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core::fragment::picking_old::vall::VallResidue Class Reference

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...
 
VallResidueoperator= (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< Realprofile_
 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

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_typeBBTorsionSRFD::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: