instruction to connect one Pose onto the right side of another More...

#include <ConnectRight.hh>

Inheritance diagram for protocols::forge::build::ConnectRight:

[legend]

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::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::Size >	Positions

typedef std::string	String

Public Member Functions
	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...

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

BuildInstructionOP	clone () const override
	clone this object 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_fixed_positions () const override
	return set of any fixed positions necessary with respect to the original interval and original Pose numbering 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...

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...

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...

Protected Member Functions
bool	dependencies_satisfied () const override
	are dependencies satisfied so that modify_impl() can complete successfully? More...

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

Private Types
typedef BuildInstruction	Super

Private Member Functions
void	init ()
	initialization on construction More...

Private Attributes
core::Size	left_position_
	connect at this position on 'pose_left' passed into modify() More...

core::Size	right_position_
	connect at this position on 'pose_right' More...

Pose	pose_right_
	connect this pose to the right of pose_left when modify( pose_left ) is called More...

bool	use_rt_
	apply the transform over the jump connection between pose_left and pose_right? default False More...

AtomNameList	left_stub_atoms_
	Use these atoms to compute the stub on pose_left. Default ["CA", "N", "CA", "C"]. More...

AtomNameList	right_stub_atoms_
	Use these atoms to compute the stub on pose_right. Default ["CA", "N", "CA", "C"]. More...

RT	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...

Interval	interval_
	tracks the numbering of the new region specifying the connected Pose More...

Detailed Description

instruction to connect one Pose onto the right side of another

Denote pose_left = [a,b] and pose_right = [c,d] and the newly connected pose_left + pose_right = pose_total = [a,d]. If 'b' of pose_left is an upper terminus or 'c' of pose_right is a lower terminus, then ConnectRight will start a new chain in the Conformation at 'c' when constructing pose_total, otherwise it will continue the chain at 'b'.

Member Typedef Documentation

◆ AtomNameList

typedef NamedStubID::AtomList protocols::forge::build::ConnectRight::AtomNameList

◆ LengthEvent

typedef Super::LengthEvent protocols::forge::build::ConnectRight::LengthEvent

◆ MoveMap

typedef Super::MoveMap protocols::forge::build::ConnectRight::MoveMap

◆ NamedStubID

typedef core::id::NamedStubID protocols::forge::build::ConnectRight::NamedStubID

◆ Pose

typedef Super::Pose protocols::forge::build::ConnectRight::Pose

◆ Positions

typedef Super::Positions protocols::forge::build::ConnectRight::Positions

◆ ResidueTypeSetCAP

typedef Super::ResidueTypeSetCAP protocols::forge::build::ConnectRight::ResidueTypeSetCAP

◆ RT

typedef core::kinematics::RT protocols::forge::build::ConnectRight::RT

◆ Size

typedef Super::Size protocols::forge::build::ConnectRight::Size

◆ String

typedef Super::String protocols::forge::build::ConnectRight::String

◆ Super

typedef BuildInstruction protocols::forge::build::ConnectRight::Super

private

Constructor & Destructor Documentation

◆ ConnectRight() [1/3]

protocols::forge::build::ConnectRight::ConnectRight ( )

default constructor

References init().

◆ ConnectRight() [2/3]

protocols::forge::build::ConnectRight::ConnectRight	(	core::Size const	left_position,
		core::Size const	right_position,
		Pose const &	pose_right
	)

position to position jump constructor

Parameters

[in]	left_position	connect at this position on 'pose_left' passed into modify()
[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
[in]	left_position	connect at this position on 'pose_left' passed into modify()
[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
[in]	start_new_chain	start new chain when connecting? does not handle termini variants

References init().

◆ ConnectRight() [3/3]

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

default

copy constructor

◆ ~ConnectRight()

protocols::forge::build::ConnectRight::~ConnectRight ( )

overridedefault

default destructor

Member Function Documentation

◆ clone()

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

overridevirtual

clone this object

Implements protocols::forge::build::BuildInstruction.

Reimplemented in protocols::forge::build::RelativeConnectRight.

◆ creates_undefined_backbone()

bool protocols::forge::build::ConnectRight::creates_undefined_backbone ( ) const

inlineoverridevirtual

does this object create undefined backbone in the modified region?

Returns: false

Implements protocols::forge::build::BuildInstruction.

◆ defined_positions()

ConnectRight::Positions protocols::forge::build::ConnectRight::defined_positions ( ) const

overridevirtual

return a copy of the set of positions within the newly modified region that has a defined conformation. E.g. existing or copied residues.

Returns: A set spanning the entire interval – all positions are defined.

This set can change wrt length changes in Pose/Conformation being watched.

Implements protocols::forge::build::BuildInstruction.

References new_positions().

◆ dependencies_satisfied()

bool protocols::forge::build::ConnectRight::dependencies_satisfied ( ) const

inlineoverrideprotectedvirtual

are dependencies satisfied so that modify_impl() can complete successfully?

Returns: always True, this BuildInstruction has no dependencies

Reimplemented from protocols::forge::build::BuildInstruction.

◆ extract_rt()

void protocols::forge::build::ConnectRight::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

Parameters

[in]	pose	The Pose to use.
[in]	jump_start_residue	The starting residue of the jump. This residue should be the equivalent of the jump position on pose_left.
[in]	jump_stop-residue	The stopping residue of the jump. This residue should be the equivalent of the jump position on pose_right.

Remarks: Uses left_stub_atoms() and right_stub_atoms() as the stub atoms to compute the transform. Remember to set use_rt() to True after calling this function if you want to actually use the transform during modify().

References core::pose::Pose::conformation(), core::conformation::Conformation::get_stub_transform(), left_named_stub_id(), core::pose::named_stub_id_to_stub_id(), right_named_stub_id(), rt_, and core::pose::Pose::size().

◆ init()

void protocols::forge::build::ConnectRight::init ( void )

private

initialization on construction

References left_stub_atoms_, and right_stub_atoms_.

Referenced by ConnectRight().

◆ interval()

Interval protocols::forge::build::ConnectRight::interval ( ) const

inlineoverridevirtual

a copy of the working range of residues specifying the modified region

before modify() holds [1, pose_right.size()]; after modify() holds [1 + pose_left.size(), pose_right.n_residue + pose_left.size()]

Remarks: This can change if listening to Conformation LengthEvents

Implements protocols::forge::build::BuildInstruction.

References interval_.

Referenced by new_positions().

◆ left_named_stub_id()

NamedStubID protocols::forge::build::ConnectRight::left_named_stub_id ( core::Size const p ) const

inlineprotected

generate the NamedStubID for the left stub atoms on position 'p'

References left_stub_atoms_.

Referenced by extract_rt(), and modify_impl().

◆ left_position() [1/2]

core::Size protocols::forge::build::ConnectRight::left_position ( ) const

inlineprotected

connect at this position on 'pose_left' passed into modify()

Remarks: this position can shift if listening to a Pose/Conformation and the number of residues changes

References left_position_.

Referenced by protocols::forge::build::RelativeConnectRight::modify_impl().

◆ left_position() [2/2]

void protocols::forge::build::ConnectRight::left_position ( core::Size const i )

inlineprotected

connect at this position on 'pose_left' passed into modify()

Remarks: this position can shift if listening to a Pose/Conformation and the number of residues changes

References left_position_.

◆ left_stub_atoms() [1/2]

AtomNameList const& protocols::forge::build::ConnectRight::left_stub_atoms ( ) const

inline

Use these atoms to compute the stub on pose_left. Default ["CA", "N", "CA", "C"].

This is an array with 4 elements in the same order as Stub initialization: 'center atom', 'point1', 'point2', 'point3'. See Stub docs for more details.

References left_stub_atoms_.

◆ left_stub_atoms() [2/2]

void protocols::forge::build::ConnectRight::left_stub_atoms ( AtomNameList const & atoms )

inline

Use these atoms to compute the stub on pose_left. Default ["CA", "N", "CA", "C"].

This is an array with 4 elements in the same order as Stub initialization: 'center atom', 'point1', 'point2', 'point3'. See Stub docs for more details.

References left_stub_atoms_.

◆ modify_impl()

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

overrideprotectedvirtual

do the actual work of modifying the Pose

Implements protocols::forge::build::BuildInstruction.

Reimplemented in protocols::forge::build::RelativeConnectRight.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::chain(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), interval_, core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer_bonded(), core::conformation::Residue::is_upper_terminus(), left_named_stub_id(), left_position_, protocols::forge::methods::merge(), merge(), protocols::mean_field::min(), core::pose::named_stub_id_to_stub_id(), core::pose::Pose::pdb_info(), pose_right_, core::pose::Pose::residue(), right_named_stub_id(), right_position_, rt_, core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::conformation::Conformation::set_stub_transform(), core::pose::Pose::size(), and use_rt_.

Referenced by protocols::forge::build::RelativeConnectRight::modify_impl().

◆ movemap()

ConnectRight::MoveMap protocols::forge::build::ConnectRight::movemap ( ) const

overridevirtual

return a copy of the MoveMap that defines the moveable/fixed positions/dofs for this instruction

Returns: a MoveMap with [interval.left, interval.right] bb set to false at the MoveMapTorsionID level

This set can change wrt length changes in Pose/Conformation being watched.

Implements protocols::forge::build::BuildInstruction.

References new_positions(), and core::kinematics::MoveMap::set_bb().

◆ new_positions()

ConnectRight::Positions protocols::forge::build::ConnectRight::new_positions ( ) const

overridevirtual

return a copy of the set of positions that are "new" and did not exist in the original Pose.

Returns: A set spanning the entire interval – all positions are new.

Implements protocols::forge::build::BuildInstruction.

References protocols::forge::methods::closed_range(), interval(), protocols::forge::build::Interval::left, and protocols::forge::build::Interval::right.

Referenced by defined_positions(), and movemap().

◆ on_residue_append()

void protocols::forge::build::ConnectRight::on_residue_append ( LengthEvent const & event )

overridevirtual

update indexing on residue append

Implements protocols::forge::build::BuildInstruction.

References interval_, protocols::forge::build::Interval::left, left_position_, protocols::forge::build::BuildInstruction::modify_was_successful(), core::conformation::signals::LengthEvent::position, and protocols::forge::build::Interval::right.

◆ on_residue_delete()

void protocols::forge::build::ConnectRight::on_residue_delete ( LengthEvent const & event )

overridevirtual

update indexing on residue delete

Implements protocols::forge::build::BuildInstruction.

References interval_, protocols::forge::build::Interval::left, left_position_, core::conformation::signals::LengthEvent::length_change, protocols::forge::build::BuildInstruction::modify_was_successful(), core::conformation::signals::LengthEvent::position, and protocols::forge::build::Interval::right.

◆ on_residue_prepend()

void protocols::forge::build::ConnectRight::on_residue_prepend ( LengthEvent const & event )

overridevirtual

update indexing on residue prepend

Implements protocols::forge::build::BuildInstruction.

References interval_, protocols::forge::build::Interval::left, left_position_, protocols::forge::build::BuildInstruction::modify_was_successful(), core::conformation::signals::LengthEvent::position, and protocols::forge::build::Interval::right.

◆ operator=()

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

copy assignment

References interval_, left_position_, left_stub_atoms_, protocols::forge::build::BuildInstruction::operator=(), pose_right_, right_position_, right_stub_atoms_, rt_, and use_rt_.

Referenced by protocols::forge::build::RelativeConnectRight::operator=().

◆ original_deleted_positions()

ConnectRight::Positions protocols::forge::build::ConnectRight::original_deleted_positions ( ) const

overridevirtual

return set of positions within the original interval that will be deleted in this BuildInstruction

Returns: An empty set – no positions are deleted.

Implements protocols::forge::build::BuildInstruction.

◆ original_fixed_positions()

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

overridevirtual

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

Remarks: Used for ensuring build regions for instructions do not overlap and so that jumps may be placed correctly.

Returns: empty set if no fixed positions

Implements protocols::forge::build::BuildInstruction.

Reimplemented in protocols::forge::build::RelativeConnectRight.

References core::sequence::left, and protocols::forge::build::BuildInstruction::original_interval().

◆ original_interval_valid()

bool protocols::forge::build::ConnectRight::original_interval_valid ( ) const

inlineoverridevirtual

is the original interval storing valid information, or is empty or being used for something else?

Returns: false, stores invalid interval

Implements protocols::forge::build::BuildInstruction.

◆ original_kept_positions()

ConnectRight::Positions protocols::forge::build::ConnectRight::original_kept_positions ( ) const

overridevirtual

return the set of positions within the original interval that will be kept in this BuildInstruction

Returns: An empty set – no positions are kept.

Implements protocols::forge::build::BuildInstruction.

◆ original_mutable_positions()

ConnectRight::Positions protocols::forge::build::ConnectRight::original_mutable_positions ( ) const

overridevirtual

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

Remarks: Used for ensuring build regions for instructions do not overlap and so that jumps may be placed correctly.

Returns: empty set if no mutable positions

Implements protocols::forge::build::BuildInstruction.

◆ pose_right()

ConnectRight::Pose const & protocols::forge::build::ConnectRight::pose_right ( )

connect this pose to the right of pose_left when modify( pose_left ) is called

References pose_right_.

◆ preexisting_positions()

ConnectRight::Positions protocols::forge::build::ConnectRight::preexisting_positions ( ) const

overridevirtual

return a copy of the set of positions within the new region that were pre-existing in the original Pose prior to modify()

Returns: An empty set – no positions are pre-existing.

Implements protocols::forge::build::BuildInstruction.

◆ reset_accounting_impl()

void protocols::forge::build::ConnectRight::reset_accounting_impl ( )

overrideprotectedvirtual

do the actual reset of intervals, positions, etc to initial state

Implements protocols::forge::build::BuildInstruction.

References interval_, protocols::forge::build::Interval::left, left_position_, protocols::forge::build::BuildInstruction::original_interval(), pose_right_, and core::pose::Pose::size().

◆ right_named_stub_id()

NamedStubID protocols::forge::build::ConnectRight::right_named_stub_id ( core::Size const p ) const

inlineprotected

generate the NamedStubID for the left right atoms on position 'p'

References right_stub_atoms_.

Referenced by extract_rt(), and modify_impl().

◆ right_position() [1/2]

core::Size protocols::forge::build::ConnectRight::right_position ( ) const

inlineprotected

connect at this position on 'pose_right'

References right_position_.

◆ right_position() [2/2]

void protocols::forge::build::ConnectRight::right_position ( core::Size const i )

inlineprotected

connect at this position on 'pose_right'

References right_position_.

◆ right_stub_atoms() [1/2]

AtomNameList const& protocols::forge::build::ConnectRight::right_stub_atoms ( ) const

inline

Use these atoms to compute the stub on pose_right. Default ["CA", "N", "CA", "C"].

This is an array with 4 elements in the same order as Stub initialization: 'center atom', 'point1', 'point2', 'point3'. See Stub docs for more details.

References right_stub_atoms_.

◆ right_stub_atoms() [2/2]

void protocols::forge::build::ConnectRight::right_stub_atoms ( AtomNameList const & atoms )

inline

Use these atoms to compute the stub on pose_right. Default ["CA", "N", "CA", "C"].

This is an array with 4 elements in the same order as Stub initialization: 'center atom', 'point1', 'point2', 'point3'. See Stub docs for more details.

References right_stub_atoms_.

◆ rt() [1/2]

RT const& protocols::forge::build::ConnectRight::rt ( )

inline

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"

References rt_.

◆ rt() [2/2]

void protocols::forge::build::ConnectRight::rt ( RT const & transform )

inline

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"

References rt_.

◆ undefined_positions()

ConnectRight::Positions protocols::forge::build::ConnectRight::undefined_positions ( ) const

overridevirtual

return a copy of the set of positions within the newly modified region that has an undefined conformation. E.g. newly created residues.

Returns: An empty set – no undefined positions.

This set can change wrt length changes in Pose/Conformation being watched.

Implements protocols::forge::build::BuildInstruction.

◆ use_rt() [1/2]

bool protocols::forge::build::ConnectRight::use_rt ( ) const

inline

apply the transform over the jump connection between pose_left and pose_right? default False

References use_rt_.

◆ use_rt() [2/2]

void protocols::forge::build::ConnectRight::use_rt ( bool const flag )

inline

apply the transform over the jump connection between pose_left and pose_right? default False

References use_rt_.

Member Data Documentation

◆ interval_

Interval protocols::forge::build::ConnectRight::interval_

private

tracks the numbering of the new region specifying the connected Pose

before modify_impl() holds [1, pose_right.size()]; after modify holds [1 + pose_left.size(), pose_right.n_residue + pose_left.size()]

Referenced by interval(), modify_impl(), on_residue_append(), on_residue_delete(), on_residue_prepend(), operator=(), and reset_accounting_impl().

◆ left_position_

core::Size protocols::forge::build::ConnectRight::left_position_

private

connect at this position on 'pose_left' passed into modify()

Remarks: this position can shift if listening to a Pose/Conformation and the number of residues changes

Referenced by left_position(), modify_impl(), on_residue_append(), on_residue_delete(), on_residue_prepend(), operator=(), and reset_accounting_impl().

◆ left_stub_atoms_

AtomNameList protocols::forge::build::ConnectRight::left_stub_atoms_

private

Use these atoms to compute the stub on pose_left. Default ["CA", "N", "CA", "C"].

This is an array with 4 elements in the same order as Stub initialization: 'center atom', 'point1', 'point2', 'point3'. See Stub docs for more details.

Referenced by init(), left_named_stub_id(), left_stub_atoms(), and operator=().

◆ pose_right_

Pose protocols::forge::build::ConnectRight::pose_right_

private

connect this pose to the right of pose_left when modify( pose_left ) is called

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

◆ right_position_

core::Size protocols::forge::build::ConnectRight::right_position_

private

connect at this position on 'pose_right'

Remarks: this position can shift if listening to a Pose/Conformation and the number of residues changes

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

◆ right_stub_atoms_

AtomNameList protocols::forge::build::ConnectRight::right_stub_atoms_

private

Use these atoms to compute the stub on pose_right. Default ["CA", "N", "CA", "C"].

This is an array with 4 elements in the same order as Stub initialization: 'center atom', 'point1', 'point2', 'point3'. See Stub docs for more details.

Referenced by init(), operator=(), right_named_stub_id(), and right_stub_atoms().

◆ rt_

RT protocols::forge::build::ConnectRight::rt_

private

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"

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

◆ use_rt_

bool protocols::forge::build::ConnectRight::use_rt_

private

apply the transform over the jump connection between pose_left and pose_right? default False

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

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

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

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ AtomNameList

◆ LengthEvent

◆ MoveMap

◆ NamedStubID

◆ Pose

◆ Positions

◆ ResidueTypeSetCAP

◆ RT

◆ Size

◆ String

◆ Super

Constructor & Destructor Documentation

◆ ConnectRight() [1/3]

◆ ConnectRight() [2/3]

◆ ConnectRight() [3/3]

◆ ~ConnectRight()

Member Function Documentation

◆ clone()

◆ creates_undefined_backbone()

◆ defined_positions()

◆ dependencies_satisfied()

◆ extract_rt()

◆ init()

◆ interval()

◆ left_named_stub_id()

◆ left_position() [1/2]

◆ left_position() [2/2]

◆ left_stub_atoms() [1/2]

◆ left_stub_atoms() [2/2]

◆ modify_impl()

◆ movemap()

◆ new_positions()

◆ on_residue_append()

◆ on_residue_delete()

◆ on_residue_prepend()

◆ operator=()

◆ original_deleted_positions()

◆ original_fixed_positions()

◆ original_interval_valid()

◆ original_kept_positions()

◆ original_mutable_positions()

◆ pose_right()

◆ preexisting_positions()

◆ reset_accounting_impl()

◆ right_named_stub_id()

◆ right_position() [1/2]

◆ right_position() [2/2]

◆ right_stub_atoms() [1/2]

◆ right_stub_atoms() [2/2]

◆ rt() [1/2]

◆ rt() [2/2]

◆ undefined_positions()

◆ use_rt() [1/2]

◆ use_rt() [2/2]

Member Data Documentation

◆ interval_

◆ left_position_

◆ left_stub_atoms_

◆ pose_right_

◆ right_position_

◆ right_stub_atoms_

◆ rt_

◆ use_rt_