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

#include <VallResidue.hh>

Inheritance diagram for protocols::frag_picker::VallResidue:

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...

VallResidue &	operator= (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::Real >	profile_
	per amino acid profile data More...

utility::vector1< core::Real >	profile_struct_
	per amino acid structure profile data More...

utility::vector1< core::Real >	sec_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

◆ BBTorsionSRFD

typedef core::fragment::BBTorsionSRFD protocols::frag_picker::VallResidue::BBTorsionSRFD

◆ BBTorsionSRFDOP

typedef core::fragment::BBTorsionSRFDOP protocols::frag_picker::VallResidue::BBTorsionSRFDOP

◆ String

typedef std::string protocols::frag_picker::VallResidue::String

Constructor & Destructor Documentation

◆ VallResidue() [1/3]

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

default constructor

◆ VallResidue() [2/3]

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

string constructor

References fill_from_string(), fill_from_string_cs(), fill_from_string_residue_depth_version1(), and fill_from_string_version1().

◆ VallResidue() [3/3]

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

copy constructor

◆ ~VallResidue()

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

overridedefault

default destructor

Member Function Documentation

◆ aa() [1/2]

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

inline

one letter amino acid code

References aa_.

◆ aa() [2/2]

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

inline

one letter amino acid code

References aa_.

◆ bbtorsion_srfd()

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_.

◆ bF() [1/2]

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

inline

b factor average for backbone

References bF_.

◆ bF() [2/2]

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

inline

b factor average for backbone

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

◆ cbx() [1/2]

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

inline

x-coordinate of C-beta

References cbx_.

◆ cbx() [2/2]

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

inline

x-coordinate of C-beta

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

◆ cby() [1/2]

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

inline

y-coordinate of C-beta

References cby_.

◆ cby() [2/2]

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

inline

y-coordinate of C-beta

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

◆ cbz() [1/2]

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

inline

z-coordinate of C-beta

References cbz_.

◆ cbz() [2/2]

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

inline

z-coordinate of C-beta

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

◆ cenx() [1/2]

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

inline

x-coordinate of centroid

References cenx_.

◆ cenx() [2/2]

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

inline

x-coordinate of centroid

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

◆ ceny() [1/2]

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

inline

y-coordinate of centroid

References ceny_.

◆ ceny() [2/2]

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

inline

y-coordinate of centroid

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

◆ cenz() [1/2]

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

inline

z-coordinate of centroid

References cenz_.

◆ cenz() [2/2]

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

inline

z-coordinate of centroid

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

◆ depth() [1/2]

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

inline

all-atom residue depth

References all_atom_residue_depth_.

Referenced by depth().

◆ depth() [2/2]

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

inline

all-atom residue depth

References all_atom_residue_depth_, and depth().

◆ distance_squared() [1/2]

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().

◆ distance_squared() [2/2]

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

References protocols::frag_picker::CA, protocols::frag_picker::CB, protocols::frag_picker::CEN, distance_squared(), distance_squared_cb(), and distance_squared_cen().

◆ distance_squared_cb()

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().

◆ distance_squared_cen()

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

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

Referenced by distance_squared().

◆ dssp_phi()

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

inline

phi backbone torsion in degrees from DSSP

References dssp_phi_.

◆ dssp_psi()

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

inline

psi backbone torsion in degrees from DSSP

References dssp_psi_.

◆ fill_from_string()

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().

◆ fill_from_string_cs()

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().

◆ fill_from_string_residue_depth_version1()

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

References aa_, all_atom_residue_depth_, format_string_residue_depth_version1(), id(), id_, resi_, ss_, ss_str_, x_, y_, and z_.

Referenced by VallResidue().

◆ fill_from_string_version1()

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().

◆ format_string()

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().

◆ format_string_cs()

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().

◆ format_string_residue_depth_version1()

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

staticprivate

References protocols::frag_picker::TR().

Referenced by fill_from_string_residue_depth_version1().

◆ format_string_version1()

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().

◆ has_chemical_shifts()

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

inline

References sec_shift_data_.

◆ has_profile()

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

inline

has profile info?

References profile_.

◆ has_profile_struct()

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

inline

has structure profile info?

References profile_struct_.

◆ id() [1/2]

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().

◆ id() [2/2]

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

inline

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

References id_.

◆ key() [1/2]

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

inline

sets the key id

References key_.

◆ key() [2/2]

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

inline

sets the key id

References key(), and key_.

Referenced by key().

◆ nali() [1/2]

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

inline

number of alignments

References nali_.

◆ nali() [2/2]

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

inline

number of alignments

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

◆ omega() [1/2]

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

inline

omega backbone torsion in degrees

References omega_.

◆ omega() [2/2]

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

inline

omega backbone torsion in degrees

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

◆ operator=()

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

copy assignment

References aa_, bF_, cbx_, cby_, cbz_, cenx_, ceny_, cenz_, dssp_phi_, dssp_psi_, id_, nali_, omega_, phi_, profile_, profile_struct_, psi_, resi_, sa_, sa_norm_, sec_shift_data_, ss_, ss_str_, x_, y_, and z_.

◆ order_vector()

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().

◆ phi() [1/2]

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

inline

phi backbone torsion in degrees

References phi_.

◆ phi() [2/2]

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

inline

phi backbone torsion in degrees

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

◆ profile() [1/2]

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

inline

per amino acid profile data

References profile_.

◆ profile() [2/2]

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

inline

per amino acid profile data

References profile_.

◆ profile_struct() [1/2]

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

inline

per amino acid structure profile data

References profile_struct_.

◆ profile_struct() [2/2]

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

inline

per amino acid structure profile data

References profile_struct_.

◆ psi() [1/2]

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

inline

psi backbone torsion in degrees

References psi_.

◆ psi() [2/2]

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

inline

psi backbone torsion in degrees

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

◆ resi() [1/2]

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

inline

residue sequence number in source

References resi_.

◆ resi() [2/2]

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

inline

residue sequence number in source

References resi_.

◆ sa() [1/2]

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

inline

solvent accessible area

References sa_.

◆ sa() [2/2]

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

inline

solvent accessible area

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

◆ sa_norm()

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

inline

solvent accessible area normalized

References sa_norm_.

◆ secondary_shifts()

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

inline

secondary chemical shifts

References sec_shift_data_.

◆ set_ss_from_str()

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

inline

References ss_, and ss_str_.

Referenced by fill_from_string_version1().

◆ ss() [1/2]

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

inline

one letter secondary structure code

References ss_.

◆ ss() [2/2]

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

inline

one letter secondary structure code

References ss_.

◆ ss_str() [1/2]

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

inline

one letter secondary structure STR code

References ss_str_.

◆ ss_str() [2/2]

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

inline

one letter secondary structure STR code

References ss_str_.

◆ x() [1/2]

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().

◆ x() [2/2]

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

inline

x-coordinate of C-alpha

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

◆ y() [1/2]

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().

◆ y() [2/2]

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

inline

y-coordinate of C-alpha

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

◆ z() [1/2]

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().

◆ z() [2/2]

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

◆ aa_

char protocols::frag_picker::VallResidue::aa_

private

one letter amino acid code

Referenced by aa(), bbtorsion_srfd(), distance_squared_cb(), fill_from_string(), fill_from_string_cs(), fill_from_string_residue_depth_version1(), fill_from_string_version1(), and operator=().

◆ all_atom_residue_depth_

core::Real protocols::frag_picker::VallResidue::all_atom_residue_depth_

private

Referenced by depth(), and fill_from_string_residue_depth_version1().

◆ bF_

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=().

◆ cbx_

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=().

◆ cby_

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=().

◆ cbz_

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=().

◆ cenx_

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

private

x-coordinate of centroid

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

◆ ceny_

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

private

y-coordinate of centroid

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

◆ cenz_

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

private

z-coordinate of centroid

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

◆ dssp_phi_

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=().

◆ dssp_psi_

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=().

◆ id_

String protocols::frag_picker::VallResidue::id_

private

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

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

◆ key_

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().

◆ nali_

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

private

number of alignments used for profile

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

◆ omega_

core::Real protocols::frag_picker::VallResidue::omega_

private

omega backbone torsion in degrees

Referenced by bbtorsion_srfd(), fill_from_string(), fill_from_string_cs(), fill_from_string_version1(), omega(), and operator=().

◆ order_

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().

◆ phi_

core::Real protocols::frag_picker::VallResidue::phi_

private

phi backbone torsion in degrees

Referenced by bbtorsion_srfd(), fill_from_string(), fill_from_string_cs(), fill_from_string_version1(), operator=(), and phi().

◆ profile_

utility::vector1<core::Real> protocols::frag_picker::VallResidue::profile_

private

per amino acid profile data

Referenced by fill_from_string(), fill_from_string_cs(), fill_from_string_version1(), has_profile(), operator=(), and profile().

◆ profile_struct_

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().

◆ psi_

core::Real protocols::frag_picker::VallResidue::psi_

private

psi backbone torsion in degrees

Referenced by bbtorsion_srfd(), fill_from_string(), fill_from_string_cs(), fill_from_string_version1(), operator=(), and psi().

◆ resi_

core::Size protocols::frag_picker::VallResidue::resi_

private

residue sequence number in source

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

◆ sa_

core::Real protocols::frag_picker::VallResidue::sa_

private

solvent accessible area

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

◆ sa_norm_

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

private

normalized solvent accessible area

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

◆ sec_shift_data_

utility::vector1<core::Real> protocols::frag_picker::VallResidue::sec_shift_data_

private

Referenced by fill_from_string_cs(), has_chemical_shifts(), operator=(), and secondary_shifts().

◆ ss_

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().

◆ ss_str_

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().

◆ x_

core::Real protocols::frag_picker::VallResidue::x_

private

x-coordinate of C-alpha

Referenced by bbtorsion_srfd(), distance_squared(), distance_squared_cb(), fill_from_string(), fill_from_string_cs(), fill_from_string_residue_depth_version1(), fill_from_string_version1(), operator=(), and x().

◆ y_

core::Real protocols::frag_picker::VallResidue::y_

private

y-coordinate of C-alpha

Referenced by bbtorsion_srfd(), distance_squared(), distance_squared_cb(), fill_from_string(), fill_from_string_cs(), fill_from_string_residue_depth_version1(), fill_from_string_version1(), operator=(), and y().

◆ z_

core::Real protocols::frag_picker::VallResidue::z_

private

z-coordinate of C-alpha

Referenced by bbtorsion_srfd(), distance_squared(), distance_squared_cb(), fill_from_string(), fill_from_string_cs(), fill_from_string_residue_depth_version1(), fill_from_string_version1(), operator=(), and z().

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

src/protocols/frag_picker/VallResidue.hh
src/protocols/frag_picker/VallResidue.cc

Public Types

Public Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ BBTorsionSRFD

◆ BBTorsionSRFDOP

◆ String

Constructor & Destructor Documentation

◆ VallResidue() [1/3]

◆ VallResidue() [2/3]

◆ VallResidue() [3/3]

◆ ~VallResidue()

Member Function Documentation

◆ aa() [1/2]

◆ aa() [2/2]

◆ bbtorsion_srfd()

◆ bF() [1/2]

◆ bF() [2/2]

◆ cbx() [1/2]

◆ cbx() [2/2]

◆ cby() [1/2]

◆ cby() [2/2]

◆ cbz() [1/2]

◆ cbz() [2/2]

◆ cenx() [1/2]

◆ cenx() [2/2]

◆ ceny() [1/2]

◆ ceny() [2/2]

◆ cenz() [1/2]

◆ cenz() [2/2]

◆ depth() [1/2]

◆ depth() [2/2]

◆ distance_squared() [1/2]

◆ distance_squared() [2/2]

◆ distance_squared_cb()

◆ distance_squared_cen()

◆ dssp_phi()

◆ dssp_psi()

◆ fill_from_string()

◆ fill_from_string_cs()

◆ fill_from_string_residue_depth_version1()

◆ fill_from_string_version1()

◆ format_string()

◆ format_string_cs()

◆ format_string_residue_depth_version1()

◆ format_string_version1()

◆ has_chemical_shifts()

◆ has_profile()

◆ has_profile_struct()

◆ id() [1/2]

◆ id() [2/2]

◆ key() [1/2]

◆ key() [2/2]

◆ nali() [1/2]

◆ nali() [2/2]

◆ omega() [1/2]

◆ omega() [2/2]

◆ operator=()

◆ order_vector()

◆ phi() [1/2]

◆ phi() [2/2]

◆ profile() [1/2]

◆ profile() [2/2]

◆ profile_struct() [1/2]

◆ profile_struct() [2/2]

◆ psi() [1/2]

◆ psi() [2/2]

◆ resi() [1/2]

◆ resi() [2/2]

◆ sa() [1/2]

◆ sa() [2/2]

◆ sa_norm()

◆ secondary_shifts()

◆ set_ss_from_str()

◆ ss() [1/2]

◆ ss() [2/2]

◆ ss_str() [1/2]