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

#include <VallResidue.hh>

Inheritance diagram for protocols::frag_picker::VallResidue:

Collaboration diagram for protocols::frag_picker::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...

virtual	~VallResidue ()
	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 (Size key)
	sets the key id More...

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...

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	cbx () const
	x-coordinate of C-beta More...

Real	cby () const
	y-coordinate of C-beta More...

Real	cbz () const
	z-coordinate of C-beta More...

Real	cenx () const
	x-coordinate of centroid More...

Real	ceny () const
	y-coordinate of centroid More...

Real	cenz () const
	z-coordinate of centroid More...

Real	sa () const
	solvent accessible area More...

Real	sa_norm () const
	solvent accessible area normalized More...

Real	dssp_phi () const
	phi backbone torsion in degrees from DSSP More...

Real	dssp_psi () const
	psi backbone torsion in degrees from DSSP More...

Real	depth () const
	all-atom residue depth More...

Size	nali () const
	number of alignments 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...

Real	bF () const
	b factor average for backbone More...

utility::vector1< Real > const &	profile () const
	per amino acid profile data More...

utility::vector1< Real > const &	profile_struct () const
	per amino acid structure profile data More...

utility::vector1< Real > const &	secondary_shifts ()
	secondary chemical shifts More...

void	profile (utility::vector1< Real > const &v)
	per amino acid profile data More...

void	profile_struct (utility::vector1< Real > const &v)
	per amino acid structure 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	ss_str (char const c)
	one letter secondary structure STR code More...

void	set_ss_from_str ()

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	cbx (Real const val)
	x-coordinate of C-beta More...

void	cby (Real const val)
	y-coordinate of C-beta More...

void	cbz (Real const val)
	z-coordinate of C-beta More...

void	cenx (Real const val)
	x-coordinate of centroid More...

void	ceny (Real const val)
	y-coordinate of centroid More...

void	cenz (Real const val)
	z-coordinate of centroid More...

void	sa (Real const val)
	solvent accessible area More...

void	nali (Size const val)
	number of alignments More...

void	depth (Real const depth)
	all-atom residue depth 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	bF (Real const val)
	b factor average for backbone 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...

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)

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)

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
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...

Size	resi_
	residue sequence number in source More...

Real	bF_
	b factor average for backbone 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	cbx_
	x-coordinate of C-beta More...

Real	cby_
	y-coordinate of C-beta More...

Real	cbz_
	z-coordinate of C-beta More...

Real	cenx_
	x-coordinate of centroid More...

Real	ceny_
	y-coordinate of centroid More...

Real	cenz_
	z-coordinate of centroid 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...

Real	sa_
	solvent accessible area More...

Real	sa_norm_
	normalized solvent accessible area More...

Real	dssp_phi_
	phi backbone torsion in degrees from DSSP program More...

Real	dssp_psi_
	psi backbone torsion in degrees from DSSP program More...

Size	nali_
	number of alignments used for profile More...

utility::vector1< Real >	profile_
	per amino acid profile data More...

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

utility::vector1< Real >	sec_shift_data_

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...

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

Definition at line 48 of file VallResidue.hh.

Member Typedef Documentation

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

Definition at line 57 of file VallResidue.hh.

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

Definition at line 58 of file VallResidue.hh.

typedef core::Real protocols::frag_picker::VallResidue::Real

Definition at line 54 of file VallResidue.hh.

typedef core::Size protocols::frag_picker::VallResidue::Size

Definition at line 53 of file VallResidue.hh.

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

Definition at line 55 of file VallResidue.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 45 of file VallResidue.cc.

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

string constructor

Definition at line 51 of file VallResidue.cc.

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

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

copy constructor

Definition at line 63 of file VallResidue.cc.

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

virtual

default destructor

Definition at line 98 of file VallResidue.cc.

Member Function Documentation

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

inline

one letter amino acid code

Definition at line 97 of file VallResidue.hh.

References aa_.

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

inline

one letter amino acid code

Definition at line 261 of file VallResidue.hh.

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

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

build a BBTorsionSRFD from this page

Definition at line 137 of file VallResidue.cc.

References aa_, omega_, phi_, psi_, core::fragment::BBTorsionSRFD::set_coordinates(), core::fragment::SecstructSRFD::set_secstruct(), core::fragment::SingleResidueFragData::set_sequence(), core::fragment::BBTorsionSRFD::set_torsion(), ss_, x_, y_, and z_.

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

inline

b factor average for backbone

Definition at line 209 of file VallResidue.hh.

References bF_.

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

inline

b factor average for backbone

Definition at line 415 of file VallResidue.hh.

References bF_.

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

inline

x-coordinate of C-beta

Definition at line 134 of file VallResidue.hh.

References cbx_.

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

inline

x-coordinate of C-beta

Definition at line 342 of file VallResidue.hh.

References cbx_.

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

inline

y-coordinate of C-beta

Definition at line 139 of file VallResidue.hh.

References cby_.

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

inline

y-coordinate of C-beta

Definition at line 348 of file VallResidue.hh.

References cby_.

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

inline

z-coordinate of C-beta

Definition at line 144 of file VallResidue.hh.

References cbz_.

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

inline

z-coordinate of C-beta

Definition at line 354 of file VallResidue.hh.

References cbz_.

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

inline

x-coordinate of centroid

Definition at line 149 of file VallResidue.hh.

References cenx_.

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

inline

x-coordinate of centroid

Definition at line 360 of file VallResidue.hh.

References cenx_.

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

inline

y-coordinate of centroid

Definition at line 154 of file VallResidue.hh.

References ceny_.

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

inline

y-coordinate of centroid

Definition at line 366 of file VallResidue.hh.

References ceny_.

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

inline

z-coordinate of centroid

Definition at line 159 of file VallResidue.hh.

References cenz_.

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

inline

z-coordinate of centroid

Definition at line 372 of file VallResidue.hh.

References cenz_.

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

inline

all-atom residue depth

Definition at line 184 of file VallResidue.hh.

References all_atom_residue_depth_.

Referenced by depth().

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

inline

all-atom residue depth

Definition at line 391 of file VallResidue.hh.

References all_atom_residue_depth_, and depth().

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

Definition at line 440 of file VallResidue.cc.

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
	)

Definition at line 478 of file VallResidue.cc.

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

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

Definition at line 447 of file VallResidue.cc.

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)

Definition at line 471 of file VallResidue.cc.

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

Referenced by distance_squared().

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

inline

phi backbone torsion in degrees from DSSP

Definition at line 174 of file VallResidue.hh.

References dssp_phi_.

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

inline

psi backbone torsion in degrees from DSSP

Definition at line 179 of file VallResidue.hh.

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

Definition at line 156 of file VallResidue.cc.

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)

Definition at line 181 of file VallResidue.cc.

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)

Definition at line 247 of file VallResidue.cc.

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

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

Definition at line 213 of file VallResidue.cc.

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

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

Definition at line 293 of file VallResidue.cc.

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.

Definition at line 329 of file VallResidue.cc.

References protocols::frag_picker::TR().

Referenced by fill_from_string_cs().

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

staticprivate

Definition at line 417 of file VallResidue.cc.

References protocols::frag_picker::TR().

Referenced by fill_from_string_residue_depth_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::Size

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

Definition at line 371 of file VallResidue.cc.

References protocols::frag_picker::TR().

Referenced by fill_from_string_version1().

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

inline

Definition at line 449 of file VallResidue.hh.

References sec_shift_data_.

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

inline

has profile info?

Definition at line 438 of file VallResidue.hh.

References profile_.

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

inline

has structure profile info?

Definition at line 444 of file VallResidue.hh.

References profile_struct_.

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

inline

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

Definition at line 85 of file VallResidue.hh.

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)

Definition at line 255 of file VallResidue.hh.

References id_.

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

inline

sets the key id

Definition at line 90 of file VallResidue.hh.

References key(), and key_.

Referenced by key().

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

inline

sets the key id

Definition at line 93 of file VallResidue.hh.

References key_.

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

inline

number of alignments

Definition at line 189 of file VallResidue.hh.

References nali_.

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

inline

number of alignments

Definition at line 385 of file VallResidue.hh.

References nali_.

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

inline

omega backbone torsion in degrees

Definition at line 204 of file VallResidue.hh.

References omega_.

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

inline

omega backbone torsion in degrees

Definition at line 409 of file VallResidue.hh.

References omega_.

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

copy assignment

Definition at line 102 of file VallResidue.cc.

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

utility::vector1< core::chemical::AA > protocols::frag_picker::VallResidue::order_vector ( )

staticprivate

return a vector specifying the order of profile data in Vall

Definition at line 262 of file VallResidue.cc.

References core::chemical::aa_from_oneletter_code(), and protocols::forge::methods::order().

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

inline

phi backbone torsion in degrees

Definition at line 194 of file VallResidue.hh.

References phi_.

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

inline

phi backbone torsion in degrees

Definition at line 397 of file VallResidue.hh.

References phi_.

Size protocols::frag_picker::VallResidue::position_index ( ) const

inline

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

Definition at line 240 of file VallResidue.hh.

References position_index_.

void protocols::frag_picker::VallResidue::position_index ( Size const idx)

inline

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

Definition at line 422 of file VallResidue.hh.

References position_index_.

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

inline

per amino acid profile data

Definition at line 214 of file VallResidue.hh.

References profile_.

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

inline

per amino acid profile data

Definition at line 229 of file VallResidue.hh.

References profile_.

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

inline

per amino acid structure profile data

Definition at line 219 of file VallResidue.hh.

References profile_struct_.

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

inline

per amino acid structure profile data

Definition at line 234 of file VallResidue.hh.

References profile_struct_.

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

inline

psi backbone torsion in degrees

Definition at line 199 of file VallResidue.hh.

References psi_.

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

inline

psi backbone torsion in degrees

Definition at line 403 of file VallResidue.hh.

References psi_.

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

inline

residue sequence number in source

Definition at line 114 of file VallResidue.hh.

References resi_.

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

inline

residue sequence number in source

Definition at line 317 of file VallResidue.hh.

References resi_.

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

inline

solvent accessible area

Definition at line 164 of file VallResidue.hh.

References sa_.

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

inline

solvent accessible area

Definition at line 379 of file VallResidue.hh.

References sa_.

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

inline

solvent accessible area normalized

Definition at line 169 of file VallResidue.hh.

References sa_norm_.

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

inline

secondary chemical shifts

Definition at line 224 of file VallResidue.hh.

References sec_shift_data_.

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 []

Definition at line 246 of file VallResidue.hh.

References section_index_.

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 []

Definition at line 429 of file VallResidue.hh.

References section_index_.

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

inline

Definition at line 278 of file VallResidue.hh.

References ss_, and ss_str_.

Referenced by fill_from_string_version1().

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

inline

one letter secondary structure code

Definition at line 103 of file VallResidue.hh.

References ss_.

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

inline

one letter secondary structure code

Definition at line 267 of file VallResidue.hh.

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

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

inline

one letter secondary structure STR code

Definition at line 109 of file VallResidue.hh.

References ss_str_.

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

inline

one letter secondary structure STR code

Definition at line 273 of file VallResidue.hh.

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

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

inline

x-coordinate of C-alpha

Definition at line 119 of file VallResidue.hh.

References x_.

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

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

inline

x-coordinate of C-alpha

Definition at line 323 of file VallResidue.hh.

References x_.

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

inline

y-coordinate of C-alpha

Definition at line 124 of file VallResidue.hh.

References y_.

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

Definition at line 329 of file VallResidue.hh.

References y_.

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

inline

z-coordinate of C-alpha

Definition at line 129 of file VallResidue.hh.

References z_.

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

Definition at line 335 of file VallResidue.hh.

References z_.

Member Data Documentation

char protocols::frag_picker::VallResidue::aa_

private

one letter amino acid code

Definition at line 510 of file VallResidue.hh.

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=().

Real protocols::frag_picker::VallResidue::all_atom_residue_depth_

private

Definition at line 591 of file VallResidue.hh.

Referenced by depth(), and fill_from_string_residue_depth_version1().

Real protocols::frag_picker::VallResidue::bF_

private

b factor average for backbone

Definition at line 522 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::cbx_

private

x-coordinate of C-beta

Definition at line 534 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::cby_

private

y-coordinate of C-beta

Definition at line 537 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::cbz_

private

z-coordinate of C-beta

Definition at line 540 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::cenx_

private

x-coordinate of centroid

Definition at line 543 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::ceny_

private

y-coordinate of centroid

Definition at line 546 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::cenz_

private

z-coordinate of centroid

Definition at line 549 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::dssp_phi_

private

phi backbone torsion in degrees from DSSP program

Definition at line 567 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::dssp_psi_

private

psi backbone torsion in degrees from DSSP program

Definition at line 570 of file VallResidue.hh.

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

String protocols::frag_picker::VallResidue::id_

private

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

Definition at line 507 of file VallResidue.hh.

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

Size protocols::frag_picker::VallResidue::key_

private

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

Definition at line 504 of file VallResidue.hh.

Referenced by key().

Size protocols::frag_picker::VallResidue::nali_

private

number of alignments used for profile

Definition at line 573 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::omega_

private

omega backbone torsion in degrees

Definition at line 558 of file VallResidue.hh.

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

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

staticprivate

order of amino acid profile data in Vall

Definition at line 597 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::phi_

private

phi backbone torsion in degrees

Definition at line 552 of file VallResidue.hh.

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

Size protocols::frag_picker::VallResidue::position_index_

private

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

Definition at line 585 of file VallResidue.hh.

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

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

private

per amino acid profile data

Definition at line 576 of file VallResidue.hh.

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

utility::vector1<Real> protocols::frag_picker::VallResidue::profile_struct_

private

per amino acid structure profile data

Definition at line 579 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::psi_

private

psi backbone torsion in degrees

Definition at line 555 of file VallResidue.hh.

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

Size protocols::frag_picker::VallResidue::resi_

private

residue sequence number in source

Definition at line 519 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::sa_

private

solvent accessible area

Definition at line 561 of file VallResidue.hh.

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

Real protocols::frag_picker::VallResidue::sa_norm_

private

normalized solvent accessible area

Definition at line 564 of file VallResidue.hh.

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

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

private

Definition at line 581 of file VallResidue.hh.

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

Size protocols::frag_picker::VallResidue::section_index_

private

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

Definition at line 589 of file VallResidue.hh.

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

char protocols::frag_picker::VallResidue::ss_

private

one letter secondary structure code (3 letter alphabet)

Definition at line 513 of file VallResidue.hh.

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.)

Definition at line 516 of file VallResidue.hh.

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().

Real protocols::frag_picker::VallResidue::x_

private

x-coordinate of C-alpha

Definition at line 525 of file VallResidue.hh.

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().

Real protocols::frag_picker::VallResidue::y_

private

y-coordinate of C-alpha

Definition at line 528 of file VallResidue.hh.

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().

Real protocols::frag_picker::VallResidue::z_

private

z-coordinate of C-alpha

Definition at line 531 of file VallResidue.hh.

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

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Constructor & Destructor Documentation

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