core::fragment::BBTorsionSRFD Class Reference

#include <BBTorsionSRFD.hh>

Public Member Functions
	BBTorsionSRFD (Size const nbb_in=3, char secstruct= 'X', char sequence= 'X')
	constructor More...
BBTorsionSRFD &	operator= (BBTorsionSRFD const &rval)
	copy assignment More...
virtual SingleResidueFragDataOP	clone () const
	clone this object More...
virtual SingleResidueFragDataOP	create () const
	create a new instance of this object More...
Size	nbb () const
	number of backbone torsions described by this fragment More...
void	set_torsion (Size const tor, Real const setting)
	set value for specific torsion in this piece of fragment. More...
Real	torsion (Size const torsion_number) const
	get the value for a specific torsion in this fragment More...
bool	has_coordinates () const
	Returns true if this instance contains cartesian coordinates, false otherwise. Coordinates are available if the <write_ca_coords> option is enabled in the new fragment picker and rosetta++ fragments are used. More...
Real	x () const
	Returns the x coordinate of this residue's CA. More...
Real	y () const
	Returns the y coordinate of this residue's CA. More...
Real	z () const
	Returns the z coordinate of this residue's CA. More...
void	set_coordinates (Real x, Real y, Real z)
	Convenience method for setting this residue's CA coordinates all at once. More...
virtual bool	apply (pose::Pose &, Size seq_pos) const
	insert all backbone torsions into pose at position seq_pos More...
virtual bool	apply (kinematics::MoveMap const &movemap, pose::Pose &pose, Size const seqpos) const
	insert all backbone torsions into pose at position seq_pos More...
virtual bool	steal (pose::Pose const &, Size seq_pos)
	insert fragment_data into pose at position seq_pos More...
virtual bool	is_compatible (SingleResidueFragData const &) const
	check weather SRFD applies to same dofs and is of same type More...
virtual bool	is_applicable (kinematics::MoveMap const &, Size seq_pos) const
	check if all backbone torsions at the sequence position moveable in the MoveMap More...
virtual void	show (std::ostream &out) const
virtual void	read_data (std::istream &in)
	Default implementation: noop. More...
virtual std::string	type () const
Public Member Functions inherited from core::fragment::SecstructSRFD
	SecstructSRFD (char secstruct= 'X', char sequence= 'X')
SingleResidueFragDataOP	clone () const
virtual char	secstruct () const
	get secstruct for this position More...
void	set_secstruct (char const ss)
virtual bool	apply_ss (std::string &, Size seq_pos) const
	insert fragment_data sec-struct into ss-string at position seq_pos More...
Public Member Functions inherited from core::fragment::SingleResidueFragData
virtual	~SingleResidueFragData ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
	SingleResidueFragData (char sequence)
	SingleResidueFragData ()
virtual bool	apply (pose::Pose &, Size const intra_frame_pos, Frame const &) const
	insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos ); More...
virtual bool	apply (kinematics::MoveMap const &movemap, pose::Pose &pose, Size const intra_frame_pos, Frame const &frame) const
	insert fragment_data into pose at position given by Frame.seqpos( intra_frame_pos ) for dofs that are allowed to move in the MoveMap More...
virtual bool	apply_ss (std::string &, Size intra_frame_pos, Frame const &) const
	insert fragment_data sec-struct into ss-string at position seq_pos More...
virtual bool	steal (pose::Pose const &, Size intra_frame_pos, Frame const &)
	insert fragment_data into pose at position seq_pos More...
virtual bool	is_applicable (kinematics::MoveMap const &, Size intra_frame_pos, Frame const &) const
	check weather dofs can be moved More...
void	set_sequence (char const sequence)
char	sequence () const

Static Public Member Functions
static std::string	_static_type_name ()
Static Public Member Functions inherited from core::fragment::SecstructSRFD
static std::string	_static_type_name ()
Static Public Member Functions inherited from core::fragment::SingleResidueFragData
static std::string	_static_type_name ()

Private Types
typedef SecstructSRFD	Parent

Private Attributes
utility::vector1< Real >	torsions_
utility::vector1< Real >	coords_
	Cartesian coordinates for CA. More...
bool	has_coords_
	Indicates whether this object contains cartesian coordinates. More...

Additional Inherited Members
Protected Attributes inherited from core::fragment::SingleResidueFragData
char	sequence_

Member Typedef Documentation

typedef SecstructSRFD core::fragment::BBTorsionSRFD::Parent

private

Constructor & Destructor Documentation

core::fragment::BBTorsionSRFD::BBTorsionSRFD ( Size const  nbb_in = 3, char  secstruct = 'X', char  sequence = 'X'  )

inline

constructor

Referenced by clone(), and create().

Member Function Documentation

static std::string core::fragment::BBTorsionSRFD::_static_type_name ( )

inlinestatic

Referenced by core::fragment::FragFactory::FragFactory(), and type().

bool core::fragment::BBTorsionSRFD::apply ( pose::Pose &  pose, Size  seq_pos  ) const

virtual

insert all backbone torsions into pose at position seq_pos

Reimplemented from core::fragment::SecstructSRFD.

Reimplemented in core::fragment::BBTorsionAndAnglesSRFD.

References core::fragment::SecstructSRFD::apply(), core::id::BB, nbb(), core::pose::Pose::set_torsion(), and torsions_.

Referenced by core::fragment::BBTorsionAndAnglesSRFD::apply().

bool core::fragment::BBTorsionSRFD::apply ( kinematics::MoveMap const &  movemap, pose::Pose &  pose, Size const  seqpos  ) const

virtual

insert all backbone torsions into pose at position seq_pos

Parameters

[in]	movemap	This MoveMap will be ignored at the BBTorsionSRFD level, but will be passed to any superclass apply().
[in,out]	pose	The pose to modify.
[in]	seqpos	Sequence position to modify.

Returns

True if apply() successful, False otherwise.

Warning

MoveMap settings at the BBTorsionSRFD level are ignored. For speed, does not check to see whether or not all backbone torsions are moveable in MoveMap – use is_applicable() for this purpose prior to calling apply().

Reimplemented from core::fragment::SecstructSRFD.

Reimplemented in core::fragment::IndependentBBTorsionSRFD, and core::fragment::BBTorsionAndAnglesSRFD.

References core::fragment::SecstructSRFD::apply(), core::id::BB, nbb(), core::pose::Pose::set_torsion(), and torsions_.

virtual SingleResidueFragDataOP core::fragment::BBTorsionSRFD::clone ( ) const

inlinevirtual

clone this object

Implements core::fragment::SingleResidueFragData.

Reimplemented in core::fragment::IndependentBBTorsionSRFD, and core::fragment::BBTorsionAndAnglesSRFD.

References BBTorsionSRFD().

virtual SingleResidueFragDataOP core::fragment::BBTorsionSRFD::create ( ) const

inlinevirtual

create a new instance of this object

Reimplemented from core::fragment::SecstructSRFD.

Reimplemented in core::fragment::IndependentBBTorsionSRFD, and core::fragment::BBTorsionAndAnglesSRFD.

References BBTorsionSRFD().

Referenced by core::fragment::picking_old::vall::VallResidue::bbtorsion_srfd().

bool core::fragment::BBTorsionSRFD::has_coordinates ( ) const

inline

Returns true if this instance contains cartesian coordinates, false otherwise. Coordinates are available if the <write_ca_coords> option is enabled in the new fragment picker and rosetta++ fragments are used.

References has_coords_.

Referenced by show().

bool core::fragment::BBTorsionSRFD::is_applicable ( kinematics::MoveMap const &  move_map, Size  seqpos  ) const

virtual

check if all backbone torsions at the sequence position moveable in the MoveMap

Returns

True if all backbone torsions moveable and is_applicable() succeeded for superclass, otherwise False.

Reimplemented from core::fragment::SecstructSRFD.

Reimplemented in core::fragment::IndependentBBTorsionSRFD, and core::fragment::BBTorsionAndAnglesSRFD.

References core::id::BB, core::kinematics::MoveMap::get(), core::fragment::SecstructSRFD::is_applicable(), nbb(), and core::fragment::tr.

Referenced by core::fragment::BBTorsionAndAnglesSRFD::is_applicable().

bool core::fragment::BBTorsionSRFD::is_compatible ( SingleResidueFragData const &  ) const

virtual

check weather SRFD applies to same dofs and is of same type

Reimplemented from core::fragment::SecstructSRFD.

Reimplemented in core::fragment::BBTorsionAndAnglesSRFD.

References nbb().

Size core::fragment::BBTorsionSRFD::nbb ( ) const

inline

number of backbone torsions described by this fragment

References torsions_.

Referenced by core::fragment::BBTorsionAndAnglesSRFD::apply(), core::fragment::IndependentBBTorsionSRFD::apply(), apply(), core::fragment::IndependentBBTorsionSRFD::is_applicable(), is_applicable(), core::fragment::BBTorsionAndAnglesSRFD::is_compatible(), is_compatible(), read_data(), show(), and steal().

BBTorsionSRFD & core::fragment::BBTorsionSRFD::operator=

(

BBTorsionSRFD const &

rval

)

copy assignment

References coords_, has_coords_, and torsions_.

Referenced by core::fragment::IndependentBBTorsionSRFD::operator=().

void core::fragment::BBTorsionSRFD::read_data ( std::istream &  )

virtual

Default implementation: noop.

Reimplemented from core::fragment::SecstructSRFD.

References nbb(), core::fragment::SecstructSRFD::read_data(), core::scoring::hbonds::t, and torsions_.

Referenced by core::fragment::BBTorsionAndAnglesSRFD::read().

void core::fragment::BBTorsionSRFD::set_coordinates ( Real  x, Real  y, Real  z  )

inline

Convenience method for setting this residue's CA coordinates all at once.

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

void core::fragment::BBTorsionSRFD::set_torsion ( Size const  tor, Real const  setting  )

inline

set value for specific torsion in this piece of fragment.

References torsions_.

void core::fragment::BBTorsionSRFD::show ( std::ostream &  out ) const

virtual

Reimplemented from core::fragment::SecstructSRFD.

Reimplemented in core::fragment::BBTorsionAndAnglesSRFD.

References core::chemical::element::F, has_coordinates(), nbb(), runtime_assert, core::fragment::SecstructSRFD::show(), torsions_, x(), y(), and z().

Referenced by core::fragment::BBTorsionAndAnglesSRFD::show().

bool core::fragment::BBTorsionSRFD::steal ( pose::Pose const &  pose, Size  seq_pos  )

virtual

insert fragment_data into pose at position seq_pos

Reimplemented from core::fragment::SecstructSRFD.

Reimplemented in core::fragment::BBTorsionAndAnglesSRFD.

References core::id::BB, nbb(), runtime_assert, core::fragment::SecstructSRFD::steal(), core::pose::Pose::torsion(), and torsions_.

Referenced by core::fragment::BBTorsionAndAnglesSRFD::steal().

Real core::fragment::BBTorsionSRFD::torsion ( Size const  torsion_number ) const

inline

get the value for a specific torsion in this fragment

References torsions_.

Referenced by core::fragment::IndependentBBTorsionSRFD::apply().

virtual std::string core::fragment::BBTorsionSRFD::type ( ) const

inlinevirtual

Reimplemented from core::fragment::SecstructSRFD.

Reimplemented in core::fragment::BBTorsionAndAnglesSRFD.

References _static_type_name().

Real core::fragment::BBTorsionSRFD::x ( ) const

inline

Returns the x coordinate of this residue's CA.

References coords_, has_coords_, and utility_exit_with_message.

Referenced by set_coordinates(), and show().

Real core::fragment::BBTorsionSRFD::y ( ) const

inline

Returns the y coordinate of this residue's CA.

References coords_, has_coords_, and utility_exit_with_message.

Referenced by set_coordinates(), and show().

Real core::fragment::BBTorsionSRFD::z ( ) const

inline

Returns the z coordinate of this residue's CA.

References coords_, has_coords_, and utility_exit_with_message.

Referenced by set_coordinates(), and show().

Member Data Documentation

utility::vector1<Real> core::fragment::BBTorsionSRFD::coords_

private

Cartesian coordinates for CA.

Referenced by operator=(), set_coordinates(), x(), y(), and z().

bool core::fragment::BBTorsionSRFD::has_coords_

private

Indicates whether this object contains cartesian coordinates.

Referenced by has_coordinates(), operator=(), set_coordinates(), x(), y(), and z().

utility::vector1<Real> core::fragment::BBTorsionSRFD::torsions_

private

Referenced by apply(), nbb(), operator=(), read_data(), set_torsion(), show(), steal(), and torsion().

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

• src/core/fragment/BBTorsionSRFD.hh
• src/core/fragment/BBTorsionSRFD.cc