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core::fragment::BBTorsionAndAnglesSRFD Class Reference

#include <BBTorsionAndAnglesSRFD.hh>

Inheritance diagram for core::fragment::BBTorsionAndAnglesSRFD:
Inheritance graph
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Public Member Functions

 BBTorsionAndAnglesSRFD ()
 default constructor More...
 
 BBTorsionAndAnglesSRFD (utility::vector1< AngleInfo > &angles_in, Size const nbb_in=3, char secstruct= 'X', char sequence= 'X')
 
SingleResidueFragDataOP clone () const override
 
SingleResidueFragDataOP create () const override
 create a new instance of this object More...
 
bool apply (pose::Pose &, Size seq_pos) const override
 insert fragment_data into pose at position seq_pos More...
 
bool apply (kinematics::MoveMap const &movemap, pose::Pose &pose, Size const seqpos) const override
 insert backbone torsions and angles into pose at position seqpos if all bb torsions are moveable in MoveMap 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
 
void show (std::ostream &out) const override
 
virtual void read (std::istream &in)
 
std::string type () const override
 
core::Size nangles () const
 
- Public Member Functions inherited from core::fragment::BBTorsionSRFD
 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::BBTorsionSRFD
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 BBTorsionSRFD Parent
 
typedef std::pair< std::vector
< Size >, Real
AngleInfo
 

Private Attributes

utility::vector1< AngleInfoangles_
 

Additional Inherited Members

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

Member Typedef Documentation

typedef std::pair<std::vector<Size>, Real> core::fragment::BBTorsionAndAnglesSRFD::AngleInfo
private

Constructor & Destructor Documentation

core::fragment::BBTorsionAndAnglesSRFD::BBTorsionAndAnglesSRFD ( )
inline

default constructor

core::fragment::BBTorsionAndAnglesSRFD::BBTorsionAndAnglesSRFD ( utility::vector1< AngleInfo > &  angles_in,
Size const  nbb_in = 3,
char  secstruct = 'X',
char  sequence = 'X' 
)
inline

Member Function Documentation

static std::string core::fragment::BBTorsionAndAnglesSRFD::_static_type_name ( )
inlinestatic

Referenced by type().

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

insert backbone torsions and angles into pose at position seqpos if all bb torsions are moveable in MoveMap

Returns
True if all torsions and angles are inserted and superclass apply() is successful, otherwise False.
Remarks
This is currently all or nothing – all torsions for seqpos must be moveable because it's not entirely clear what the behavior of partial angle insertion is. In addition, DOF_IDs are not made explicitly available within this class, meaning there is no way to look them up within the MoveMap; the implementation in this class must be changed if this is desired.

Implements core::fragment::SingleResidueFragData.

References angles_, core::fragment::BBTorsionSRFD::apply(), core::id::BB, core::pose::Pose::conformation(), core::kinematics::MoveMap::get(), core::fragment::BBTorsionSRFD::nbb(), and core::conformation::Conformation::set_bond_angle().

SingleResidueFragDataOP core::fragment::BBTorsionAndAnglesSRFD::clone ( ) const
inlineoverridevirtual
SingleResidueFragDataOP core::fragment::BBTorsionAndAnglesSRFD::create ( ) const
inlineoverridevirtual

create a new instance of this object

Implements core::fragment::SingleResidueFragData.

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

there is no information in the MoveMap as to which angles can be moved, so this function

will return its value solely based on the parent

Implements core::fragment::SingleResidueFragData.

References core::fragment::BBTorsionSRFD::is_applicable().

bool core::fragment::BBTorsionAndAnglesSRFD::is_compatible ( SingleResidueFragData const &  ) const
overridevirtual

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

Implements core::fragment::SingleResidueFragData.

References nangles(), and core::fragment::BBTorsionSRFD::nbb().

core::Size core::fragment::BBTorsionAndAnglesSRFD::nangles ( ) const
inline

References angles_.

Referenced by is_compatible().

void core::fragment::BBTorsionAndAnglesSRFD::read ( std::istream &  in)
virtual
void core::fragment::BBTorsionAndAnglesSRFD::show ( std::ostream &  out) const
overridevirtual
bool core::fragment::BBTorsionAndAnglesSRFD::steal ( pose::Pose const &  pose,
Size  seq_pos 
)
overridevirtual
std::string core::fragment::BBTorsionAndAnglesSRFD::type ( ) const
inlineoverridevirtual

Member Data Documentation

utility::vector1< AngleInfo > core::fragment::BBTorsionAndAnglesSRFD::angles_
private

Referenced by apply(), nangles(), and steal().


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