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core::fragment::BBTorsionSRFD Class Reference

#include <BBTorsionSRFD.hh>

Inheritance diagram for core::fragment::BBTorsionSRFD:
Inheritance graph
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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< Realtorsions_
 
utility::vector1< Realcoords_
 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

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
bool core::fragment::BBTorsionSRFD::apply ( pose::Pose pose,
Size  seq_pos 
) const
overridevirtual
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]movemapThis MoveMap will be ignored at the BBTorsionSRFD level, but will be passed to any superclass apply().
[in,out]poseThe pose to modify.
[in]seqposSequence 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
SingleResidueFragDataOP core::fragment::BBTorsionSRFD::create ( ) const
inlineoverridevirtual
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
void core::fragment::BBTorsionSRFD::read_data ( std::istream &  )
overridevirtual
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
bool core::fragment::BBTorsionSRFD::steal ( pose::Pose const &  pose,
Size  seq_pos 
)
overridevirtual
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
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

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