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

#include <VallResidue.hh>

Collaboration diagram for core::fragment::picking_old::vall::VallResidue:

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=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...

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...

Detailed Description

class for managing a line of the Vall fragment library

Definition at line 47 of file VallResidue.hh.

Member Typedef Documentation

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

Definition at line 57 of file VallResidue.hh.

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

Definition at line 58 of file VallResidue.hh.

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

Definition at line 54 of file VallResidue.hh.

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

Definition at line 53 of file VallResidue.hh.

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

Definition at line 55 of file VallResidue.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 50 of file VallResidue.cc.

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

string constructor

Definition at line 67 of file VallResidue.cc.

References fill_from_string().

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

copy constructor

Definition at line 73 of file VallResidue.cc.

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

default destructor

Definition at line 91 of file VallResidue.cc.

Member Function Documentation

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

inline

one letter amino acid code

Definition at line 109 of file VallResidue.hh.

References aa_.

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

inline

one letter amino acid code

Definition at line 205 of file VallResidue.hh.

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

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

Definition at line 119 of file VallResidue.cc.

References aa_, core::fragment::BBTorsionSRFD::create(), omega_, phi_, psi_, 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)

Definition at line 138 of file VallResidue.cc.

References aa_, format_, 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.

Definition at line 210 of file VallResidue.cc.

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

inline

has profile info?

Definition at line 294 of file VallResidue.hh.

References profile_.

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

inline

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

Definition at line 102 of file VallResidue.hh.

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)

Definition at line 198 of file VallResidue.hh.

References id_.

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

inline

omega backbone torsion in degrees

Definition at line 165 of file VallResidue.hh.

References omega_.

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

inline

omega backbone torsion in degrees

Definition at line 261 of file VallResidue.hh.

References omega_.

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

copy assignment

Definition at line 95 of file VallResidue.cc.

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

Definition at line 178 of file VallResidue.cc.

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

Definition at line 151 of file VallResidue.hh.

References phi_.

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

inline

phi backbone torsion in degrees

Definition at line 247 of file VallResidue.hh.

References phi_.

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

inline

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

Definition at line 180 of file VallResidue.hh.

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 []

Definition at line 276 of file VallResidue.hh.

References position_index_.

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

inline

per amino acid profile data

Definition at line 172 of file VallResidue.hh.

References profile_.

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

inline

per amino acid profile data

Definition at line 268 of file VallResidue.hh.

References profile_.

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

inline

psi backbone torsion in degrees

Definition at line 158 of file VallResidue.hh.

References psi_.

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

inline

psi backbone torsion in degrees

Definition at line 254 of file VallResidue.hh.

References psi_.

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

inline

residue sequence number in source

Definition at line 123 of file VallResidue.hh.

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

Definition at line 219 of file VallResidue.hh.

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 []

Definition at line 188 of file VallResidue.hh.

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 []

Definition at line 284 of file VallResidue.hh.

References section_index_.

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

inline

one letter secondary structure code

Definition at line 116 of file VallResidue.hh.

References ss_.

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

inline

one letter secondary structure code

Definition at line 212 of file VallResidue.hh.

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

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

inline

x-coordinate of C-alpha

Definition at line 130 of file VallResidue.hh.

References x_.

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

inline

x-coordinate of C-alpha

Definition at line 226 of file VallResidue.hh.

References x_.

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

inline

y-coordinate of C-alpha

Definition at line 137 of file VallResidue.hh.

References y_.

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

inline

y-coordinate of C-alpha

Definition at line 233 of file VallResidue.hh.

References y_.

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

inline

z-coordinate of C-alpha

Definition at line 144 of file VallResidue.hh.

References z_.

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

inline

z-coordinate of C-alpha

Definition at line 240 of file VallResidue.hh.

References z_.

Member Data Documentation

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

private

one letter amino acid code

Definition at line 328 of file VallResidue.hh.

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()

Definition at line 385 of file VallResidue.hh.

Referenced by fill_from_string().

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

private

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

Definition at line 324 of file VallResidue.hh.

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

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

private

omega backbone torsion in degrees

Definition at line 360 of file VallResidue.hh.

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

Definition at line 381 of file VallResidue.hh.

Referenced by fill_from_string().

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

private

phi backbone torsion in degrees

Definition at line 352 of file VallResidue.hh.

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 []

Definition at line 369 of file VallResidue.hh.

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

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

private

per amino acid profile data

Definition at line 364 of file VallResidue.hh.

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

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

private

psi backbone torsion in degrees

Definition at line 356 of file VallResidue.hh.

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

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

private

residue sequence number in source

Definition at line 336 of file VallResidue.hh.

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 []

Definition at line 374 of file VallResidue.hh.

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

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

private

one letter secondary structure code

Definition at line 332 of file VallResidue.hh.

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

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

private

x-coordinate of C-alpha

Definition at line 340 of file VallResidue.hh.

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

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

private

y-coordinate of C-alpha

Definition at line 344 of file VallResidue.hh.

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

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

private

z-coordinate of C-alpha

Definition at line 348 of file VallResidue.hh.

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