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

#include <RelativeConnectRight.hh>

Inheritance diagram for protocols::forge::build::RelativeConnectRight:

Collaboration diagram for protocols::forge::build::RelativeConnectRight:

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::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< Size >	Positions

typedef std::string	String

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

	RelativeConnectRight (RelativeSequencePositionOP const &rp, Size const right_position, Pose const &pose_right)
	RelativeSequencePosition + position on-right jump constructor. More...

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

virtual	~RelativeConnectRight ()
	default destructor More...

RelativeConnectRight &	operator= (RelativeConnectRight const &rval)
	copy assignment More...

virtual BuildInstructionOP	clone () const
	clone this object More...

virtual void	modify_impl (Pose &pose_left)
	do the actual work of modifying the Pose More...

virtual Positions	original_fixed_positions () const
	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 (Size const left_position, Size const right_position, Pose const &pose_right)
	position to position jump constructor More...

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

virtual	~ConnectRight ()
	default destructor More...

ConnectRight &	operator= (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...

virtual bool	original_interval_valid () const
	is the original interval storing valid information, or is empty or being used for something else? More...

virtual Interval	interval () const
	a copy of the working range of residues specifying the modified region More...

virtual Positions	preexisting_positions () const
	return a copy of the set of positions within the new region that were pre-existing in the original Pose prior to modify() More...

virtual Positions	new_positions () const
	return a copy of the set of positions that are "new" and did not exist in the original Pose. More...

virtual Positions	defined_positions () const
	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...

virtual Positions	undefined_positions () const
	return a copy of the set of positions within the newly modified region that has an undefined conformation. E.g. newly created residues. More...

virtual MoveMap	movemap () const
	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, Size const jump_start_residue, 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...

virtual void	on_residue_append (LengthEvent const &event)
	update indexing on residue append More...

virtual void	on_residue_prepend (LengthEvent const &event)
	update indexing on residue prepend More...

virtual void	on_residue_delete (LengthEvent const &event)
	update indexing on residue delete More...

virtual Positions	original_kept_positions () const
	return the set of positions within the original interval that will be kept in this BuildInstruction More...

virtual Positions	original_deleted_positions () const
	return set of positions within the original interval that will be deleted in this BuildInstruction More...

virtual Positions	original_mutable_positions () const
	return set of any mutable positions necessary with respect to the original interval and original Pose numbering More...

virtual bool	creates_undefined_backbone () const
	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...

virtual	~BuildInstruction ()
	default destructor More...

BuildInstruction &	operator= (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...

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
virtual bool	dependencies_satisfied () const
	are dependencies satisfied so that modify_impl() can complete successfully? More...

Size	left_position () const
	connect at this position on 'pose_left' passed into modify() More...

Size	right_position () const
	connect at this position on 'pose_right' More...

NamedStubID	left_named_stub_id (Size const p) const
	generate the NamedStubID for the left stub atoms on position 'p' More...

NamedStubID	right_named_stub_id (Size const p) const
	generate the NamedStubID for the left right atoms on position 'p' More...

void	left_position (Size const i)
	connect at this position on 'pose_left' passed into modify() More...

void	right_position (Size const i)
	connect at this position on 'pose_right' More...

virtual void	reset_accounting_impl ()
	do the actual reset of intervals, positions, etc to initial state More...

Detailed Description

version of ConnectRight instruction that depends upon results from another BuildInstruction

Definition at line 38 of file RelativeConnectRight.hh.

Member Typedef Documentation

typedef core::kinematics::Jump protocols::forge::build::RelativeConnectRight::Jump

Definition at line 60 of file RelativeConnectRight.hh.

typedef Super::LengthEvent protocols::forge::build::RelativeConnectRight::LengthEvent

Definition at line 53 of file RelativeConnectRight.hh.

typedef Super::MoveMap protocols::forge::build::RelativeConnectRight::MoveMap

Definition at line 54 of file RelativeConnectRight.hh.

typedef Super::Pose protocols::forge::build::RelativeConnectRight::Pose

Definition at line 55 of file RelativeConnectRight.hh.

typedef Super::Positions protocols::forge::build::RelativeConnectRight::Positions

Definition at line 57 of file RelativeConnectRight.hh.

typedef Super::ResidueTypeSetCAP protocols::forge::build::RelativeConnectRight::ResidueTypeSetCAP

Definition at line 52 of file RelativeConnectRight.hh.

typedef Super::Size protocols::forge::build::RelativeConnectRight::Size

Definition at line 50 of file RelativeConnectRight.hh.

typedef Super::String protocols::forge::build::RelativeConnectRight::String

Definition at line 58 of file RelativeConnectRight.hh.

typedef ConnectRight protocols::forge::build::RelativeConnectRight::Super

private

Definition at line 44 of file RelativeConnectRight.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 37 of file RelativeConnectRight.cc.

Referenced by clone().

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

RelativeSequencePosition + position on-right jump constructor.

Parameters

[in]	rp	RelativeSequencePosition defining the type of computation to perform. (will be cloned)
[in]	right_position	connect at this position on 'pose_right'
[in]	pose_right	connect this pose to the right of pose_left when modify( pose_left ) is called

Definition at line 48 of file RelativeConnectRight.cc.

protocols::forge::build::RelativeConnectRight::RelativeConnectRight ( RelativeConnectRight const & rval)

copy constructor

Definition at line 59 of file RelativeConnectRight.cc.

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

virtual

default destructor

Definition at line 66 of file RelativeConnectRight.cc.

Member Function Documentation

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

virtual

clone this object

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

Definition at line 81 of file RelativeConnectRight.cc.

References RelativeConnectRight().

void protocols::forge::build::RelativeConnectRight::modify_impl ( Pose & pose_left)

virtual

do the actual work of modifying the Pose

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

Definition at line 87 of file RelativeConnectRight.cc.

References protocols::forge::build::BuildInstruction::dependencies(), protocols::forge::build::ConnectRight::left_position(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::BuildInstruction::n_dependencies(), and rp_.

RelativeConnectRight & protocols::forge::build::RelativeConnectRight::operator= ( RelativeConnectRight const & rval)

copy assignment

Definition at line 70 of file RelativeConnectRight.cc.

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

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

virtual

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.

Definition at line 105 of file RelativeConnectRight.cc.

Member Data Documentation

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

private

function object used to compute the 'left_position' in ConnectRight

Definition at line 134 of file RelativeConnectRight.hh.

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

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

src/protocols/forge/build/RelativeConnectRight.hh
src/protocols/forge/build/RelativeConnectRight.cc

Public Types

Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation