A version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD). More...

#include <IndependentBBTorsionSRFD.hh>

Inheritance diagram for core::fragment::IndependentBBTorsionSRFD:

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Collaboration diagram for core::fragment::IndependentBBTorsionSRFD:

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Public Types
typedef core::Size	Size

typedef core::kinematics::MoveMap	MoveMap

typedef core::pose::Pose	Pose

Public Member Functions
	IndependentBBTorsionSRFD ()
	default constructor More...

	IndependentBBTorsionSRFD (Size const n_bbtorsions, char const secstruct, char const sequence)
	constructor More...

	IndependentBBTorsionSRFD (IndependentBBTorsionSRFD const &rval)
	copy constructor More...

virtual	~IndependentBBTorsionSRFD ()
	default destructor More...

IndependentBBTorsionSRFD &	operator= (IndependentBBTorsionSRFD 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...

virtual bool	apply (MoveMap const &movemap, Pose &pose, Size const seqpos) const
	apply only torsions in this fragment marked as moveable in the given MoveMap More...

virtual bool	is_applicable (MoveMap const &movemap, Size seqpos) const
	is at least one torsion marked as moveable in the given MoveMap? More...

Public Member Functions inherited from core::fragment::BBTorsionSRFD
	BBTorsionSRFD (Size const nbb_in=3, char secstruct= 'X', char sequence= 'X')
	constructor More...

BBTorsionSRFD &	operator= (BBTorsionSRFD const &rval)
	copy assignment 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	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 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

Private Types
typedef BBTorsionSRFD	Super

typedef SecstructSRFD	Super2

Additional Inherited Members
Static Public Member Functions inherited from core::fragment::BBTorsionSRFD
static std::string	_static_type_name ()

Protected Attributes inherited from core::fragment::SingleResidueFragData
char	sequence_

Detailed Description

A version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD).

Definition at line 43 of file IndependentBBTorsionSRFD.hh.

Member Typedef Documentation

typedef core::kinematics::MoveMap core::fragment::IndependentBBTorsionSRFD::MoveMap

Definition at line 57 of file IndependentBBTorsionSRFD.hh.

typedef core::pose::Pose core::fragment::IndependentBBTorsionSRFD::Pose

Definition at line 58 of file IndependentBBTorsionSRFD.hh.

typedef core::Size core::fragment::IndependentBBTorsionSRFD::Size

Definition at line 56 of file IndependentBBTorsionSRFD.hh.

typedef BBTorsionSRFD core::fragment::IndependentBBTorsionSRFD::Super

private

Definition at line 49 of file IndependentBBTorsionSRFD.hh.

typedef SecstructSRFD core::fragment::IndependentBBTorsionSRFD::Super2

private

Definition at line 50 of file IndependentBBTorsionSRFD.hh.

Constructor & Destructor Documentation

core::fragment::IndependentBBTorsionSRFD::IndependentBBTorsionSRFD ( )

default constructor

Definition at line 37 of file IndependentBBTorsionSRFD.cc.

Referenced by clone(), and create().

core::fragment::IndependentBBTorsionSRFD::IndependentBBTorsionSRFD	(	Size const	n_bbtorsions,
		char const	secstruct,
		char const	sequence
	)

constructor

Parameters

[in]	n_bbtorsions	Number of backbone torsions.
[in]	secstruct	The single character secondary structure type.
[in]	sequence	The single character sequence type.

Definition at line 46 of file IndependentBBTorsionSRFD.cc.

core::fragment::IndependentBBTorsionSRFD::IndependentBBTorsionSRFD ( IndependentBBTorsionSRFD const & rval)

copy constructor

Definition at line 56 of file IndependentBBTorsionSRFD.cc.

core::fragment::IndependentBBTorsionSRFD::~IndependentBBTorsionSRFD ( )

virtual

default destructor

Definition at line 62 of file IndependentBBTorsionSRFD.cc.

Member Function Documentation

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

virtual

apply only torsions in this fragment marked as moveable in the given MoveMap

Parameters

[in]	movemap	Check for moveable torsions in this MoveMap.
[in,out]	pose	The Pose to modify.
[in]	seqpos	Insert at this sequence position.

Returns: True if at least one torsion inserted and second level superclass SecstructSRFD::apply() succeeded, otherwise false.

Parameters

[in]	movemap	Check for moveable torsions in this MoveMap.
[in,out]	pose	The Pose to modify.
[in]	seqpos	Insert at this sequence position.

Returns: True if at least one torsion inserted and second level superclass SecstructSRFD::apply() succeeded, otherwise false.

Skips the initial call to primary superclass BBTorsionSRFD::apply() because it contains all-or-nothing behavior we want to override. Instead will go directly to second level SecstructSRFD::apply(), and afterwards execute the rest of the procedure.

Reimplemented from core::fragment::BBTorsionSRFD.

Definition at line 97 of file IndependentBBTorsionSRFD.cc.

References core::fragment::SecstructSRFD::apply(), core::id::BB, core::kinematics::MoveMap::get(), core::fragment::BBTorsionSRFD::nbb(), core::pose::Pose::set_torsion(), and core::fragment::BBTorsionSRFD::torsion().

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

virtual

clone this object

Reimplemented from core::fragment::BBTorsionSRFD.

Definition at line 75 of file IndependentBBTorsionSRFD.cc.

References IndependentBBTorsionSRFD().

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

virtual

create a new instance of this object

Reimplemented from core::fragment::BBTorsionSRFD.

Definition at line 81 of file IndependentBBTorsionSRFD.cc.

References IndependentBBTorsionSRFD().

bool core::fragment::IndependentBBTorsionSRFD::is_applicable	(	MoveMap const &	movemap,
		Size	seqpos
	)		const

virtual

is at least one torsion marked as moveable in the given MoveMap?

Parameters

[in]	movemap	Check for moveable torsions in this MoveMap.
[in]	seqpos	Check at this sequence position.

Returns: True if at least one torsion moveable and second level superclass SecstructSRFD::is_applicable(), otherwise False.

Parameters

[in]	movemap	Check for moveable torsions in this MoveMap.
[in]	seqpos	Check at this sequence position.

Returns: True if at least one torsion moveable and second level superclass SecstructSRFD::is_applicable(), otherwise False.

Skips the initial call to primary superclass BBTorsionSRFD::is_applicable() because it contains all-or-nothing behavior we want to override. Instead will go directly to second level SecstructSRFD::is_applicable(), and afterwards execute the rest of the procedure.

Reimplemented from core::fragment::BBTorsionSRFD.

Definition at line 133 of file IndependentBBTorsionSRFD.cc.

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

IndependentBBTorsionSRFD & core::fragment::IndependentBBTorsionSRFD::operator= ( IndependentBBTorsionSRFD const & rval)

copy assignment

Definition at line 66 of file IndependentBBTorsionSRFD.cc.

References core::fragment::BBTorsionSRFD::operator=().

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

src/core/fragment/IndependentBBTorsionSRFD.hh
src/core/fragment/IndependentBBTorsionSRFD.cc

Public Types

Public Member Functions

Private Types

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation