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

#include <CartesianBondedEnergy.hh>

Inheritance diagram for core::scoring::methods::IdealParametersDatabase:

Collaboration diagram for core::scoring::methods::IdealParametersDatabase:

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_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_

Detailed Description

Definition at line 205 of file CartesianBondedEnergy.hh.

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
	)

Definition at line 267 of file CartesianBondedEnergy.cc.

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

Definition at line 259 of file CartesianBondedEnergy.hh.

References bbdep_bond_devs_.

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

inline

Definition at line 258 of file CartesianBondedEnergy.hh.

References bbdep_bond_params_.

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

private

Definition at line 1114 of file CartesianBondedEnergy.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, 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::chemical::ResidueType::dihedral(), core::chemical::ResidueType::has(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_protein(), lookup_angle(), lookup_length(), lookup_torsion(), core::chemical::ResidueType::lower_connect_id(), core::chemical::LOWER_TERMINUS, core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbrs(), core::chemical::ResidueType::ndihe(), nonprepro_restype_data_, core::chemical::ResidueType::num_bondangles(), core::chemical::num_canonical_aas, prepro_restype_data_, core::chemical::ResidueType::upper_connect_id(), and core::chemical::UPPER_TERMINUS.

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
	)

Definition at line 306 of file CartesianBondedEnergy.cc.

References bbdep_bond_devs_, bbdep_bond_params_, bondangles_bbdep_def_, bondangles_bbdep_gly_, bondangles_bbdep_prepro_, bondangles_bbdep_pro_, bondangles_bbdep_valile_, bondangles_indep_, bondlengths_bbdep_def_, bondlengths_bbdep_gly_, bondlengths_bbdep_prepro_, bondlengths_bbdep_pro_, bondlengths_bbdep_valile_, bondlengths_indep_, k_angle_, k_length_, k_torsion_, k_torsion_improper_, k_torsion_proton_, read_bbdep_table(), torsions_indep_, 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

Definition at line 740 of file CartesianBondedEnergy.cc.

References core::chemical::ResidueType::aa(), 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
	)

Definition at line 973 of file CartesianBondedEnergy.cc.

References core::chemical::aa_ala, core::chemical::aa_gly, core::chemical::aa_pro, core::conformation::ResidueFactory::create_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::scoring::methods::get_restag(), 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

Definition at line 596 of file CartesianBondedEnergy.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_ala, 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

Definition at line 659 of file CartesianBondedEnergy.cc.

References core::chemical::ResidueType::aa(), 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

Definition at line 801 of file CartesianBondedEnergy.cc.

References core::chemical::ResidueType::aa(), 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_, 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
	)

Definition at line 1048 of file CartesianBondedEnergy.cc.

References core::chemical::aa_pro, core::conformation::ResidueFactory::create_residue(), core::scoring::methods::get_restag(), 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.

Definition at line 704 of file CartesianBondedEnergy.cc.

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
	)

Definition at line 863 of file CartesianBondedEnergy.cc.

References core::chemical::ResidueType::aa(), core::chemical::aa_arg, core::chemical::aa_cys, 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::scoring::methods::get_restag(), 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, 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!).

Definition at line 1094 of file CartesianBondedEnergy.cc.

References create_parameters_for_restype(), nonprepro_restype_data_, and prepro_restype_data_.

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

Definition at line 391 of file CartesianBondedEnergy.cc.

References bbdep_bond_devs_, bondangles_indep_, and bondlengths_indep_.

Referenced by init().

Member Data Documentation

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

private

Definition at line 322 of file CartesianBondedEnergy.hh.

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

bool core::scoring::methods::IdealParametersDatabase::bbdep_bond_params_

private

Definition at line 322 of file CartesianBondedEnergy.hh.

Referenced by bbdep_bond_params(), and init().

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

private

Definition at line 317 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_angle().

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

private

Definition at line 317 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_angle().

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

private

Definition at line 317 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_angle().

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

private

Definition at line 317 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_angle().

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

private

Definition at line 317 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_angle().

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

private

Definition at line 312 of file CartesianBondedEnergy.hh.

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

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

private

Definition at line 319 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_length().

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

private

Definition at line 319 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_length().

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

private

Definition at line 319 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_length().

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

private

Definition at line 319 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_length().

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

private

Definition at line 319 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_length().

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

private

Definition at line 313 of file CartesianBondedEnergy.hh.

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

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

private

Definition at line 308 of file CartesianBondedEnergy.hh.

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

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

private

Definition at line 308 of file CartesianBondedEnergy.hh.

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

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

private

Definition at line 308 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_torsion_legacy().

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

private

Definition at line 308 of file CartesianBondedEnergy.hh.

Referenced by init().

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

private

Definition at line 308 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_torsion_legacy().

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

private

Definition at line 326 of file CartesianBondedEnergy.hh.

Referenced by create_parameters_for_restype(), and parameters_for_restype().

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

private

Definition at line 325 of file CartesianBondedEnergy.hh.

Referenced by create_parameters_for_restype(), and parameters_for_restype().

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

private

Definition at line 311 of file CartesianBondedEnergy.hh.

Referenced by init(), and lookup_torsion().

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

• src/core/scoring/methods/CartesianBondedEnergy.hh
• src/core/scoring/methods/CartesianBondedEnergy.cc