protocols::minimization_packing::MinimalRotamer Class Reference

#include <GreenPacker.hh>

Inheritance diagram for protocols::minimization_packing::MinimalRotamer:

Public Types
typedef core::chemical::AA	AA
typedef core::chemical::ResidueType	ResidueType
typedef core::conformation::Residue	Residue
typedef core::Size	Size
typedef core::Vector	Vector
typedef core::Real	Real

Public Member Functions
	~MinimalRotamer () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
	MinimalRotamer (Residue const &)
bool	same (MinimalRotamer const &) const
bool	same_residue_type (MinimalRotamer const &) const
AA	aa () const

Private Member Functions
bool	has_ideal_geometry (core::conformation::Residue const &res) const
bool	atom_is_ideal (core::conformation::Residue const &res, core::Size const atom_id) const
void	record_chi (core::conformation::Residue const &res)
void	record_internal_geometry (core::conformation::Residue const &res)
void	record_internal_geometry (core::conformation::Residue const &res, core::Size const atom_id)
bool	chi_matches_coords (core::conformation::Residue const &res, core::Size chi_index) const
bool	same_chi (MinimalRotamer const &other) const
	@detail This tolerance may need fiddling with More...
bool	same_nonideal_geometry (MinimalRotamer const &other) const
	@detail These tolerances may need fiddling with More...
	MinimalRotamer ()
MinimalRotamer const &	operator= (MinimalRotamer const &)

Private Attributes
ResidueType const &	residue_type_
bool	ideal_geometry_
utility::vector1< Real >	chi_
utility::vector1< Vector >	internal_geometry_

Static Private Attributes
static core::Size const	d = 0
static core::Size const	theta = 1
static core::Size const	phi = 2

Member Typedef Documentation

AA

typedef core::chemical::AA protocols::minimization_packing::MinimalRotamer::AA

Real

typedef core::Real protocols::minimization_packing::MinimalRotamer::Real

Residue

typedef core::conformation::Residue protocols::minimization_packing::MinimalRotamer::Residue

ResidueType

typedef core::chemical::ResidueType protocols::minimization_packing::MinimalRotamer::ResidueType

Size

typedef core::Size protocols::minimization_packing::MinimalRotamer::Size

Vector

typedef core::Vector protocols::minimization_packing::MinimalRotamer::Vector

Constructor & Destructor Documentation

~MinimalRotamer()

protocols::minimization_packing::MinimalRotamer::~MinimalRotamer ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

MinimalRotamer() [1/2]

protocols::minimization_packing::MinimalRotamer::MinimalRotamer

(

Residue const &

res

)

References has_ideal_geometry(), ideal_geometry_, record_chi(), and record_internal_geometry().

MinimalRotamer() [2/2]

protocols::minimization_packing::MinimalRotamer::MinimalRotamer ( )

private

No default constructor or assignment operator copy c-tor is fine

Member Function Documentation

aa()

core::chemical::AA protocols::minimization_packing::MinimalRotamer::aa

(

)

const

References core::chemical::ResidueTypeBase::aa(), and residue_type_.

atom_is_ideal()

bool protocols::minimization_packing::MinimalRotamer::atom_is_ideal ( core::conformation::Residue const &  res, core::Size const  atom_id  ) const

private

Assumption: sidechain ideal coordinates do not depend on other residues ( as opposed to the backbone O for example, which depends on the coordinates of i+1.)

References core::chemical::ICoorAtomID::atomno(), core::chemical::ResidueType::chi_atoms(), core::chemical::AtomICoor::d(), core::chemical::ResidueType::icoor(), core::chemical::AtomICoor::phi(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::theta(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by has_ideal_geometry().

chi_matches_coords()

bool protocols::minimization_packing::MinimalRotamer::chi_matches_coords ( core::conformation::Residue const &  res, core::Size  chi_index  ) const

private

References core::conformation::Residue::chi(), core::chemical::ResidueType::chi_atoms(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by record_chi().

has_ideal_geometry()

bool protocols::minimization_packing::MinimalRotamer::has_ideal_geometry ( core::conformation::Residue const &  res ) const

private

References atom_is_ideal(), core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::nheavyatoms(), and core::conformation::Residue::type().

Referenced by MinimalRotamer().

operator=()

MinimalRotamer const& protocols::minimization_packing::MinimalRotamer::operator= ( MinimalRotamer const &  )

private

record_chi()

void protocols::minimization_packing::MinimalRotamer::record_chi ( core::conformation::Residue const &  res )

private

References core::conformation::Residue::chi(), chi_, chi_matches_coords(), core::chemical::ResidueType::nchi(), and core::conformation::Residue::type().

Referenced by MinimalRotamer().

record_internal_geometry() [1/2]

void protocols::minimization_packing::MinimalRotamer::record_internal_geometry ( core::conformation::Residue const &  res )

private

only record internal geometry for sidechain atoms

References core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), core::chemical::ResidueType::first_sidechain_atom(), internal_geometry_, core::conformation::Residue::natoms(), core::chemical::ResidueType::nheavyatoms(), and core::conformation::Residue::type().

Referenced by MinimalRotamer().

record_internal_geometry() [2/2]

void protocols::minimization_packing::MinimalRotamer::record_internal_geometry ( core::conformation::Residue const &  res, core::Size const  atom_id  )

private

References core::chemical::ICoorAtomID::atomno(), d, core::chemical::ResidueType::icoor(), internal_geometry_, phi, core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), theta, core::conformation::Residue::type(), and core::conformation::Residue::xyz().

same()

bool protocols::minimization_packing::MinimalRotamer::same

(

MinimalRotamer const &

other

)

const

References ideal_geometry_, residue_type_, same_chi(), and same_nonideal_geometry().

same_chi()

bool protocols::minimization_packing::MinimalRotamer::same_chi ( MinimalRotamer const &  other ) const

private

@detail This tolerance may need fiddling with

References chi_, and ideal_geometry_.

Referenced by same().

same_nonideal_geometry()

bool protocols::minimization_packing::MinimalRotamer::same_nonideal_geometry ( MinimalRotamer const &  other ) const

private

@detail These tolerances may need fiddling with

References d, ideal_geometry_, internal_geometry_, phi, and theta.

Referenced by same().

same_residue_type()

bool protocols::minimization_packing::MinimalRotamer::same_residue_type

(

MinimalRotamer const &

other

)

const

References residue_type_.

Member Data Documentation

chi_

utility::vector1< Real > protocols::minimization_packing::MinimalRotamer::chi_

private

Referenced by record_chi(), and same_chi().

d

core::Size const protocols::minimization_packing::MinimalRotamer::d = 0

staticprivate

Referenced by record_internal_geometry(), and same_nonideal_geometry().

ideal_geometry_

bool protocols::minimization_packing::MinimalRotamer::ideal_geometry_

private

Referenced by MinimalRotamer(), same(), same_chi(), and same_nonideal_geometry().

internal_geometry_

utility::vector1< Vector > protocols::minimization_packing::MinimalRotamer::internal_geometry_

private

Referenced by record_internal_geometry(), and same_nonideal_geometry().

phi

core::Size const protocols::minimization_packing::MinimalRotamer::phi = 2

staticprivate

Referenced by record_internal_geometry(), and same_nonideal_geometry().

residue_type_

ResidueType const& protocols::minimization_packing::MinimalRotamer::residue_type_

private

Referenced by aa(), same(), and same_residue_type().

theta

core::Size const protocols::minimization_packing::MinimalRotamer::theta = 1

staticprivate

Referenced by record_internal_geometry(), and same_nonideal_geometry().

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

• src/protocols/minimization_packing/GreenPacker.hh
• src/protocols/minimization_packing/GreenPacker.cc