Rosetta 3.4
Public Types | Public Member Functions
protocols::frag_picker::VallResidue Class Reference

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

#include <VallResidue.hh>

Inheritance diagram for protocols::frag_picker::VallResidue:
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List of all members.

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
 VallResidue (String const &line)
 string constructor
 VallResidue (VallResidue const &rval)
 copy constructor
 ~VallResidue ()
 default destructor
VallResidueoperator= (VallResidue const &rval)
 copy assignment
BBTorsionSRFDOP bbtorsion_srfd () const
 build a BBTorsionSRFD from this page
String const & id () const
 id of fragment source (e.g. pdb name)
void key (Size key)
 sets the key id
Size key ()
 sets the key id
char aa () const
 one letter amino acid code
char ss () const
 one letter secondary structure code
char ss_str () const
 one letter secondary structure STR code
Size resi () const
 residue sequence number in source
Real x () const
 x-coordinate of C-alpha
Real y () const
 y-coordinate of C-alpha
Real z () const
 z-coordinate of C-alpha
Real cbx () const
 x-coordinate of C-beta
Real cby () const
 y-coordinate of C-beta
Real cbz () const
 z-coordinate of C-beta
Real cenx () const
 x-coordinate of centroid
Real ceny () const
 y-coordinate of centroid
Real cenz () const
 z-coordinate of centroid
Real sa () const
 solvent accessible area
Real sa_norm () const
 solvent accessible area normalized
Real dssp_phi () const
 phi backbone torsion in degrees from DSSP
Real dssp_psi () const
 psi backbone torsion in degrees from DSSP
Real depth () const
 all-atom residue depth
Size nali () const
 number of alignments
Real phi () const
 phi backbone torsion in degrees
Real psi () const
 psi backbone torsion in degrees
Real omega () const
 omega backbone torsion in degrees
Real bF () const
 b factor average for backbone
utility::vector1< Real > const & profile () const
 per amino acid profile data
utility::vector1< Real > const & profile_struct () const
 per amino acid structure profile data
utility::vector1< Real > const & secondary_shifts ()
 secondary chemical shifts
void profile (utility::vector1< Real > const &v)
 per amino acid profile data
void profile_struct (utility::vector1< Real > const &v)
 per amino acid structure profile data
Size position_index () const
 stores the 1-based indexing for accessing this residue via VallSection::operator []
Size section_index () const
 stores the 1-based indexing for accessing the VallSection this residue is located in via VallLibrary::operator []
void id (String const &s)
 id of fragment source (e.g. pdb name)
void aa (char const c)
 one letter amino acid code
void ss (char const c)
 one letter secondary structure code
void ss_str (char const c)
 one letter secondary structure STR code
void set_ss_from_str ()
void resi (Size const i)
 residue sequence number in source
void x (Real const val)
 x-coordinate of C-alpha
void y (Real const val)
 y-coordinate of C-alpha
void z (Real const val)
 z-coordinate of C-alpha
void cbx (Real const val)
 x-coordinate of C-beta
void cby (Real const val)
 y-coordinate of C-beta
void cbz (Real const val)
 z-coordinate of C-beta
void cenx (Real const val)
 x-coordinate of centroid
void ceny (Real const val)
 y-coordinate of centroid
void cenz (Real const val)
 z-coordinate of centroid
void sa (Real const val)
 solvent accessible area
void nali (Size const val)
 number of alignments
void depth (Real const depth)
 all-atom residue depth
void phi (Real const val)
 phi backbone torsion in degrees
void psi (Real const val)
 psi backbone torsion in degrees
void omega (Real const val)
 omega backbone torsion in degrees
void bF (Real const val)
 b factor average for backbone
void position_index (Size const idx)
 stores the 1-based indexing for accessing this residue via VallSection::operator []
void section_index (Size const idx)
 stores the 1-based indexing for accessing the VallSection this residue is located in via VallLibrary::operator []
bool has_profile () const
 has profile info?
bool has_profile_struct () const
 has structure profile info?
bool has_chemical_shifts () const
void fill_from_string (String const &line)
 fill internal data from string
void fill_from_string_cs (String const &line)
 fill internal data from string
void fill_from_string_version1 (String const &line)
 fill internal data from string
void fill_from_string_residue_depth_version1 (String const &line)
Real distance_squared (VallResidueCOP r)
Real distance_squared_cb (VallResidueCOP r)
Real distance_squared_cen (VallResidueCOP r)
Real distance_squared (VallResidueCOP r, ContactType const &type)

Detailed Description

class for managing a line of the Vall fragment library


Member Typedef Documentation


Constructor & Destructor Documentation

protocols::frag_picker::VallResidue::VallResidue ( )

default constructor

protocols::frag_picker::VallResidue::VallResidue ( String const &  line)
protocols::frag_picker::VallResidue::VallResidue ( VallResidue const &  rval)

copy constructor

protocols::frag_picker::VallResidue::~VallResidue ( )

default destructor


Member Function Documentation

char protocols::frag_picker::VallResidue::aa ( ) const [inline]

one letter amino acid code

void protocols::frag_picker::VallResidue::aa ( char const  c) [inline]

one letter amino acid code

References core::pack::dunbrack::c.

VallResidue::BBTorsionSRFDOP protocols::frag_picker::VallResidue::bbtorsion_srfd ( ) const
Real protocols::frag_picker::VallResidue::bF ( ) const [inline]

b factor average for backbone

void protocols::frag_picker::VallResidue::bF ( Real const  val) [inline]

b factor average for backbone

void protocols::frag_picker::VallResidue::cbx ( Real const  val) [inline]

x-coordinate of C-beta

Real protocols::frag_picker::VallResidue::cbx ( ) const [inline]

x-coordinate of C-beta

void protocols::frag_picker::VallResidue::cby ( Real const  val) [inline]

y-coordinate of C-beta

Real protocols::frag_picker::VallResidue::cby ( ) const [inline]

y-coordinate of C-beta

void protocols::frag_picker::VallResidue::cbz ( Real const  val) [inline]

z-coordinate of C-beta

Real protocols::frag_picker::VallResidue::cbz ( ) const [inline]

z-coordinate of C-beta

Real protocols::frag_picker::VallResidue::cenx ( ) const [inline]

x-coordinate of centroid

void protocols::frag_picker::VallResidue::cenx ( Real const  val) [inline]

x-coordinate of centroid

Real protocols::frag_picker::VallResidue::ceny ( ) const [inline]

y-coordinate of centroid

void protocols::frag_picker::VallResidue::ceny ( Real const  val) [inline]

y-coordinate of centroid

Real protocols::frag_picker::VallResidue::cenz ( ) const [inline]

z-coordinate of centroid

void protocols::frag_picker::VallResidue::cenz ( Real const  val) [inline]

z-coordinate of centroid

Real protocols::frag_picker::VallResidue::depth ( ) const [inline]

all-atom residue depth

Referenced by depth().

void protocols::frag_picker::VallResidue::depth ( Real const  depth) [inline]

all-atom residue depth

References depth().

core::Real protocols::frag_picker::VallResidue::distance_squared ( VallResidueCOP  r)

References x(), y(), and z().

Referenced by distance_squared(), and distance_squared_cb().

core::Real protocols::frag_picker::VallResidue::distance_squared ( VallResidueCOP  r,
ContactType const &  type 
)
core::Real protocols::frag_picker::VallResidue::distance_squared_cb ( VallResidueCOP  r)

References distance_squared(), x(), y(), and z().

Referenced by distance_squared().

core::Real protocols::frag_picker::VallResidue::distance_squared_cen ( VallResidueCOP  r)

References x(), y(), and z().

Referenced by distance_squared().

Real protocols::frag_picker::VallResidue::dssp_phi ( ) const [inline]

phi backbone torsion in degrees from DSSP

Real protocols::frag_picker::VallResidue::dssp_psi ( ) const [inline]

psi backbone torsion in degrees from DSSP

void protocols::frag_picker::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) BFactor

References id().

Referenced by VallResidue().

void protocols::frag_picker::VallResidue::fill_from_string_cs ( 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) (CS data, 12 columns)

References id().

Referenced by VallResidue().

void protocols::frag_picker::VallResidue::fill_from_string_residue_depth_version1 ( String const &  line)

References id().

Referenced by VallResidue().

void protocols::frag_picker::VallResidue::fill_from_string_version1 ( String const &  line)

fill internal data from string

Values are delimited by whitespace. Ordering is: id aa ss resi dummy dummy x y z cbz cby cbz cenx ceny cenz phi psi omega dssp_phi dssp_psi sa nali (aa profile_info, 20 columns) BFactor

References id(), protocols::frag_picker::sa_faraggi_max(), and set_ss_from_str().

Referenced by VallResidue().

bool protocols::frag_picker::VallResidue::has_chemical_shifts ( ) const [inline]
bool protocols::frag_picker::VallResidue::has_profile ( ) const [inline]

has profile info?

bool protocols::frag_picker::VallResidue::has_profile_struct ( ) const [inline]

has structure profile info?

void protocols::frag_picker::VallResidue::id ( String const &  s) [inline]

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

String const& protocols::frag_picker::VallResidue::id ( ) const [inline]
void protocols::frag_picker::VallResidue::key ( Size  key) [inline]

sets the key id

References key().

Referenced by key().

Size protocols::frag_picker::VallResidue::key ( ) [inline]

sets the key id

Size protocols::frag_picker::VallResidue::nali ( ) const [inline]

number of alignments

void protocols::frag_picker::VallResidue::nali ( Size const  val) [inline]

number of alignments

Real protocols::frag_picker::VallResidue::omega ( ) const [inline]

omega backbone torsion in degrees

void protocols::frag_picker::VallResidue::omega ( Real const  val) [inline]

omega backbone torsion in degrees

VallResidue & protocols::frag_picker::VallResidue::operator= ( VallResidue const &  rval)

copy assignment

void protocols::frag_picker::VallResidue::phi ( Real const  val) [inline]

phi backbone torsion in degrees

Real protocols::frag_picker::VallResidue::phi ( ) const [inline]

phi backbone torsion in degrees

void protocols::frag_picker::VallResidue::position_index ( Size const  idx) [inline]

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

Size protocols::frag_picker::VallResidue::position_index ( ) const [inline]

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

utility::vector1<Real> const& protocols::frag_picker::VallResidue::profile ( ) const [inline]

per amino acid profile data

void protocols::frag_picker::VallResidue::profile ( utility::vector1< Real > const &  v) [inline]

per amino acid profile data

utility::vector1<Real> const& protocols::frag_picker::VallResidue::profile_struct ( ) const [inline]

per amino acid structure profile data

void protocols::frag_picker::VallResidue::profile_struct ( utility::vector1< Real > const &  v) [inline]

per amino acid structure profile data

void protocols::frag_picker::VallResidue::psi ( Real const  val) [inline]

psi backbone torsion in degrees

Real protocols::frag_picker::VallResidue::psi ( ) const [inline]

psi backbone torsion in degrees

Size protocols::frag_picker::VallResidue::resi ( ) const [inline]

residue sequence number in source

void protocols::frag_picker::VallResidue::resi ( Size const  i) [inline]

residue sequence number in source

void protocols::frag_picker::VallResidue::sa ( Real const  val) [inline]

solvent accessible area

Real protocols::frag_picker::VallResidue::sa ( ) const [inline]

solvent accessible area

Real protocols::frag_picker::VallResidue::sa_norm ( ) const [inline]

solvent accessible area normalized

utility::vector1<Real> const& protocols::frag_picker::VallResidue::secondary_shifts ( ) [inline]

secondary chemical shifts

void protocols::frag_picker::VallResidue::section_index ( Size const  idx) [inline]

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

Size protocols::frag_picker::VallResidue::section_index ( ) const [inline]

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

void protocols::frag_picker::VallResidue::set_ss_from_str ( ) [inline]
void protocols::frag_picker::VallResidue::ss ( char const  c) [inline]

one letter secondary structure code

References core::pack::dunbrack::c.

char protocols::frag_picker::VallResidue::ss ( ) const [inline]

one letter secondary structure code

void protocols::frag_picker::VallResidue::ss_str ( char const  c) [inline]

one letter secondary structure STR code

References core::pack::dunbrack::c.

char protocols::frag_picker::VallResidue::ss_str ( ) const [inline]

one letter secondary structure STR code

void protocols::frag_picker::VallResidue::x ( Real const  val) [inline]

x-coordinate of C-alpha

Real protocols::frag_picker::VallResidue::x ( ) const [inline]

x-coordinate of C-alpha

Referenced by distance_squared(), distance_squared_cb(), and distance_squared_cen().

void protocols::frag_picker::VallResidue::y ( Real const  val) [inline]

y-coordinate of C-alpha

Real protocols::frag_picker::VallResidue::y ( ) const [inline]

y-coordinate of C-alpha

Referenced by distance_squared(), distance_squared_cb(), and distance_squared_cen().

Real protocols::frag_picker::VallResidue::z ( ) const [inline]

z-coordinate of C-alpha

Referenced by distance_squared(), distance_squared_cb(), and distance_squared_cen().

void protocols::frag_picker::VallResidue::z ( Real const  val) [inline]

z-coordinate of C-alpha


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