tracks modifications to be made and is capable of making residue length changes on a Pose More...

#include <BuildInstruction.hh>

Inheritance diagram for protocols::forge::build::BuildInstruction:

Collaboration diagram for protocols::forge::build::BuildInstruction:

Public Types
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
	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...

virtual BuildInstructionOP	clone () const =0
	clone this object 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...

virtual void	on_residue_append (LengthEvent const &event)=0
	update indexing on residue append More...

virtual void	on_residue_prepend (LengthEvent const &event)=0
	update indexing on residue prepend More...

virtual void	on_residue_delete (LengthEvent const &event)=0
	update indexing on residue delete 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...

virtual bool	original_interval_valid () const =0
	is the original interval storing valid information, or is empty or being used for something else? More...

virtual Interval	interval () const =0
	a copy of the working range of residues specifying the modified region More...

virtual Positions	preexisting_positions () const =0
	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 =0
	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 =0
	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 =0
	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 =0
	return a copy of the MoveMap that defines the moveable/fixed positions/dofs for this instruction 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 Positions	original_kept_positions () const =0
	return the set of positions within the original interval that will be kept in this BuildInstruction More...

virtual Positions	original_deleted_positions () const =0
	return set of positions within the original interval that will be deleted in this BuildInstruction More...

virtual bool	compatible_with (BuildInstruction const &rval) const
	compares fixed and mutable positions to determine compatibility with another instruction More...

virtual Positions	original_fixed_positions () const =0
	return set of any fixed positions necessary with respect to the original interval and original Pose numbering More...

virtual Positions	original_mutable_positions () const =0
	return set of any mutable positions necessary with respect to the original interval and original Pose numbering More...

virtual bool	creates_undefined_backbone () const =0
	does this object create undefined backbone in the modified region? More...

Protected Member Functions
Link const &	length_obs_link () const
	access to the Conformation length observer link More...

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

virtual void	modify_impl (Pose &pose)=0
	do the actual work of modifying the Pose More...

void	state (BuildInstructionState::Enum const s)
	set the BuildInstruction's current state More...

virtual void	reset_accounting_impl ()=0
	do the actual reset of intervals, positions, etc to initial state More...

Private Types
typedef utility::pointer::ReferenceCount	Super

Private Attributes
BuildInstructionState::Enum	state_
	Describes the state of the BuildInstruction. More...

Interval	original_interval_
	defines the original residue range via closed interval [first, second] or an original anchor position [anchor, anchor] that's marked as invalid More...

ResidueTypeSetCAP	rts_
	the residue type set to use More...

Link	length_obs_link_
	Conformation length observer link. More...

bool	detach_after_modify_
	detach after performing modify() More...

BuildInstructionCAPs	dependencies_
	if this BuildInstruction's modify() is dependent on any other BuildInstructions whose modify() must complete first, we store access to those instructions here More...

Detailed Description

tracks modifications to be made and is capable of making residue length changes on a Pose

Definition at line 68 of file BuildInstruction.hh.

Member Typedef Documentation

typedef utility::vector1< BuildInstructionCAP > protocols::forge::build::BuildInstruction::BuildInstructionCAPs

Definition at line 88 of file BuildInstruction.hh.

typedef core::conformation::signals::LengthEvent protocols::forge::build::BuildInstruction::LengthEvent

Definition at line 84 of file BuildInstruction.hh.

typedef utility::signals::Link protocols::forge::build::BuildInstruction::Link

Definition at line 90 of file BuildInstruction.hh.

typedef core::kinematics::MoveMap protocols::forge::build::BuildInstruction::MoveMap

Definition at line 85 of file BuildInstruction.hh.

typedef core::pose::Pose protocols::forge::build::BuildInstruction::Pose

Definition at line 86 of file BuildInstruction.hh.

typedef std::set< Size > protocols::forge::build::BuildInstruction::Positions

Definition at line 92 of file BuildInstruction.hh.

typedef core::Real protocols::forge::build::BuildInstruction::Real

Definition at line 81 of file BuildInstruction.hh.

typedef core::chemical::ResidueTypeSet protocols::forge::build::BuildInstruction::ResidueTypeSet

Definition at line 82 of file BuildInstruction.hh.

typedef core::chemical::ResidueTypeSetCAP protocols::forge::build::BuildInstruction::ResidueTypeSetCAP

Definition at line 83 of file BuildInstruction.hh.

typedef core::Size protocols::forge::build::BuildInstruction::Size

Definition at line 80 of file BuildInstruction.hh.

typedef std::string protocols::forge::build::BuildInstruction::String

Definition at line 93 of file BuildInstruction.hh.

typedef utility::pointer::ReferenceCount protocols::forge::build::BuildInstruction::Super

private

Definition at line 74 of file BuildInstruction.hh.

Constructor & Destructor Documentation

protocols::forge::build::BuildInstruction::BuildInstruction ( )

default constructor

Definition at line 51 of file BuildInstruction.cc.

protocols::forge::build::BuildInstruction::BuildInstruction	(	Interval const &	i,
		ResidueTypeSetCAP	rts = `core::chemical::ChemicalManager::get_instance()->residue_type_set( core::chemical::FA_STANDARD )`
	)

interval constructor

Parameters

[in]	i	the residue range to operate on
[in]	rts	the residue type set to use, default FA_STANDARD

Definition at line 62 of file BuildInstruction.cc.

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

copy constructor

Definition at line 75 of file BuildInstruction.cc.

protocols::forge::build::BuildInstruction::~BuildInstruction ( )

virtual

default destructor

Definition at line 88 of file BuildInstruction.cc.

References detach_from().

Member Function Documentation

void protocols::forge::build::BuildInstruction::add_dependency_to ( BuildInstructionCAP i)

virtual

add an instruction to this BuildInstruction's dependency list

Remarks: before this instruction's modify() may complete properly, all instructions in the dependency list must have completed modify() first

Definition at line 236 of file BuildInstruction.cc.

References dependencies_, and dependent_on().

void protocols::forge::build::BuildInstruction::attach_to ( Pose & pose)

attach to a Pose's conformation

Definition at line 169 of file BuildInstruction.cc.

References core::conformation::Conformation::attach_length_obs(), core::pose::Pose::conformation(), detach_from(), length_obs_link_, and on_length_change().

Referenced by modify(), and protocols::forge::build::SegmentRebuild::modify_impl().

void protocols::forge::build::BuildInstruction::clear_dependencies ( )

inline

clear the list of dependencies

Definition at line 345 of file BuildInstruction.hh.

References dependencies_.

virtual BuildInstructionOP protocols::forge::build::BuildInstruction::clone ( ) const

pure virtual

clone this object

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::SegmentRebuild, protocols::forge::build::Bridge, protocols::forge::build::ConnectRight, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::RelativeConnectRight, and protocols::forge::build::SegmentSwap.

bool protocols::forge::build::BuildInstruction::compatible_with ( BuildInstruction const & rval) const

virtual

compares fixed and mutable positions to determine compatibility with another instruction

Remarks: override this to obtain custom compatibility check

Definition at line 252 of file BuildInstruction.cc.

References original_fixed_positions(), original_mutable_positions(), rts_, and protocols::forge::build::TR().

virtual bool protocols::forge::build::BuildInstruction::creates_undefined_backbone ( ) const

pure virtual

does this object create undefined backbone in the modified region?

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

virtual Positions protocols::forge::build::BuildInstruction::defined_positions ( ) const

pure virtual

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

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by protocols::forge::build::BuildManager::intervals_containing_defined_positions(), and protocols::forge::build::BuildManager::modified_i2p_defined().

BuildInstructionCAPs const& protocols::forge::build::BuildInstruction::dependencies ( ) const

inline

the list of instructions whose modify() must complete before the modify() for this instruction may be called successfully

Definition at line 252 of file BuildInstruction.hh.

References dependencies_.

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

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

protectedvirtual

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

Returns: True if modify_impl() can be called, False otherwise.

Remarks: This function will automatically be checked within modify() prior to running modify_impl().

Reimplemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Definition at line 221 of file BuildInstruction.cc.

References dependencies_.

Referenced by modify().

bool protocols::forge::build::BuildInstruction::dependent_on ( BuildInstructionCAP i) const

virtual

is this instruction dependent upon the given instruction?

Definition at line 244 of file BuildInstruction.cc.

References dependencies_.

Referenced by add_dependency_to().

bool protocols::forge::build::BuildInstruction::detach_after_modify ( ) const

inline

detach after modify()?

Ordinarily a modify() call consists of attaching as a length obs of the Pose, actually doing the modify, and then detaching as a length obs of the Pose. This flag governs whether the last detach occurs.

Definition at line 216 of file BuildInstruction.hh.

References detach_after_modify_.

void protocols::forge::build::BuildInstruction::detach_after_modify ( bool const flag)

inline

set detach after modify()

Ordinarily a modify() call consists of attaching as a length obs of the Pose, actually doing the modify, and then detaching as a length obs of the Pose. This flag governs whether the last detach occurs.

Definition at line 318 of file BuildInstruction.hh.

References detach_after_modify_.

void protocols::forge::build::BuildInstruction::detach_from ( )

detach from a Pose's conformation

Definition at line 176 of file BuildInstruction.cc.

References length_obs_link_.

Referenced by attach_to(), modify(), on_length_change(), reset_accounting(), and ~BuildInstruction().

bool protocols::forge::build::BuildInstruction::has_dependencies ( ) const

inline

does this BuildInstruction have dependencies?

Definition at line 237 of file BuildInstruction.hh.

References dependencies_.

Referenced by protocols::forge::build::SegmentRebuild::original_fixed_positions().

virtual Interval protocols::forge::build::BuildInstruction::interval ( ) const

pure virtual

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

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Link const& protocols::forge::build::BuildInstruction::length_obs_link ( ) const

inlineprotected

access to the Conformation length observer link

Definition at line 405 of file BuildInstruction.hh.

References length_obs_link_.

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

BuildInstructionState::Enum protocols::forge::build::BuildInstruction::modify ( Pose & pose)

modify this pose

Returns: the state of the BuildInstruction

Definition at line 109 of file BuildInstruction.cc.

References attach_to(), core::scoring::Energies::clear(), dependencies_satisfied(), detach_after_modify_, detach_from(), core::pose::Pose::energies(), modify_impl(), protocols::forge::build::BuildInstructionState::MODIFY_WAS_SUCCESSFUL, modify_was_successful(), state(), state_, and protocols::forge::build::BuildInstructionState::WAITING_ON_DEPENDENCIES.

Referenced by protocols::forge::build::BuildManager::modify(), and protocols::forge::build::Bridge::modify_impl().

virtual void protocols::forge::build::BuildInstruction::modify_impl ( Pose & pose)

protectedpure virtual

do the actual work of modifying the Pose

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, protocols::forge::build::SegmentSwap, and protocols::forge::build::RelativeConnectRight.

Referenced by modify().

bool protocols::forge::build::BuildInstruction::modify_was_successful ( ) const

Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL?

Remarks: MODIFY_WAS_SUCCESSFUL indicates the BuildInstruction has finished modifications to the Pose, and its residue indexing is now consistent with the newly modified Pose.

Definition at line 163 of file BuildInstruction.cc.

References protocols::forge::build::BuildInstructionState::MODIFY_WAS_SUCCESSFUL, and state_.

Referenced by modify(), protocols::forge::build::BuildManager::modify(), protocols::forge::build::ConnectRight::on_residue_append(), protocols::forge::build::ConnectRight::on_residue_delete(), and protocols::forge::build::ConnectRight::on_residue_prepend().

virtual MoveMap protocols::forge::build::BuildInstruction::movemap ( ) const

pure virtual

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

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by protocols::forge::build::BuildManager::modified_interval2movemap().

Size protocols::forge::build::BuildInstruction::n_dependencies ( ) const

inline

the number of dependencies this BuildInstruction has

Definition at line 244 of file BuildInstruction.hh.

References dependencies_.

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

virtual Positions protocols::forge::build::BuildInstruction::new_positions ( ) const

pure virtual

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by protocols::forge::build::BuildManager::intervals_containing_new_positions(), protocols::forge::build::BuildManager::modified_i2p_new(), and protocols::forge::build::BuildManager::modify().

void protocols::forge::build::BuildInstruction::on_length_change ( LengthEvent const & event)

update any indexing wrt length change to Pose/Conformation being watched

Definition at line 182 of file BuildInstruction.cc.

References detach_from(), core::conformation::signals::LengthEvent::INVALIDATE, on_residue_append(), on_residue_delete(), on_residue_prepend(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, core::conformation::signals::LengthEvent::RESIDUE_DELETE, core::conformation::signals::LengthEvent::RESIDUE_PREPEND, and core::conformation::signals::LengthEvent::tag.

Referenced by attach_to().

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

pure virtual

update indexing on residue append

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by on_length_change().

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

pure virtual

update indexing on residue delete

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by on_length_change().

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

pure virtual

update indexing on residue prepend

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by on_length_change().

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

copy assignment

Definition at line 94 of file BuildInstruction.cc.

References detach_after_modify_, original_interval_, rts_, and state_.

Referenced by protocols::forge::build::SegmentSwap::operator=(), protocols::forge::build::GrowRight::operator=(), protocols::forge::build::GrowLeft::operator=(), protocols::forge::build::ConnectRight::operator=(), protocols::forge::build::Bridge::operator=(), protocols::forge::build::SegmentRebuild::operator=(), and protocols::forge::build::SegmentInsert::operator=().

virtual Positions protocols::forge::build::BuildInstruction::original_deleted_positions ( ) const

pure virtual

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by protocols::forge::build::BuildManager::modify(), protocols::forge::build::BuildManager::original_i2p_deleted(), and protocols::forge::build::BuildManager::original_intervals_containing_deleted_positions().

virtual Positions protocols::forge::build::BuildInstruction::original_fixed_positions ( ) const

pure virtual

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 necessary

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, protocols::forge::build::SegmentSwap, and protocols::forge::build::RelativeConnectRight.

Referenced by compatible_with().

Interval const& protocols::forge::build::BuildInstruction::original_interval ( ) const

inline

return original residue range of this instruction

Definition at line 223 of file BuildInstruction.hh.

References original_interval_.

virtual bool protocols::forge::build::BuildInstruction::original_interval_valid ( ) const

pure virtual

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by protocols::forge::build::BuildManager::intervals_without_valid_original_equivalents(), protocols::forge::build::BuildManager::modified2original_interval_endpoints(), protocols::forge::build::BuildManager::modified2original_intervals(), protocols::forge::build::BuildManager::original2modified_interval_endpoints(), and protocols::forge::build::BuildManager::original2modified_intervals().

virtual Positions protocols::forge::build::BuildInstruction::original_kept_positions ( ) const

pure virtual

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by protocols::forge::build::BuildManager::original_i2p_kept(), and protocols::forge::build::BuildManager::original_intervals_containing_kept_positions().

virtual Positions protocols::forge::build::BuildInstruction::original_mutable_positions ( ) const

pure virtual

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.

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by compatible_with().

virtual Positions protocols::forge::build::BuildInstruction::preexisting_positions ( ) const

pure virtual

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by protocols::forge::build::BuildManager::intervals_containing_preexisting_positions(), and protocols::forge::build::BuildManager::modified_i2p_preexisting().

bool protocols::forge::build::BuildInstruction::ready ( ) const

Is the BuildInstruction's state at READY?

Remarks: READY indicates the BuildInstruction has been reset and is ready to modify a Pose.

Definition at line 145 of file BuildInstruction.cc.

References protocols::forge::build::BuildInstructionState::READY, and state_.

void protocols::forge::build::BuildInstruction::reset_accounting ( )

reset intervals, positions, etc to initial state and drop observers. State set to READY.

Reset intervals, positions, etc to initial state and drop observers. State set to READY.

Definition at line 209 of file BuildInstruction.cc.

References detach_from(), protocols::forge::build::BuildInstructionState::READY, reset_accounting_impl(), and state().

virtual void protocols::forge::build::BuildInstruction::reset_accounting_impl ( )

protectedpure virtual

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

Implemented in protocols::forge::build::ConnectRight, protocols::forge::build::SegmentInsert, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by reset_accounting().

ResidueTypeSet const& protocols::forge::build::BuildInstruction::residue_type_set ( ) const

inline

the residue type set being used

Definition at line 230 of file BuildInstruction.hh.

References rts_.

Referenced by protocols::forge::build::Bridge::modify_impl(), protocols::forge::build::GrowLeft::modify_impl(), protocols::forge::build::GrowRight::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), and protocols::forge::build::SegmentInsert::modify_impl().

BuildInstructionState::Enum protocols::forge::build::BuildInstruction::state ( ) const

inline

return the state of this BuildInstruction

Definition at line 149 of file BuildInstruction.hh.

References state_.

Referenced by modify(), and reset_accounting().

void protocols::forge::build::BuildInstruction::state ( BuildInstructionState::Enum const s)

inlineprotected

set the BuildInstruction's current state

Definition at line 435 of file BuildInstruction.hh.

References state_.

virtual Positions protocols::forge::build::BuildInstruction::undefined_positions ( ) const

pure virtual

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

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

Implemented in protocols::forge::build::SegmentInsert, protocols::forge::build::ConnectRight, protocols::forge::build::SegmentRebuild, protocols::forge::build::GrowLeft, protocols::forge::build::GrowRight, protocols::forge::build::Bridge, and protocols::forge::build::SegmentSwap.

Referenced by protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::build::BuildManager::modified_i2p_undefined(), and protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions().

bool protocols::forge::build::BuildInstruction::waiting_on_dependencies ( ) const

Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES?

Remarks: WAITING_ON_DEPENDENCIES indicates the BuildInstruction is waiting for its dependencies to be satisfied before allowing modifications to proceed.

Definition at line 154 of file BuildInstruction.cc.

References state_, and protocols::forge::build::BuildInstructionState::WAITING_ON_DEPENDENCIES.

Member Data Documentation

BuildInstructionCAPs protocols::forge::build::BuildInstruction::dependencies_

private

if this BuildInstruction's modify() is dependent on any other BuildInstructions whose modify() must complete first, we store access to those instructions here

Warning: Due to copy ambiguities, dependencies are currently not copied! They must be externally rebuilt, e.g. by the BuildManager.

Definition at line 485 of file BuildInstruction.hh.

Referenced by add_dependency_to(), clear_dependencies(), dependencies(), dependencies_satisfied(), dependent_on(), has_dependencies(), and n_dependencies().

bool protocols::forge::build::BuildInstruction::detach_after_modify_

private

detach after performing modify()

Ordinarily a modify() call consists of attaching as a length obs of the Pose, actually doing the modify, and then detaching as a length obs of the Pose. This flag governs whether the last detach occurs.

Definition at line 477 of file BuildInstruction.hh.

Referenced by detach_after_modify(), modify(), and operator=().

Link protocols::forge::build::BuildInstruction::length_obs_link_

private

Conformation length observer link.

Definition at line 469 of file BuildInstruction.hh.

Referenced by attach_to(), detach_from(), and length_obs_link().

Interval protocols::forge::build::BuildInstruction::original_interval_

private

defines the original residue range via closed interval [first, second] or an original anchor position [anchor, anchor] that's marked as invalid