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protocols::forge::build::RelativeConnectRight Class Reference

version of ConnectRight instruction that depends upon results from another BuildInstruction More...

#include <RelativeConnectRight.hh>

Inheritance diagram for protocols::forge::build::RelativeConnectRight:
Inheritance graph
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Public Types

typedef Super::Size Size
 
typedef Super::ResidueTypeSetCAP ResidueTypeSetCAP
 
typedef Super::LengthEvent LengthEvent
 
typedef Super::MoveMap MoveMap
 
typedef Super::Pose Pose
 
typedef Super::Positions Positions
 
typedef Super::String String
 
typedef core::kinematics::Jump Jump
 
- Public Types inherited from protocols::forge::build::ConnectRight
typedef Super::Size Size
 
typedef Super::ResidueTypeSetCAP ResidueTypeSetCAP
 
typedef Super::LengthEvent LengthEvent
 
typedef Super::MoveMap MoveMap
 
typedef Super::Pose Pose
 
typedef Super::Positions Positions
 
typedef Super::String String
 
typedef core::kinematics::RT RT
 
typedef core::id::NamedStubID NamedStubID
 
typedef NamedStubID::AtomList AtomNameList
 
- Public Types inherited from protocols::forge::build::BuildInstruction
typedef core::Size Size
 
typedef core::Real Real
 
typedef
core::chemical::ResidueTypeSet 
ResidueTypeSet
 
typedef
core::chemical::ResidueTypeSetCAP 
ResidueTypeSetCAP
 
typedef
core::chemical::ResidueTypeSetCOP 
ResidueTypeSetCOP
 
typedef
core::conformation::signals::LengthEvent 
LengthEvent
 
typedef core::kinematics::MoveMap MoveMap
 
typedef core::pose::Pose Pose
 
typedef utility::vector1
< BuildInstructionCAP
BuildInstructionCAPs
 
typedef utility::signals::Link Link
 
typedef std::set< core::SizePositions
 
typedef std::string String
 

Public Member Functions

 RelativeConnectRight ()
 default constructor More...
 
 RelativeConnectRight (RelativeSequencePositionOP const &rp, core::Size const right_position, Pose const &pose_right)
 RelativeSequencePosition + position on-right jump constructor. More...
 
 RelativeConnectRight (RelativeConnectRight const &rval)
 copy constructor More...
 
 ~RelativeConnectRight () override
 default destructor More...
 
RelativeConnectRightoperator= (RelativeConnectRight const &rval)
 copy assignment More...
 
BuildInstructionOP clone () const override
 clone this object More...
 
void modify_impl (Pose &pose_left) override
 do the actual work of modifying the Pose More...
 
Positions original_fixed_positions () const override
 return set of any fixed positions necessary with respect to the original interval and original Pose numbering More...
 
- Public Member Functions inherited from protocols::forge::build::ConnectRight
 ConnectRight ()
 default constructor More...
 
 ConnectRight (core::Size const left_position, core::Size const right_position, Pose const &pose_right)
 position to position jump constructor More...
 
 ConnectRight (ConnectRight const &rval)
 copy constructor More...
 
 ~ConnectRight () override
 default destructor More...
 
ConnectRightoperator= (ConnectRight const &rval)
 copy assignment More...
 
Pose const & pose_right ()
 connect this pose to the right of pose_left when modify( pose_left ) is called More...
 
bool use_rt () const
 apply the transform over the jump connection between pose_left and pose_right? default False More...
 
AtomNameList const & left_stub_atoms () const
 Use these atoms to compute the stub on pose_left. Default ["CA", "N", "CA", "C"]. More...
 
AtomNameList const & right_stub_atoms () const
 Use these atoms to compute the stub on pose_right. Default ["CA", "N", "CA", "C"]. More...
 
RT const & rt ()
 the rotation-translation representing an explicit transform from the stub on pose_left to the stub on pose_right, i.e. the representation of the "jump" More...
 
bool original_interval_valid () const override
 is the original interval storing valid information, or is empty or being used for something else? More...
 
Interval interval () const override
 a copy of the working range of residues specifying the modified region More...
 
Positions preexisting_positions () const override
 return a copy of the set of positions within the new region that were pre-existing in the original Pose prior to modify() More...
 
Positions new_positions () const override
 return a copy of the set of positions that are "new" and did not exist in the original Pose. More...
 
Positions defined_positions () const override
 return a copy of the set of positions within the newly modified region that has a defined conformation. E.g. existing or copied residues. More...
 
Positions undefined_positions () const override
 return a copy of the set of positions within the newly modified region that has an undefined conformation. E.g. newly created residues. More...
 
MoveMap movemap () const override
 return a copy of the MoveMap that defines the moveable/fixed positions/dofs for this instruction More...
 
void use_rt (bool const flag)
 apply the transform over the jump connection between pose_left and pose_right? default False More...
 
void extract_rt (Pose const &pose, core::Size const jump_start_residue, core::Size const jump_stop_residue)
 extract appropriately computed transform between two stubs that represent a jump in the given Pose between the two residues and set it as the rt for this ConnectRight More...
 
void left_stub_atoms (AtomNameList const &atoms)
 Use these atoms to compute the stub on pose_left. Default ["CA", "N", "CA", "C"]. More...
 
void right_stub_atoms (AtomNameList const &atoms)
 Use these atoms to compute the stub on pose_right. Default ["CA", "N", "CA", "C"]. More...
 
void rt (RT const &transform)
 the rotation-translation representing an explicit transform from the stub on pose_left to the stub on pose_right, i.e. the representation of the "jump" More...
 
void on_residue_append (LengthEvent const &event) override
 update indexing on residue append More...
 
void on_residue_prepend (LengthEvent const &event) override
 update indexing on residue prepend More...
 
void on_residue_delete (LengthEvent const &event) override
 update indexing on residue delete More...
 
Positions original_kept_positions () const override
 return the set of positions within the original interval that will be kept in this BuildInstruction More...
 
Positions original_deleted_positions () const override
 return set of positions within the original interval that will be deleted in this BuildInstruction More...
 
Positions original_mutable_positions () const override
 return set of any mutable positions necessary with respect to the original interval and original Pose numbering More...
 
bool creates_undefined_backbone () const override
 does this object create undefined backbone in the modified region? More...
 
- Public Member Functions inherited from protocols::forge::build::BuildInstruction
 BuildInstruction ()
 default constructor More...
 
 BuildInstruction (Interval const &i, ResidueTypeSetCAP rts=core::chemical::ChemicalManager::get_instance() ->residue_type_set(core::chemical::FA_STANDARD))
 interval constructor More...
 
 BuildInstruction (BuildInstruction const &rval)
 copy constructor More...
 
 ~BuildInstruction () override
 default destructor More...
 
BuildInstructionoperator= (BuildInstruction const &rval)
 copy assignment More...
 
BuildInstructionState::Enum modify (Pose &pose)
 modify this pose More...
 
BuildInstructionState::Enum state () const
 return the state of this BuildInstruction More...
 
bool ready () const
 Is the BuildInstruction's state at READY? More...
 
bool waiting_on_dependencies () const
 Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES? More...
 
bool modify_was_successful () const
 Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL? More...
 
void attach_to (Pose &pose)
 attach to a Pose's conformation More...
 
void detach_from ()
 detach from a Pose's conformation More...
 
void on_length_change (LengthEvent const &event)
 update any indexing wrt length change to Pose/Conformation being watched More...
 
bool detach_after_modify () const
 detach after modify()? More...
 
Interval const & original_interval () const
 return original residue range of this instruction More...
 
ResidueTypeSet const & residue_type_set () const
 the residue type set being used More...
 
bool has_dependencies () const
 does this BuildInstruction have dependencies? More...
 
core::Size n_dependencies () const
 the number of dependencies this BuildInstruction has More...
 
BuildInstructionCAPs const & dependencies () const
 the list of instructions whose modify() must complete before the modify() for this instruction may be called successfully More...
 
void detach_after_modify (bool const flag)
 set detach after modify() More...
 
void reset_accounting ()
 reset intervals, positions, etc to initial state and drop observers. State set to READY. More...
 
virtual void add_dependency_to (BuildInstructionCAP i)
 add an instruction to this BuildInstruction's dependency list More...
 
virtual bool dependent_on (BuildInstructionCAP i) const
 is this instruction dependent upon the given instruction? More...
 
void clear_dependencies ()
 clear the list of dependencies More...
 
virtual bool compatible_with (BuildInstruction const &rval) const
 compares fixed and mutable positions to determine compatibility with another instruction More...
 

Private Types

typedef ConnectRight Super
 

Private Attributes

RelativeSequencePositionOP rp_
 function object used to compute the 'left_position' in ConnectRight More...
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::forge::build::ConnectRight
bool dependencies_satisfied () const override
 are dependencies satisfied so that modify_impl() can complete successfully? More...
 
core::Size left_position () const
 connect at this position on 'pose_left' passed into modify() More...
 
core::Size right_position () const
 connect at this position on 'pose_right' More...
 
NamedStubID left_named_stub_id (core::Size const p) const
 generate the NamedStubID for the left stub atoms on position 'p' More...
 
NamedStubID right_named_stub_id (core::Size const p) const
 generate the NamedStubID for the left right atoms on position 'p' More...
 
void left_position (core::Size const i)
 connect at this position on 'pose_left' passed into modify() More...
 
void right_position (core::Size const i)
 connect at this position on 'pose_right' More...
 
void reset_accounting_impl () override
 do the actual reset of intervals, positions, etc to initial state More...
 
- Protected Member Functions inherited from protocols::forge::build::BuildInstruction
Link const & length_obs_link () const
 access to the Conformation length observer link More...
 
void state (BuildInstructionState::Enum const s)
 set the BuildInstruction's current state More...
 

Detailed Description

version of ConnectRight instruction that depends upon results from another BuildInstruction

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::forge::build::RelativeConnectRight::RelativeConnectRight ( )

default constructor

protocols::forge::build::RelativeConnectRight::RelativeConnectRight ( RelativeSequencePositionOP const &  rp,
core::Size const  right_position,
Pose const &  pose_right 
)

RelativeSequencePosition + position on-right jump constructor.

Parameters
[in]rpRelativeSequencePosition defining the type of computation to perform. (will be cloned)
[in]right_positionconnect at this position on 'pose_right'
[in]pose_rightconnect this pose to the right of pose_left when modify( pose_left ) is called
protocols::forge::build::RelativeConnectRight::RelativeConnectRight ( RelativeConnectRight const &  rval)

copy constructor

protocols::forge::build::RelativeConnectRight::~RelativeConnectRight ( )
overridedefault

default destructor

Member Function Documentation

BuildInstructionOP protocols::forge::build::RelativeConnectRight::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::forge::build::ConnectRight.

void protocols::forge::build::RelativeConnectRight::modify_impl ( Pose pose_left)
overridevirtual
RelativeConnectRight & protocols::forge::build::RelativeConnectRight::operator= ( RelativeConnectRight const &  rval)

copy assignment

References protocols::forge::build::ConnectRight::operator=(), and rp_.

RelativeConnectRight::Positions protocols::forge::build::RelativeConnectRight::original_fixed_positions ( ) const
overridevirtual

return set of any fixed positions necessary with respect to the original interval and original Pose numbering

Returns
always empty set, no fixed positions
Remarks
Used for ensuring build regions for instructions do not overlap and so that jumps may be placed correctly. There is currently no way to represent the dependent fixed position, so we're forced to return an empty set.

Reimplemented from protocols::forge::build::ConnectRight.

Member Data Documentation

RelativeSequencePositionOP protocols::forge::build::RelativeConnectRight::rp_
private

function object used to compute the 'left_position' in ConnectRight

Referenced by modify_impl(), and operator=().


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