class for managing a line of the Vall fragment library More...

#include <VallResidue.hh>

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef std::string	String

typedef core::fragment::BBTorsionSRFD	BBTorsionSRFD

typedef core::fragment::BBTorsionSRFDOP	BBTorsionSRFDOP

Public Member Functions
	VallResidue ()
	default constructor More...

	VallResidue (String const &line)
	string constructor More...

	VallResidue (VallResidue const &rval)
	copy constructor More...

	~VallResidue ()
	default destructor More...

VallResidue &	operator= (VallResidue const &rval)
	copy assignment More...

BBTorsionSRFDOP	bbtorsion_srfd (BBTorsionSRFD const &srfd_type=core::fragment::BBTorsionSRFD()) const
	build a BBTorsionSRFD of the given type from this page More...

String const &	id () const
	id of fragment source (e.g. pdb name) More...

char	aa () const
	one letter amino acid code More...

char	ss () const
	one letter secondary structure code More...

Size	resi () const
	residue sequence number in source More...

Real	x () const
	x-coordinate of C-alpha More...

Real	y () const
	y-coordinate of C-alpha More...

Real	z () const
	z-coordinate of C-alpha More...

Real	phi () const
	phi backbone torsion in degrees More...

Real	psi () const
	psi backbone torsion in degrees More...

Real	omega () const
	omega backbone torsion in degrees More...

utility::vector1< Real > const &	profile () const
	per amino acid profile data More...

Size	position_index () const
	stores the 1-based indexing for accessing this residue via VallSection::operator [] More...

Size	section_index () const
	stores the 1-based indexing for accessing the VallSection this residue is located in via VallLibrary::operator [] More...

void	id (String const &s)
	id of fragment source (e.g. pdb name) More...

void	aa (char const c)
	one letter amino acid code More...

void	ss (char const c)
	one letter secondary structure code More...

void	resi (Size const i)
	residue sequence number in source More...

void	x (Real const val)
	x-coordinate of C-alpha More...

void	y (Real const val)
	y-coordinate of C-alpha More...

void	z (Real const val)
	z-coordinate of C-alpha More...

void	phi (Real const val)
	phi backbone torsion in degrees More...

void	psi (Real const val)
	psi backbone torsion in degrees More...

void	omega (Real const val)
	omega backbone torsion in degrees More...

void	profile (utility::vector1< Real > const &v)
	per amino acid profile data More...

void	position_index (Size const idx)
	stores the 1-based indexing for accessing this residue via VallSection::operator [] More...

void	section_index (Size const idx)
	stores the 1-based indexing for accessing the VallSection this residue is located in via VallLibrary::operator [] More...

bool	has_profile () const
	has profile info? More...

void	fill_from_string (String const &line)
	fill internal data from string More...

Static Private Member Functions
static utility::vector1 < core::chemical::AA >	order_vector ()
	return a vector specifying the order of profile data in Vall More...

static String	format_string ()
	return a formatting string for fill_from_string() dependent upon actual type of core::Real and core::Size More...

static String	format_string_2011 ()
	return a formatting string for fill_from_string() dependent upon actual type of core::Real and core::Size More...

Private Attributes
String	id_
	id of fragment source (e.g. pdb name) More...

char	aa_
	one letter amino acid code More...

char	ss_
	one letter secondary structure code More...

Size	resi_
	residue sequence number in source More...

Real	x_
	x-coordinate of C-alpha More...

Real	y_
	y-coordinate of C-alpha More...

Real	z_
	z-coordinate of C-alpha More...

Real	phi_
	phi backbone torsion in degrees More...

Real	psi_
	psi backbone torsion in degrees More...

Real	omega_
	omega backbone torsion in degrees More...

utility::vector1< Real >	profile_
	per amino acid profile data More...

Size	position_index_
	stores the 1-based indexing for accessing this residue via VallSection::operator [] More...

Size	section_index_
	stores the 1-based indexing for accessing the VallSection this residue is located in via VallLibrary::operator [] More...

Static Private Attributes
static utility::vector1 < core::chemical::AA >	order_ = order_vector()
	order of amino acid profile data in Vall More...

static String	format_ = format_string()
	formatting string for fill_from_string() More...

static String	format_2011_ = format_string_2011()

Detailed Description

class for managing a line of the Vall fragment library

Member Typedef Documentation

typedef core::fragment::BBTorsionSRFD core::fragment::picking_old::vall::VallResidue::BBTorsionSRFD

typedef core::fragment::BBTorsionSRFDOP core::fragment::picking_old::vall::VallResidue::BBTorsionSRFDOP

typedef core::Real core::fragment::picking_old::vall::VallResidue::Real

typedef core::Size core::fragment::picking_old::vall::VallResidue::Size

typedef std::string core::fragment::picking_old::vall::VallResidue::String

Constructor & Destructor Documentation

core::fragment::picking_old::vall::VallResidue::VallResidue ( )

default constructor

core::fragment::picking_old::vall::VallResidue::VallResidue ( String const & line )

string constructor

References fill_from_string().

core::fragment::picking_old::vall::VallResidue::VallResidue ( VallResidue const & rval )

default

copy constructor

core::fragment::picking_old::vall::VallResidue::~VallResidue ( )

default

default destructor

Member Function Documentation

char core::fragment::picking_old::vall::VallResidue::aa ( ) const

inline

one letter amino acid code

References aa_.

void core::fragment::picking_old::vall::VallResidue::aa ( char const c )

inline

one letter amino acid code

References aa_, and core::pack::dunbrack::c.

VallResidue::BBTorsionSRFDOP core::fragment::picking_old::vall::VallResidue::bbtorsion_srfd ( BBTorsionSRFD const & srfd_type = core::fragment::BBTorsionSRFD() ) const

build a BBTorsionSRFD of the given type from this page

Parameters

[in] srfd_type BBTorsionSRFD::create() will be called from this object.

Returns: A BBTorsionSRFD of the given type initialized with the backbone torsion information from this page.

References aa_, core::fragment::BBTorsionSRFD::create(), omega_, phi_, psi_, core::fragment::SingleResidueFragData::set_sequence(), and ss_.

void core::fragment::picking_old::vall::VallResidue::fill_from_string ( String const & line )

fill internal data from string

Values are delimited by whitespace. Ordering is: id aa ss resi dummy dummy x y z phi psi omega dummy dummy dummy dummy (aa profile_info, 20 columns)

References aa_, format_, format_2011_, id(), id_, omega_, order_, phi_, profile_, psi_, resi_, ss_, x_, y_, and z_.

Referenced by core::fragment::picking_old::vall::vall_library_from_file(), and VallResidue().

VallResidue::String core::fragment::picking_old::vall::VallResidue::format_string ( )

staticprivate

return a formatting string for fill_from_string() dependent upon actual type of core::Real and core::Size

Remarks: This is necessary for sscanf; wrong type can give wrong input.

VallResidue::String core::fragment::picking_old::vall::VallResidue::format_string_2011 ( )

staticprivate

return a formatting string for fill_from_string() dependent upon actual type of core::Real and core::Size

Remarks: This is necessary for sscanf; wrong type can give wrong input.

bool core::fragment::picking_old::vall::VallResidue::has_profile ( ) const

inline

has profile info?

References profile_.

String const& core::fragment::picking_old::vall::VallResidue::id ( ) const

inline

id of fragment source (e.g. pdb name)

References id_.

Referenced by fill_from_string(), and core::fragment::picking_old::vall::vall_library_from_file().

void core::fragment::picking_old::vall::VallResidue::id ( String const & s )

inline

id of fragment source (e.g. pdb name)

References id_.

Real core::fragment::picking_old::vall::VallResidue::omega ( ) const

inline

omega backbone torsion in degrees

References omega_.

void core::fragment::picking_old::vall::VallResidue::omega ( Real const val )

inline

omega backbone torsion in degrees

References omega_, and protocols::hybridization::val.

VallResidue & core::fragment::picking_old::vall::VallResidue::operator= ( VallResidue const & rval )

copy assignment

References aa_, id_, omega_, phi_, position_index_, profile_, psi_, resi_, section_index_, ss_, x_, y_, and z_.

utility::vector1< core::chemical::AA > core::fragment::picking_old::vall::VallResidue::order_vector ( )

staticprivate

return a vector specifying the order of profile data in Vall

References core::chemical::aa_from_oneletter_code(), and protocols::forge::methods::order().

Real core::fragment::picking_old::vall::VallResidue::phi ( ) const

inline

phi backbone torsion in degrees

References phi_.

void core::fragment::picking_old::vall::VallResidue::phi ( Real const val )

inline

phi backbone torsion in degrees

References phi_, and protocols::hybridization::val.

Size core::fragment::picking_old::vall::VallResidue::position_index ( ) const

inline

stores the 1-based indexing for accessing this residue via VallSection::operator []

References position_index_.

void core::fragment::picking_old::vall::VallResidue::position_index ( Size const idx )

inline

stores the 1-based indexing for accessing this residue via VallSection::operator []

References position_index_.

utility::vector1< Real > const& core::fragment::picking_old::vall::VallResidue::profile ( ) const

inline

per amino acid profile data

References profile_.

void core::fragment::picking_old::vall::VallResidue::profile ( utility::vector1< Real > const & v )

inline

per amino acid profile data

References profile_.

Real core::fragment::picking_old::vall::VallResidue::psi ( ) const

inline

psi backbone torsion in degrees

References psi_.

void core::fragment::picking_old::vall::VallResidue::psi ( Real const val )

inline

psi backbone torsion in degrees

References psi_, and protocols::hybridization::val.

Size core::fragment::picking_old::vall::VallResidue::resi ( ) const

inline

residue sequence number in source

References resi_.

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

void core::fragment::picking_old::vall::VallResidue::resi ( Size const i )

inline

residue sequence number in source

References resi_.

Size core::fragment::picking_old::vall::VallResidue::section_index ( ) const

inline

stores the 1-based indexing for accessing the VallSection this residue is located in via VallLibrary::operator []

References section_index_.

void core::fragment::picking_old::vall::VallResidue::section_index ( Size const idx )

inline

stores the 1-based indexing for accessing the VallSection this residue is located in via VallLibrary::operator []

References section_index_.

char core::fragment::picking_old::vall::VallResidue::ss ( ) const

inline

one letter secondary structure code

References ss_.

void core::fragment::picking_old::vall::VallResidue::ss ( char const c )

inline

one letter secondary structure code

References core::pack::dunbrack::c, and ss_.

Real core::fragment::picking_old::vall::VallResidue::x ( ) const

inline

x-coordinate of C-alpha

References x_.

void core::fragment::picking_old::vall::VallResidue::x ( Real const val )

inline

x-coordinate of C-alpha

References protocols::hybridization::val, and x_.

Real core::fragment::picking_old::vall::VallResidue::y ( ) const

inline

y-coordinate of C-alpha

References y_.

void core::fragment::picking_old::vall::VallResidue::y ( Real const val )

inline

y-coordinate of C-alpha

References protocols::hybridization::val, and y_.

Real core::fragment::picking_old::vall::VallResidue::z ( ) const

inline

z-coordinate of C-alpha

References z_.

void core::fragment::picking_old::vall::VallResidue::z ( Real const val )

inline

z-coordinate of C-alpha

References protocols::hybridization::val, and z_.

Member Data Documentation

char core::fragment::picking_old::vall::VallResidue::aa_

private

one letter amino acid code

Referenced by aa(), bbtorsion_srfd(), fill_from_string(), and operator=().

VallResidue::String core::fragment::picking_old::vall::VallResidue::format_ = format_string()

staticprivate

formatting string for fill_from_string()

Referenced by fill_from_string().

VallResidue::String core::fragment::picking_old::vall::VallResidue::format_2011_ = format_string_2011()

staticprivate

Referenced by fill_from_string().

String core::fragment::picking_old::vall::VallResidue::id_

private

id of fragment source (e.g. pdb name)

Referenced by fill_from_string(), id(), and operator=().

Real core::fragment::picking_old::vall::VallResidue::omega_

private

omega backbone torsion in degrees

Referenced by bbtorsion_srfd(), fill_from_string(), omega(), and operator=().

utility::vector1< core::chemical::AA > core::fragment::picking_old::vall::VallResidue::order_ = order_vector()

staticprivate

order of amino acid profile data in Vall

Referenced by fill_from_string().

Real core::fragment::picking_old::vall::VallResidue::phi_

private

phi backbone torsion in degrees

Referenced by bbtorsion_srfd(), fill_from_string(), operator=(), and phi().

Size core::fragment::picking_old::vall::VallResidue::position_index_

private

stores the 1-based indexing for accessing this residue via VallSection::operator []

Referenced by operator=(), and position_index().

utility::vector1< Real > core::fragment::picking_old::vall::VallResidue::profile_

private

per amino acid profile data

Referenced by fill_from_string(), has_profile(), operator=(), and profile().

Real core::fragment::picking_old::vall::VallResidue::psi_

private

psi backbone torsion in degrees

Referenced by bbtorsion_srfd(), fill_from_string(), operator=(), and psi().

Size core::fragment::picking_old::vall::VallResidue::resi_

private

residue sequence number in source

Referenced by fill_from_string(), operator=(), and resi().

Size core::fragment::picking_old::vall::VallResidue::section_index_

private

stores the 1-based indexing for accessing the VallSection this residue is located in via VallLibrary::operator []

Referenced by operator=(), and section_index().

char core::fragment::picking_old::vall::VallResidue::ss_

private

one letter secondary structure code

Referenced by bbtorsion_srfd(), fill_from_string(), operator=(), and ss().

Real core::fragment::picking_old::vall::VallResidue::x_

private

x-coordinate of C-alpha

Referenced by fill_from_string(), operator=(), and x().

Real core::fragment::picking_old::vall::VallResidue::y_

private

y-coordinate of C-alpha

Referenced by fill_from_string(), operator=(), and y().

Real core::fragment::picking_old::vall::VallResidue::z_

private

z-coordinate of C-alpha

Referenced by fill_from_string(), operator=(), and z().

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

src/core/fragment/picking_old/vall/VallResidue.hh
src/core/fragment/picking_old/vall/VallResidue.cc

Public Types

Public Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation