core::fragment::BBTorsionSRFD Class Reference

#include <BBTorsionSRFD.hh>

Inheritance diagram for core::fragment::BBTorsionSRFD:

Public Member Functions
	BBTorsionSRFD (Size const nbb_in=3, char secstruct= 'X', char sequence= 'X')
	constructor More...
SingleResidueFragDataOP	clone () const override
	clone this object More...
SingleResidueFragDataOP	create () const override
	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...
bool	apply (pose::Pose &, Size seq_pos) const override
	insert all backbone torsions into pose at position seq_pos More...
bool	apply (kinematics::MoveMap const &movemap, pose::Pose &pose, Size const seqpos) const override
	insert all backbone torsions into pose at position seq_pos More...
bool	steal (pose::Pose const &, Size seq_pos) override
	insert fragment_data into pose at position seq_pos More...
bool	is_compatible (SingleResidueFragData const &) const override
	check weather SRFD applies to same dofs and is of same type More...
bool	is_applicable (kinematics::MoveMap const &, Size seq_pos) const override
	check if all backbone torsions at the sequence position moveable in the MoveMap More...
void	show (std::ostream &out) const override
void	read_data (std::istream &in) override
	Default implementation: noop. More...
std::string	type () const override
Public Member Functions inherited from core::fragment::SecstructSRFD
	SecstructSRFD (char secstruct= 'X', char sequence= 'X')
SingleResidueFragDataOP	clone () const override
SingleResidueFragDataOP	create () const override
	create a new instance of this object More...
char	secstruct () const override
	get secstruct for this position More...
void	set_secstruct (char const ss)
bool	apply (pose::Pose &, Size seq_pos) const override
	insert fragment_data into pose at position seq_pos More...
bool	apply (kinematics::MoveMap const &, pose::Pose &pose, Size const seqpos) const override
	apply secondary structure fragment data to the pose, movemap has no effect More...
bool	apply_ss (std::string &, Size seq_pos) const override
	insert fragment_data sec-struct into ss-string at position seq_pos More...
bool	steal (pose::Pose const &, Size seq_pos) override
	insert fragment_data into pose at position seq_pos More...
bool	is_compatible (SingleResidueFragData const &) const override
	check weather SRFD applies to same dofs and is of same type More...
bool	is_applicable (kinematics::MoveMap const &, Size seq_pos) const override
	check whether dofs can be moved More...
void	show (std::ostream &out) const override
void	read_data (std::istream &in) override
	Default implementation: noop. More...
std::string	type () const override
Public Member Functions inherited from core::fragment::SingleResidueFragData
	~SingleResidueFragData () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. 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

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

overridevirtual

insert all backbone torsions into pose at position seq_pos

Implements core::fragment::SingleResidueFragData.

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

overridevirtual

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().

Implements core::fragment::SingleResidueFragData.

Reimplemented in core::fragment::IndependentBBTorsionSRFD.

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

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

inlineoverridevirtual

clone this object

Implements core::fragment::SingleResidueFragData.

Reimplemented in core::fragment::IndependentBBTorsionSRFD.

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

inlineoverridevirtual

create a new instance of this object

Implements core::fragment::SingleResidueFragData.

Reimplemented in core::fragment::IndependentBBTorsionSRFD.

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

overridevirtual

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.

Implements core::fragment::SingleResidueFragData.

Reimplemented in core::fragment::IndependentBBTorsionSRFD.

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

overridevirtual

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

Implements core::fragment::SingleResidueFragData.

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(), protocols::loop_grower::FragmentExtension::cluster_fragments(), core::fragment::IndependentBBTorsionSRFD::is_applicable(), is_applicable(), core::fragment::BBTorsionAndAnglesSRFD::is_compatible(), is_compatible(), read_data(), show(), and steal().

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

overridevirtual

Default implementation: noop.

Reimplemented from core::fragment::SingleResidueFragData.

References nbb(), core::fragment::SecstructSRFD::read_data(), protocols::hybridization::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

overridevirtual

Reimplemented from core::fragment::SingleResidueFragData.

References core::chemical::element::F, has_coordinates(), nbb(), 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  )

overridevirtual

insert fragment_data into pose at position seq_pos

Implements core::fragment::SingleResidueFragData.

References core::id::BB, nbb(), 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(), and protocols::loop_grower::FragmentExtension::cluster_fragments().

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

inlineoverridevirtual

Reimplemented from core::fragment::SingleResidueFragData.

References _static_type_name().

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

inline

Returns the x coordinate of this residue's CA.

References coords_, and has_coords_.

Referenced by set_coordinates(), and show().

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

inline

Returns the y coordinate of this residue's CA.

References coords_, and has_coords_.

Referenced by set_coordinates(), and show().

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

inline

Returns the z coordinate of this residue's CA.

References coords_, and has_coords_.

Referenced by set_coordinates(), and show().

Member Data Documentation

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

private

Cartesian coordinates for CA.

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

bool core::fragment::BBTorsionSRFD::has_coords_

private

Indicates whether this object contains cartesian coordinates.

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

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

private

Referenced by apply(), nbb(), 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