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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:
Inheritance graph
[legend]

Public Types

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

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_cs ()
 return a formatting string for fill_from_string() dependent upon actual type of core::Real and core::Size More...
 
static String format_string_version1 ()
 return a formatting string for fill_from_string() dependent upon actual type of core::Real and core::Size More...
 
static String format_string_residue_depth_version1 ()
 

Private Attributes

core::Size key_
 integer key for a residue is simply the line number in a vall file More...
 
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 (3 letter alphabet) More...
 
char ss_str_
 one letter secondary structure code (STR alphabet - Karplus et. al.) More...
 
core::Size resi_
 residue sequence number in source More...
 
core::Real bF_
 b factor average for backbone More...
 
core::Real x_
 x-coordinate of C-alpha More...
 
core::Real y_
 y-coordinate of C-alpha More...
 
core::Real z_
 z-coordinate of C-alpha More...
 
core::Real cbx_
 x-coordinate of C-beta More...
 
core::Real cby_
 y-coordinate of C-beta More...
 
core::Real cbz_
 z-coordinate of C-beta More...
 
core::Real cenx_
 x-coordinate of centroid More...
 
core::Real ceny_
 y-coordinate of centroid More...
 
core::Real cenz_
 z-coordinate of centroid More...
 
core::Real phi_
 phi backbone torsion in degrees More...
 
core::Real psi_
 psi backbone torsion in degrees More...
 
core::Real omega_
 omega backbone torsion in degrees More...
 
core::Real sa_
 solvent accessible area More...
 
core::Real sa_norm_
 normalized solvent accessible area More...
 
core::Real dssp_phi_
 phi backbone torsion in degrees from DSSP program More...
 
core::Real dssp_psi_
 psi backbone torsion in degrees from DSSP program More...
 
core::Size nali_
 number of alignments used for profile More...
 
utility::vector1< core::Realprofile_
 per amino acid profile data More...
 
utility::vector1< core::Realprofile_struct_
 per amino acid structure profile data More...
 
utility::vector1< core::Realsec_shift_data_
 
core::Real all_atom_residue_depth_
 

Static Private Attributes

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

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 ( )
overridedefault

default destructor

Member Function Documentation

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

one letter amino acid code

References aa_.

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

one letter amino acid code

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

VallResidue::BBTorsionSRFDOP protocols::frag_picker::VallResidue::bbtorsion_srfd ( ) const

build a BBTorsionSRFD from this page

References aa_, omega_, phi_, psi_, ss_, x_, y_, and z_.

core::Real protocols::frag_picker::VallResidue::bF ( ) const
inline

b factor average for backbone

References bF_.

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

b factor average for backbone

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

core::Real protocols::frag_picker::VallResidue::cbx ( ) const
inline

x-coordinate of C-beta

References cbx_.

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

x-coordinate of C-beta

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

core::Real protocols::frag_picker::VallResidue::cby ( ) const
inline

y-coordinate of C-beta

References cby_.

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

y-coordinate of C-beta

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

core::Real protocols::frag_picker::VallResidue::cbz ( ) const
inline

z-coordinate of C-beta

References cbz_.

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

z-coordinate of C-beta

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

core::Real protocols::frag_picker::VallResidue::cenx ( ) const
inline

x-coordinate of centroid

References cenx_.

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

x-coordinate of centroid

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

core::Real protocols::frag_picker::VallResidue::ceny ( ) const
inline

y-coordinate of centroid

References ceny_.

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

y-coordinate of centroid

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

core::Real protocols::frag_picker::VallResidue::cenz ( ) const
inline

z-coordinate of centroid

References cenz_.

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

z-coordinate of centroid

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

core::Real protocols::frag_picker::VallResidue::depth ( ) const
inline

all-atom residue depth

References all_atom_residue_depth_.

Referenced by depth().

void protocols::frag_picker::VallResidue::depth ( core::Real const  depth)
inline

all-atom residue depth

References all_atom_residue_depth_, and depth().

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

References x(), x_, y(), y_, z(), 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 aa_, cbx_, cby_, cbz_, distance_squared(), x(), x_, y(), y_, z(), and z_.

Referenced by distance_squared().

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

References cenx_, ceny_, cenz_, x(), y(), and z().

Referenced by distance_squared().

core::Real protocols::frag_picker::VallResidue::dssp_phi ( ) const
inline

phi backbone torsion in degrees from DSSP

References dssp_phi_.

core::Real protocols::frag_picker::VallResidue::dssp_psi ( ) const
inline

psi backbone torsion in degrees from DSSP

References dssp_psi_.

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 aa_, format_string(), id(), id_, omega_, order_, phi_, profile_, psi_, resi_, ss_, ss_str_, x_, y_, and z_.

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 aa_, bF_, format_string_cs(), id(), id_, omega_, order_, phi_, profile_, psi_, resi_, sec_shift_data_, ss_, ss_str_, x_, y_, and z_.

Referenced by VallResidue().

void protocols::frag_picker::VallResidue::fill_from_string_residue_depth_version1 ( String const &  line)
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 aa_, bF_, cbx_, cby_, cbz_, cenx_, ceny_, cenz_, dssp_phi_, dssp_psi_, format_string_version1(), id(), id_, nali_, omega_, order_, phi_, profile_, profile_struct_, psi_, resi_, sa_, protocols::frag_picker::sa_faraggi_max(), sa_norm_, set_ss_from_str(), ss_str_, x_, y_, and z_.

Referenced by VallResidue().

VallResidue::String protocols::frag_picker::VallResidue::format_string ( )
staticprivate

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

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

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

References protocols::frag_picker::TR().

Referenced by fill_from_string().

VallResidue::String protocols::frag_picker::VallResidue::format_string_cs ( )
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.

References protocols::frag_picker::TR().

Referenced by fill_from_string_cs().

VallResidue::String protocols::frag_picker::VallResidue::format_string_residue_depth_version1 ( )
staticprivate
VallResidue::String protocols::frag_picker::VallResidue::format_string_version1 ( )
staticprivate

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

return a formatting string for fill_from_string_version1() dependent upon actual type of core::Real and core::core::Size

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

References protocols::frag_picker::TR().

Referenced by fill_from_string_version1().

bool protocols::frag_picker::VallResidue::has_chemical_shifts ( ) const
inline

References sec_shift_data_.

bool protocols::frag_picker::VallResidue::has_profile ( ) const
inline

has profile info?

References profile_.

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

has structure profile info?

References profile_struct_.

String const& protocols::frag_picker::VallResidue::id ( ) const
inline

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

References id_.

Referenced by fill_from_string(), fill_from_string_cs(), fill_from_string_residue_depth_version1(), and fill_from_string_version1().

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

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

References id_.

void protocols::frag_picker::VallResidue::key ( core::Size  key)
inline

sets the key id

References key(), and key_.

Referenced by key().

core::Size protocols::frag_picker::VallResidue::key ( )
inline

sets the key id

References key_.

core::Size protocols::frag_picker::VallResidue::nali ( ) const
inline

number of alignments

References nali_.

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

number of alignments

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

core::Real protocols::frag_picker::VallResidue::omega ( ) const
inline

omega backbone torsion in degrees

References omega_.

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

omega backbone torsion in degrees

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

VallResidue & protocols::frag_picker::VallResidue::operator= ( VallResidue const &  rval)
utility::vector1< core::chemical::AA > protocols::frag_picker::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().

core::Real protocols::frag_picker::VallResidue::phi ( ) const
inline

phi backbone torsion in degrees

References phi_.

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

phi backbone torsion in degrees

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

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

per amino acid profile data

References profile_.

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

per amino acid profile data

References profile_.

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

per amino acid structure profile data

References profile_struct_.

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

per amino acid structure profile data

References profile_struct_.

core::Real protocols::frag_picker::VallResidue::psi ( ) const
inline

psi backbone torsion in degrees

References psi_.

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

psi backbone torsion in degrees

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

core::Size protocols::frag_picker::VallResidue::resi ( ) const
inline

residue sequence number in source

References resi_.

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

residue sequence number in source

References resi_.

core::Real protocols::frag_picker::VallResidue::sa ( ) const
inline

solvent accessible area

References sa_.

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

solvent accessible area

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

core::Real protocols::frag_picker::VallResidue::sa_norm ( ) const
inline

solvent accessible area normalized

References sa_norm_.

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

secondary chemical shifts

References sec_shift_data_.

void protocols::frag_picker::VallResidue::set_ss_from_str ( )
inline

References ss_, and ss_str_.

Referenced by fill_from_string_version1().

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

one letter secondary structure code

References ss_.

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

one letter secondary structure code

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

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

one letter secondary structure STR code

References ss_str_.

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

one letter secondary structure STR code

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

core::Real protocols::frag_picker::VallResidue::x ( ) const
inline

x-coordinate of C-alpha

References x_.

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

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

x-coordinate of C-alpha

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

core::Real protocols::frag_picker::VallResidue::y ( ) const
inline

y-coordinate of C-alpha

References y_.

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

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

y-coordinate of C-alpha

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

core::Real protocols::frag_picker::VallResidue::z ( ) const
inline

z-coordinate of C-alpha

References z_.

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

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

z-coordinate of C-alpha

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

Member Data Documentation

char protocols::frag_picker::VallResidue::aa_
private
core::Real protocols::frag_picker::VallResidue::all_atom_residue_depth_
private
core::Real protocols::frag_picker::VallResidue::bF_
private

b factor average for backbone

Referenced by bF(), fill_from_string_cs(), fill_from_string_version1(), and operator=().

core::Real protocols::frag_picker::VallResidue::cbx_
private

x-coordinate of C-beta

Referenced by cbx(), distance_squared_cb(), fill_from_string_version1(), and operator=().

core::Real protocols::frag_picker::VallResidue::cby_
private

y-coordinate of C-beta

Referenced by cby(), distance_squared_cb(), fill_from_string_version1(), and operator=().

core::Real protocols::frag_picker::VallResidue::cbz_
private

z-coordinate of C-beta

Referenced by cbz(), distance_squared_cb(), fill_from_string_version1(), and operator=().

core::Real protocols::frag_picker::VallResidue::cenx_
private

x-coordinate of centroid

Referenced by cenx(), distance_squared_cen(), fill_from_string_version1(), and operator=().

core::Real protocols::frag_picker::VallResidue::ceny_
private

y-coordinate of centroid

Referenced by ceny(), distance_squared_cen(), fill_from_string_version1(), and operator=().

core::Real protocols::frag_picker::VallResidue::cenz_
private

z-coordinate of centroid

Referenced by cenz(), distance_squared_cen(), fill_from_string_version1(), and operator=().

core::Real protocols::frag_picker::VallResidue::dssp_phi_
private

phi backbone torsion in degrees from DSSP program

Referenced by dssp_phi(), fill_from_string_version1(), and operator=().

core::Real protocols::frag_picker::VallResidue::dssp_psi_
private

psi backbone torsion in degrees from DSSP program

Referenced by dssp_psi(), fill_from_string_version1(), and operator=().

String protocols::frag_picker::VallResidue::id_
private
core::Size protocols::frag_picker::VallResidue::key_
private

integer key for a residue is simply the line number in a vall file

Referenced by key().

core::Size protocols::frag_picker::VallResidue::nali_
private

number of alignments used for profile

Referenced by fill_from_string_version1(), nali(), and operator=().

core::Real protocols::frag_picker::VallResidue::omega_
private
utility::vector1< core::chemical::AA > protocols::frag_picker::VallResidue::order_ = order_vector()
staticprivate

order of amino acid profile data in Vall

Referenced by fill_from_string(), fill_from_string_cs(), and fill_from_string_version1().

core::Real protocols::frag_picker::VallResidue::phi_
private
utility::vector1<core::Real> protocols::frag_picker::VallResidue::profile_
private
utility::vector1<core::Real> protocols::frag_picker::VallResidue::profile_struct_
private

per amino acid structure profile data

Referenced by fill_from_string_version1(), has_profile_struct(), operator=(), and profile_struct().

core::Real protocols::frag_picker::VallResidue::psi_
private
core::Size protocols::frag_picker::VallResidue::resi_
private
core::Real protocols::frag_picker::VallResidue::sa_
private

solvent accessible area

Referenced by fill_from_string_version1(), operator=(), and sa().

core::Real protocols::frag_picker::VallResidue::sa_norm_
private

normalized solvent accessible area

Referenced by fill_from_string_version1(), operator=(), and sa_norm().

utility::vector1<core::Real> protocols::frag_picker::VallResidue::sec_shift_data_
private
char protocols::frag_picker::VallResidue::ss_
private

one letter secondary structure code (3 letter alphabet)

Referenced by bbtorsion_srfd(), fill_from_string(), fill_from_string_cs(), fill_from_string_residue_depth_version1(), operator=(), set_ss_from_str(), and ss().

char protocols::frag_picker::VallResidue::ss_str_
private

one letter secondary structure code (STR alphabet - Karplus et. al.)

Referenced by fill_from_string(), fill_from_string_cs(), fill_from_string_residue_depth_version1(), fill_from_string_version1(), operator=(), set_ss_from_str(), and ss_str().

core::Real protocols::frag_picker::VallResidue::x_
private
core::Real protocols::frag_picker::VallResidue::y_
private
core::Real protocols::frag_picker::VallResidue::z_
private

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