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:

Collaboration diagram for protocols::frag_picker::VallResidue:

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
VallResidue &	operator= (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

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

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

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

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

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

---

Constructor & Destructor Documentation

protocols::frag_picker::VallResidue::VallResidue

(

)

default constructor

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().

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

build a BBTorsionSRFD from this page

References core::fragment::BBTorsionSRFD::set_coordinates(), core::fragment::SecstructSRFD::set_secstruct(), core::fragment::SingleResidueFragData::set_sequence(), and core::fragment::BBTorsionSRFD::set_torsion().

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
	)

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

)

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]

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

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::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]

Referenced by fill_from_string_version1().

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:

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