_bbdep_valile_
boost::unordered_map < atm_name_single, core::scoring::methods::CartBondedParametersOP >	bondlengths_bbdep_prepro_
boost::unordered_map < atm_name_single, core::scoring::methods::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

typedef boost::unordered_map< atm_name_quad, core::scoring::methods::CartBondedParametersOP > core::energy_methods::IdealParametersDatabase::TorsionsIndepSubmap

Constructor & Destructor Documentation

core::energy_methods::IdealParametersDatabase::IdealParametersDatabase	(	Real	k_len,
		Real	k_ang,
		Real	k_tors,
		Real	k_tors_prot,
		Real	k_tors_improper
	)

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

core::energy_methods::IdealParametersDatabase::IdealParametersDatabase ( IdealParametersDatabase const &  )

delete

core::energy_methods::IdealParametersDatabase::~IdealParametersDatabase ( )

override

References nonprepro_restype_data_, prepro_restype_data_, and restype_destruction_observer().

Member Function Documentation

void core::energy_methods::IdealParametersDatabase::add_impropers_from_stream ( std::istream &  instream )

private

References impropers_indep_.

Referenced by read_improper_database().

bool core::energy_methods::IdealParametersDatabase::bbdep_bond_devs ( ) const

inline

References bbdep_bond_devs_.

bool core::energy_methods::IdealParametersDatabase::bbdep_bond_params ( ) const

inline

References bbdep_bond_params_.

ResidueCartBondedParametersCOP core::energy_methods::IdealParametersDatabase::create_parameters_for_restype ( core::chemical::ResidueType const &  restype, bool  prepro  )

private

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().

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

private

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().

Real core::energy_methods::IdealParametersDatabase::k_angle ( ) const

inline

References k_angle_.

Real core::energy_methods::IdealParametersDatabase::k_length ( ) const

inline

References k_length_.

Real core::energy_methods::IdealParametersDatabase::k_torsion ( ) const

inline

References k_torsion_.

Real core::energy_methods::IdealParametersDatabase::k_torsion_improper ( ) const

inline

References k_torsion_improper_.

Real core::energy_methods::IdealParametersDatabase::k_torsion_proton ( ) const

inline

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

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::energy_methods::IdealParametersDatabase::lookup_bondangle_buildideal ( core::chemical::ResidueType const &  restype, int  atm1, int  atm2, int  atm3, Real &  Ktheta, Real &  theta0  ) const

private

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().

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

private

References core::chemical::ResidueTypeBase::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().

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

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

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().

IdealParametersDatabase& core::energy_methods::IdealParametersDatabase::operator= ( IdealParametersDatabase const &  )

delete

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().

void core::energy_methods::IdealParametersDatabase::read_angle_database ( std::string const &  infile, bool const  symmetrize_gly  )

private

References bondangles_indep_, core::chemical::element::K, and core::energy_methods::TR().

Referenced by init().

void core::energy_methods::IdealParametersDatabase::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 &  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::energy_methods::IdealParametersDatabase::read_improper_database ( std::string const &  infile, bool const  symmetrize_gly  )

private

References add_impropers_from_stream(), impropers_indep_, and core::energy_methods::TR().

Referenced by init().

void core::energy_methods::IdealParametersDatabase::read_length_database ( std::string const &  infile, bool const  symmetrize_gly  )

private

References bondlengths_indep_, and core::energy_methods::TR().

Referenced by init().

void core::energy_methods::IdealParametersDatabase::read_torsion_database ( std::string const &  infile, bool const  symmetrize_gly  )

private

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().

void core::energy_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::energy_methods::TR().

Referenced by read_bbdep_table().

Member Data Documentation

bool core::energy_methods::IdealParametersDatabase::bbdep_bond_devs_

private

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

bool core::energy_methods::IdealParametersDatabase::bbdep_bond_params_

private

Referenced by bbdep_bond_params(), and init().

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

private

Referenced by init(), and lookup_angle().

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

private

Referenced by init(), and lookup_angle().

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

private

Referenced by init(), and lookup_angle().

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

private

Referenced by init(), and lookup_angle().

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

private

Referenced by init(), and lookup_angle().

boost::unordered_map< atm_name_triple, core::scoring::methods::CartBondedParametersOP > core::energy_methods::IdealParametersDatabase::bondangles_indep_

private

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

boost::unordered_map< atm_name_single, core::scoring::methods::CartBondedParametersOP > core::energy_methods::IdealParametersDatabase::bondlengths_bbdep_def_

private

Referenced by init(), and lookup_length().

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

private

Referenced by init(), and lookup_length().

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

private

Referenced by init(), and lookup_length().

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

private

Referenced by init(), and lookup_length().

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

private

Referenced by init(), and lookup_length().

boost::unordered_map< atm_name_pair, core::scoring::methods::CartBondedParametersOP > core::energy_methods::IdealParametersDatabase::bondlengths_indep_

private

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

boost::unordered_map< atm_name_quad, core::scoring::methods::CartBondedParametersOP > core::energy_methods::IdealParametersDatabase::impropers_indep_

private

Referenced by add_impropers_from_stream(), create_parameters_for_restype(), lookup_improper(), and read_improper_database().

Real core::energy_methods::IdealParametersDatabase::k_angle_

private

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

Real core::energy_methods::IdealParametersDatabase::k_length_

private

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

Real core::energy_methods::IdealParametersDatabase::k_torsion_

private

Referenced by generate_impropers_map_res(), init(), k_torsion(), and lookup_torsion_legacy().

Real core::energy_methods::IdealParametersDatabase::k_torsion_improper_

private

Referenced by init(), and k_torsion_improper().

Real core::energy_methods::IdealParametersDatabase::k_torsion_proton_

private

Referenced by init(), k_torsion_proton(), and lookup_torsion_legacy().

std::map< chemical::ResidueType const *, ResidueCartBondedParametersCOP > core::energy_methods::IdealParametersDatabase::nonprepro_restype_data_

private

Referenced by parameters_for_restype(), restype_destruction_observer(), and ~IdealParametersDatabase().

std::map< chemical::ResidueType const *, ResidueCartBondedParametersCOP > core::energy_methods::IdealParametersDatabase::prepro_restype_data_

private

Referenced by parameters_for_restype(), restype_destruction_observer(), and ~IdealParametersDatabase().

boost::unordered_multimap< atm_name_quad, core::scoring::methods::CartBondedParametersOP > core::energy_methods::IdealParametersDatabase::torsions_indep_

private

Referenced by create_parameters_for_restype(), and read_torsion_database().

---

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

• src/core/energy_methods/CartesianBondedEnergy.hh
• src/core/energy_methods/CartesianBondedEnergy.cc