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core::fragment::IndependentBBTorsionSRFD Class Reference

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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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...
 
 ~IndependentBBTorsionSRFD () override
 default destructor More...
 
IndependentBBTorsionSRFDoperator= (IndependentBBTorsionSRFD const &rval)
 copy assignment More...
 
SingleResidueFragDataOP clone () const override
 clone this object More...
 
SingleResidueFragDataOP create () const override
 create a new instance of this object More...
 
bool apply (MoveMap const &movemap, Pose &pose, Size const seqpos) const override
 apply only torsions in this fragment marked as moveable in the given MoveMap More...
 
bool is_applicable (MoveMap const &movemap, Size seqpos) const override
 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...
 
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 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...
 
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
 

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 ()
 
- 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 ()
 
- 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).

Member Typedef Documentation

Constructor & Destructor Documentation

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

default constructor

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

constructor

Parameters
[in]n_bbtorsionsNumber of backbone torsions.
[in]secstructThe single character secondary structure type.
[in]sequenceThe single character sequence type.
core::fragment::IndependentBBTorsionSRFD::IndependentBBTorsionSRFD ( IndependentBBTorsionSRFD const &  rval)
default

copy constructor

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

default destructor

Member Function Documentation

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

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

apply only torsions in this fragment marked as moveable in the given MoveMap for D-amino acids

Parameters
[in]movemapCheck for moveable torsions in this MoveMap.
[in,out]poseThe Pose to modify.
[in]seqposInsert at this sequence position.
Returns
True if at least one torsion inserted and second level superclass SecstructSRFD::apply() succeeded, otherwise false.
Parameters
[in]movemapCheck for moveable torsions in this MoveMap.
[in,out]poseThe Pose to modify.
[in]seqposInsert 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.

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

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

clone this object

Reimplemented from core::fragment::BBTorsionSRFD.

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

create a new instance of this object

Reimplemented from core::fragment::BBTorsionSRFD.

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

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

Parameters
[in]movemapCheck for moveable torsions in this MoveMap.
[in]seqposCheck at this sequence position.
Returns
True if at least one torsion moveable and second level superclass SecstructSRFD::is_applicable(), otherwise False.
Parameters
[in]movemapCheck for moveable torsions in this MoveMap.
[in]seqposCheck 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.

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


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