a container for managing BuildInstructions More...

#include <BuildManager.hh>

Inheritance diagram for protocols::forge::build::BuildManager:

Collaboration diagram for protocols::forge::build::BuildManager:

Public Types
typedef core::Size	Size

typedef core::kinematics::MoveMap	MoveMap

typedef core::kinematics::MoveMapOP	MoveMapOP

typedef core::pose::Pose	Pose

typedef core::id::SequenceMapping	SequenceMapping

typedef core::id::SequenceMappingOP	SequenceMappingOP

typedef core::id::SequenceMappingCOP	SequenceMappingCOP

typedef utility::vector1 < BuildInstructionOP >	BuildInstructionOPs

typedef BuildInstructionOPs::iterator	BIOPIterator

typedef BuildInstructionOPs::const_iterator	BIOPConstIterator

typedef std::pair< Size, Size >	DependencyEdge

typedef utility::vector1 < DependencyEdge >	DependencyEdges

typedef std::set< Size >	Positions

typedef std::map< Size, Size >	Original2Modified

typedef std::map< Size, Size >	Modified2Original

typedef std::map< Interval, Positions >	Interval2Positions

typedef std::map< Interval, Interval >	Interval2Interval

typedef std::map< Interval, MoveMap >	Interval2MoveMap

typedef std::string	String

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

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

virtual	~BuildManager ()
	default destructor More...

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

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

virtual BuildManagerOP	create () const
	create a new instance of this type of object More...

void	reset_accounting ()
	reset all accounting info (intervals, positions, etc) to initial state More...

void	add (BuildInstructionOP bi)
	add an instruction directly (no copy) More...

void	clear ()
	clear all instructions More...

Size	size () const
	current number of instructions More...

bool	empty () const
	no instructions? More...

BIOPConstIterator	begin () const
	const iterator pointing to the first instruction More...

BIOPConstIterator	end () const
	const iterator pointing just beyond the last instruction More...

void	create_directed_dependency (BuildInstructionOP u, BuildInstructionOP v)
	create a directed dependency: instruction 'u' must complete before instruction 'v' can complete, i.e. 'v' depends on 'u' More...

Size	n_dependencies () const
	the number of dependencies currently defined (i.e. # of edges in the dependency graph) More...

bool	dependencies_exist () const
	have dependencies been defined? More...

Size	clear_dependencies ()
	clear all dependencies More...

Original2Modified	modify (Pose &pose)
	modify the pose using the instructions in this container More...

Size	dummy_modify (Size const nres)
	a dry run of modify() with an all-ala helical Pose of the given length More...

bool	compatibility_check () const
	check if instruction regions are compatible with each other More...

MoveMap	movemap () const
	return the combined movemap from all instructions in this manager More...

MoveMapOP	movemap_as_OP () const

SequenceMappingCOP	sequence_mapping () const
	SequenceMapping consistent with the original -> modified mapping from the most recent modify() call. More...

Original2Modified const &	original2modified () const
	return a map translating original residue -> modified residue for positions that existed within both the original Pose and modified Pose More...

Interval2Interval	original2modified_intervals () const
	return a map translating original intervals to modified intervals More...

Original2Modified	original2modified_interval_endpoints () const
	return a map translating original interval endpoints to modified interval endpoints More...

Interval2Interval	modified2original_intervals () const
	return a map translating modified intervals to original intervals More...

Modified2Original	modified2original_interval_endpoints () const
	return a map translating modified interval endpoints to original interval endpoints More...

std::set< Interval >	intervals () const
	return all modified intervals More...

std::set< Interval >	intervals_without_valid_original_equivalents () const
	return modified intervals that have no equivalent original interval in their BuildInstructions (original_interval_valid() = false) More...

std::set< Interval >	intervals_containing_preexisting_positions () const
	return all intervals containing positions that were pre-existing in the original Pose prior to calling modify() More...

std::set< Interval >	intervals_containing_new_positions () const
	return all intervals containing positions that are "new" and did not exist in the original Pose More...

std::set< Interval >	intervals_containing_defined_positions () const
	return all intervals containing positions with defined conformation More...

std::set< Interval >	intervals_containing_undefined_positions () const
	return all intervals containing positions with undefined conformation More...

std::set< Interval >	original_intervals_containing_kept_positions () const
	return all original intervals containing positions that will be kept by the BuildInstructions More...

std::set< Interval >	original_intervals_containing_deleted_positions () const
	return all original intervals containing positions that will be deleted by the BuildInstructions More...

Positions	positions () const
	return all positions within the modified intervals More...

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

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

Positions	defined_positions () const
	return a copy of the set of positions within the newly modified regions that have a defined conformation. E.g. existing or copied residues. More...

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

Positions	union_of_intervals_containing_undefined_positions () const
	the positions representing the union of all intervals containing positions with undefined conformation More...

Positions	original_kept_positions () const
	return the set of positions within the original intervals that will be kept by the BuildInstructions More...

Positions	original_deleted_positions () const
	return set of positions within the original intervals that will be deleted by the BuildInstructions More...

Interval2Positions	modified_i2p_preexisting () const
	return a map from modified intervals to the set of pre-existing positions inside them More...

Interval2Positions	modified_i2p_new () const
	return a map from modified intervals to the set of "new" positions inside them that were not present in the original Pose More...

Interval2Positions	modified_i2p_defined () const
	return a map from modified intervals to the set of positions inside them that have defined conformation More...

Interval2Positions	modified_i2p_undefined () const
	return a map from modified intervals to the set of positions inside them that have undefined conformation More...

Interval2MoveMap	modified_interval2movemap () const
	return a map from modified intervals to their individual movemaps More...

Interval2Positions	original_i2p_kept () const
	return a map from original intervals to the set of positions inside them that will be kept by the BuildInstructions More...

Interval2Positions	original_i2p_deleted () const
	return a map from original intervals to the set of positions inside them that will be deleted by the BuildInstructions More...

Private Types
typedef utility::pointer::ReferenceCount	Super

Private Member Functions
BIOPIterator	find_instruction (BuildInstructionCOP u)
	find the given instruction More...

BIOPConstIterator	find_instruction (BuildInstructionCOP u) const
	find the given instruction More...

DependencyEdges::iterator	find_dependency (BuildInstructionCOP u, BuildInstructionCOP v)
	find the given dependency More...

DependencyEdges::const_iterator	find_dependency (BuildInstructionCOP u, BuildInstructionCOP v) const
	find the given dependency More...

void	reconstruct_dependencies (DependencyEdges const &dependency_list)
	clear the current dependency list and reconstruct the dependencies using the given list More...

Private Attributes
BuildInstructionOPs	instructions_
	the list of BuildInstructions to apply More...

DependencyEdges	instruction_dependencies_
	list recording BuildInstruction inter-dependencies by index into instructions_ array More...

Original2Modified	original2modified_
	map translation old residue -> new residue for non-modified regions only More...

SequenceMappingOP	seqmap_
	SequenceMapping consistent with the old -> new mapping from the most recent modify() call. More...

bool	modify_was_successful_
	indicates modify() has been called and succeeded More...

Detailed Description

a container for managing BuildInstructions

Note: Compatibility checks wrt dependencies currently do not exist. It remains to be seen how to handle this.

Definition at line 55 of file BuildManager.hh.

Member Typedef Documentation

typedef BuildInstructionOPs::const_iterator protocols::forge::build::BuildManager::BIOPConstIterator

Definition at line 78 of file BuildManager.hh.

typedef BuildInstructionOPs::iterator protocols::forge::build::BuildManager::BIOPIterator

Definition at line 77 of file BuildManager.hh.

typedef utility::vector1< BuildInstructionOP > protocols::forge::build::BuildManager::BuildInstructionOPs

Definition at line 76 of file BuildManager.hh.

typedef std::pair< Size, Size > protocols::forge::build::BuildManager::DependencyEdge

Definition at line 79 of file BuildManager.hh.

typedef utility::vector1< DependencyEdge > protocols::forge::build::BuildManager::DependencyEdges

Definition at line 80 of file BuildManager.hh.

typedef std::map< Interval, Interval > protocols::forge::build::BuildManager::Interval2Interval

Definition at line 85 of file BuildManager.hh.

typedef std::map< Interval, MoveMap > protocols::forge::build::BuildManager::Interval2MoveMap

Definition at line 86 of file BuildManager.hh.

typedef std::map< Interval, Positions > protocols::forge::build::BuildManager::Interval2Positions

Definition at line 84 of file BuildManager.hh.

typedef std::map< Size, Size > protocols::forge::build::BuildManager::Modified2Original

Definition at line 83 of file BuildManager.hh.

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

Definition at line 68 of file BuildManager.hh.

typedef core::kinematics::MoveMapOP protocols::forge::build::BuildManager::MoveMapOP

Definition at line 69 of file BuildManager.hh.

typedef std::map< Size, Size > protocols::forge::build::BuildManager::Original2Modified

Definition at line 82 of file BuildManager.hh.

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

Definition at line 70 of file BuildManager.hh.

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

Definition at line 81 of file BuildManager.hh.

typedef core::id::SequenceMapping protocols::forge::build::BuildManager::SequenceMapping

Definition at line 72 of file BuildManager.hh.

typedef core::id::SequenceMappingCOP protocols::forge::build::BuildManager::SequenceMappingCOP

Definition at line 74 of file BuildManager.hh.

typedef core::id::SequenceMappingOP protocols::forge::build::BuildManager::SequenceMappingOP

Definition at line 73 of file BuildManager.hh.

typedef core::Size protocols::forge::build::BuildManager::Size

Definition at line 67 of file BuildManager.hh.

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

Definition at line 88 of file BuildManager.hh.

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

private

Definition at line 61 of file BuildManager.hh.

Constructor & Destructor Documentation

protocols::forge::build::BuildManager::BuildManager ( )

default constructor

Definition at line 71 of file BuildManager.cc.

Referenced by clone(), and create().

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

copy constructor

Definition at line 78 of file BuildManager.cc.

References add(), begin(), end(), instruction_dependencies_, and reconstruct_dependencies().

protocols::forge::build::BuildManager::~BuildManager ( )

virtual

default destructor

Definition at line 95 of file BuildManager.cc.

Member Function Documentation

void protocols::forge::build::BuildManager::add ( BuildInstructionOP bi)

add an instruction directly (no copy)

Definition at line 146 of file BuildManager.cc.

References instructions_.

Referenced by protocols::fldsgn::BluePrintBDR::add_instruction(), protocols::forge::components::BDR::add_instruction(), BuildManager(), and operator=().

BIOPConstIterator protocols::forge::build::BuildManager::begin ( ) const

inline

const iterator pointing to the first instruction

Definition at line 162 of file BuildManager.hh.

References instructions_.

Referenced by protocols::forge::components::VarLengthBuild::apply(), BuildManager(), compatibility_check(), defined_positions(), intervals(), intervals_containing_defined_positions(), intervals_containing_new_positions(), intervals_containing_preexisting_positions(), intervals_containing_undefined_positions(), intervals_without_valid_original_equivalents(), modified2original_interval_endpoints(), modified2original_intervals(), modified_i2p_defined(), modified_i2p_new(), modified_i2p_preexisting(), modified_i2p_undefined(), modified_interval2movemap(), modify(), movemap_as_OP(), new_positions(), operator=(), original2modified_interval_endpoints(), original2modified_intervals(), original_deleted_positions(), original_i2p_deleted(), original_i2p_kept(), original_intervals_containing_deleted_positions(), original_intervals_containing_kept_positions(), original_kept_positions(), positions(), preexisting_positions(), undefined_positions(), and union_of_intervals_containing_undefined_positions().

void protocols::forge::build::BuildManager::clear ( )

clear all instructions

Definition at line 158 of file BuildManager.cc.

References instruction_dependencies_, and instructions_.

Referenced by operator=().

BuildManager::Size protocols::forge::build::BuildManager::clear_dependencies ( )

clear all dependencies

Returns: number of dependencies dropped

Definition at line 188 of file BuildManager.cc.

References instruction_dependencies_, and instructions_.

Referenced by reconstruct_dependencies().

BuildManagerOP protocols::forge::build::BuildManager::clone ( ) const

virtual

clone this object

Definition at line 122 of file BuildManager.cc.

References BuildManager().

bool protocols::forge::build::BuildManager::compatibility_check ( ) const

check if instruction regions are compatible with each other

Returns: true if regions compatible, false if regions incompatible

Definition at line 431 of file BuildManager.cc.

References begin(), and end().

Referenced by modify().

BuildManagerOP protocols::forge::build::BuildManager::create ( ) const

virtual

create a new instance of this type of object

Definition at line 128 of file BuildManager.cc.

References BuildManager().

void protocols::forge::build::BuildManager::create_directed_dependency	(	BuildInstructionOP	u,
		BuildInstructionOP	v
	)

create a directed dependency: instruction 'u' must complete before instruction 'v' can complete, i.e. 'v' depends on 'u'

Definition at line 166 of file BuildManager.cc.

References core::kinematics::distance(), find_instruction(), instruction_dependencies_, and instructions_.

Referenced by protocols::fldsgn::BluePrintBDR::create_directed_dependency(), protocols::forge::components::BDR::create_directed_dependency(), and reconstruct_dependencies().

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

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

Returns: If modify() has not been called will return an empty set.

Definition at line 808 of file BuildManager.cc.

References begin(), end(), and modify_was_successful_.

bool protocols::forge::build::BuildManager::dependencies_exist ( ) const

inline

have dependencies been defined?

Definition at line 192 of file BuildManager.hh.

References instruction_dependencies_.

BuildManager::Size protocols::forge::build::BuildManager::dummy_modify ( Size const nres)

a dry run of modify() with an all-ala helical Pose of the given length

Parameters

[in] nres The length of the dummy structure to use.

Returns: The final length of the modified Pose.

Remarks: Use this to do a fake run of modify() if you need any position or mapping information prior to actually calling modify().

Definition at line 400 of file BuildManager.cc.

References instructions_, core::pose::make_pose_from_sequence(), and modify().

bool protocols::forge::build::BuildManager::empty ( ) const

inline

no instructions?

Definition at line 155 of file BuildManager.hh.

References instructions_.

Referenced by protocols::forge::components::VarLengthBuild::apply().

BIOPConstIterator protocols::forge::build::BuildManager::end ( ) const

inline

const iterator pointing just beyond the last instruction

Definition at line 169 of file BuildManager.hh.

References instructions_.

Referenced by BuildManager(), compatibility_check(), defined_positions(), intervals(), intervals_containing_defined_positions(), intervals_containing_new_positions(), intervals_containing_preexisting_positions(), intervals_containing_undefined_positions(), intervals_without_valid_original_equivalents(), modified2original_interval_endpoints(), modified2original_intervals(), modified_i2p_defined(), modified_i2p_new(), modified_i2p_preexisting(), modified_i2p_undefined(), modified_interval2movemap(), modify(), movemap_as_OP(), new_positions(), operator=(), original2modified_interval_endpoints(), original2modified_intervals(), original_deleted_positions(), original_i2p_deleted(), original_i2p_kept(), original_intervals_containing_deleted_positions(), original_intervals_containing_kept_positions(), original_kept_positions(), positions(), preexisting_positions(), undefined_positions(), and union_of_intervals_containing_undefined_positions().

BuildManager::DependencyEdges::iterator protocols::forge::build::BuildManager::find_dependency	(	BuildInstructionCOP	u,
		BuildInstructionCOP	v
	)

private

find the given dependency

find the edge specifying the given dependency

Returns: iterator pointing to the DependencyEdge if found, otherwise the 'end' iterator

Definition at line 1043 of file BuildManager.cc.

References instruction_dependencies_, and instructions_.

BuildManager::DependencyEdges::const_iterator protocols::forge::build::BuildManager::find_dependency	(	BuildInstructionCOP	u,
		BuildInstructionCOP	v
	)		const

private

find the given dependency

Returns: const iterator pointing to the DependencyEdge if found, otherwise the 'end' const iterator

Definition at line 1057 of file BuildManager.cc.

References instruction_dependencies_, and instructions_.

BuildManager::BIOPIterator protocols::forge::build::BuildManager::find_instruction ( BuildInstructionCOP u)

private

find the given instruction

Returns: iterator pointing to the BuildInstructionOP if found, otherwise the 'end' iterator

Definition at line 1027 of file BuildManager.cc.

References instructions_.

Referenced by create_directed_dependency().

BuildManager::BIOPConstIterator protocols::forge::build::BuildManager::find_instruction ( BuildInstructionCOP u) const

private

find the given instruction

Returns: iterator pointing to the BuildInstructionCOP if found, otherwise the 'end' iterator

Definition at line 1035 of file BuildManager.cc.

References instructions_.

std::set< Interval > protocols::forge::build::BuildManager::intervals ( ) const

return all modified intervals

Remarks: Since this encompasses everything this is typically not useful except for overall tracking purposes.

Returns: If modify() has not been called will return an empty set.

Definition at line 586 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), and modify_was_successful_.

Referenced by intervals_containing_defined_positions(), intervals_containing_new_positions(), intervals_containing_preexisting_positions(), intervals_containing_undefined_positions(), intervals_without_valid_original_equivalents(), original_intervals_containing_deleted_positions(), and original_intervals_containing_kept_positions().

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_defined_positions ( ) const

return all intervals containing positions with defined conformation

Returns: If modify() has not been called will return an empty set.

Definition at line 672 of file BuildManager.cc.

References begin(), protocols::forge::build::BuildInstruction::defined_positions(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), and modify_was_successful_.

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_new_positions ( ) const

return all intervals containing positions that are "new" and did not exist in the original Pose

Returns: If modify() has not been called will return an empty set.

Definition at line 652 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), modify_was_successful_, and protocols::forge::build::BuildInstruction::new_positions().

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_preexisting_positions ( ) const

return all intervals containing positions that were pre-existing in the original Pose prior to calling modify()

Returns: If modify() has not been called will return an empty set.

Definition at line 631 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), modify_was_successful_, and protocols::forge::build::BuildInstruction::preexisting_positions().

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_undefined_positions ( ) const

return all intervals containing positions with undefined conformation

Remarks: typically used to define intervals appropriate for loop modeling

Returns: If modify() has not been called will return an empty set.

Definition at line 693 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), modify_was_successful_, and protocols::forge::build::BuildInstruction::undefined_positions().

Referenced by protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), and protocols::forge::remodel::RemodelMover::design_refine_seq_relax().

std::set< Interval > protocols::forge::build::BuildManager::intervals_without_valid_original_equivalents ( ) const

return modified intervals that have no equivalent original interval in their BuildInstructions (original_interval_valid() = false)

Remarks: This is for cases such as insertions where there is no equivalent original region.

Returns: If modify() has not been called will return an empty set.

Definition at line 607 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), modify_was_successful_, and protocols::forge::build::BuildInstruction::original_interval_valid().

BuildManager::Modified2Original protocols::forge::build::BuildManager::modified2original_interval_endpoints ( ) const

return a map translating modified interval endpoints to original interval endpoints

Remarks: modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map

Returns: map; empty if modify() has not yet been called

Remarks: modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map

Definition at line 561 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::Interval::left, modify_was_successful_, protocols::forge::build::BuildInstruction::original_interval(), protocols::forge::build::BuildInstruction::original_interval_valid(), and protocols::forge::build::Interval::right.

BuildManager::Interval2Interval protocols::forge::build::BuildManager::modified2original_intervals ( ) const

return a map translating modified intervals to original intervals

Remarks: modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map

Returns: map; empty if modify() has not yet been called

Definition at line 537 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, protocols::forge::build::BuildInstruction::original_interval(), and protocols::forge::build::BuildInstruction::original_interval_valid().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::modified_i2p_defined ( ) const

return a map from modified intervals to the set of positions inside them that have defined conformation

Returns: If modify() has not been called will return an empty map.

Definition at line 941 of file BuildManager.cc.

References begin(), protocols::forge::build::BuildInstruction::defined_positions(), end(), protocols::forge::build::BuildInstruction::interval(), and modify_was_successful_.

BuildManager::Interval2Positions protocols::forge::build::BuildManager::modified_i2p_new ( ) const

return a map from modified intervals to the set of "new" positions inside them that were not present in the original Pose

Returns: If modify() has not been called will return an empty map.

Definition at line 922 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, and protocols::forge::build::BuildInstruction::new_positions().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::modified_i2p_preexisting ( ) const

return a map from modified intervals to the set of pre-existing positions inside them

Returns: If modify() has not been called will return an empty map.

Definition at line 903 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, and protocols::forge::build::BuildInstruction::preexisting_positions().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::modified_i2p_undefined ( ) const

return a map from modified intervals to the set of positions inside them that have undefined conformation

Returns: If modify() has not been called will return an empty map.

Definition at line 960 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, and protocols::forge::build::BuildInstruction::undefined_positions().

BuildManager::Interval2MoveMap protocols::forge::build::BuildManager::modified_interval2movemap ( ) const

return a map from modified intervals to their individual movemaps

Returns: If modify() has not been called will return an empty map.

Definition at line 978 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, and protocols::forge::build::BuildInstruction::movemap().

BuildManager::Original2Modified protocols::forge::build::BuildManager::modify ( Pose & pose)

modify the pose using the instructions in this container

Parameters

[in,out] pose the Pose to modify

Returns: a map translating original residue -> modified residue for positions that existed within both the original Pose and modified Pose

Definition at line 207 of file BuildManager.cc.

References core::chemical::aa_vrt, protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_jump(), begin(), protocols::forge::methods::closed_range(), compatibility_check(), core::conformation::ResidueFactory::create_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, end(), core::pose::Pose::fold_tree(), core::conformation::get_anchor_atomno(), instructions_, protocols::forge::methods::make_star_foldtree(), protocols::forge::build::BuildInstruction::modify(), protocols::forge::build::BuildInstruction::modify_was_successful(), modify_was_successful_, core::pose::Pose::n_residue(), core::chemical::ResidueTypeSet::name_map(), protocols::forge::build::BuildInstruction::new_positions(), original2modified_, original2modified_interval_endpoints(), protocols::forge::build::BuildInstruction::original_deleted_positions(), reset_accounting(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), seqmap_, core::pose::Pose::total_residue(), and protocols::forge::build::TR().

Referenced by protocols::forge::components::VarLengthBuild::apply(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), and dummy_modify().

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

return the combined movemap from all instructions in this manager

Returns: If modify() has not been called will return an empty MoveMap.

Definition at line 445 of file BuildManager.cc.

References movemap_as_OP().

Referenced by protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::forge::remodel::RemodelMover::confirm_sequence(), and protocols::forge::remodel::RemodelMover::design_refine().

BuildManager::MoveMapOP protocols::forge::build::BuildManager::movemap_as_OP ( ) const

Definition at line 449 of file BuildManager.cc.

References begin(), end(), and modify_was_successful_.

Referenced by protocols::forge::components::BDR::design_refine(), and movemap().

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

inline

the number of dependencies currently defined (i.e. # of edges in the dependency graph)

Definition at line 185 of file BuildManager.hh.

References instruction_dependencies_.

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

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

Returns: If modify() has not been called will return an empty set.

Definition at line 789 of file BuildManager.cc.

References begin(), end(), and modify_was_successful_.

Referenced by protocols::forge::components::VarLengthBuild::centroid_build(), and protocols::forge::components::BDR::design_refine().

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

copy assignment

Definition at line 99 of file BuildManager.cc.

References add(), begin(), clear(), end(), instruction_dependencies_, modify_was_successful_, original2modified_, reconstruct_dependencies(), and seqmap_.

BuildManager::Original2Modified const & protocols::forge::build::BuildManager::original2modified ( ) const

return a map translating original residue -> modified residue for positions that existed within both the original Pose and modified Pose

Returns: map; empty if modify() has not yet been called

Definition at line 478 of file BuildManager.cc.

References original2modified_.

Referenced by protocols::forge::components::VarLengthBuild::apply(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), and protocols::forge::components::VarLengthBuild::centroid_build().

BuildManager::Original2Modified protocols::forge::build::BuildManager::original2modified_interval_endpoints ( ) const

return a map translating original interval endpoints to modified interval endpoints

Remarks: modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map

Returns: map; empty if modify() has not yet been called

Definition at line 512 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::Interval::left, modify_was_successful_, protocols::forge::build::BuildInstruction::original_interval(), protocols::forge::build::BuildInstruction::original_interval_valid(), and protocols::forge::build::Interval::right.

Referenced by protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), and modify().

BuildManager::Interval2Interval protocols::forge::build::BuildManager::original2modified_intervals ( ) const

return a map translating original intervals to modified intervals

Remarks: modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map

Returns: map; empty if modify() has not yet been called

Remarks: modified intervals with no equivalent original intervals (e.g. cases such as insertions) will not appear in this map

Returns: map; empty if modify() has not yet been called

Definition at line 487 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, protocols::forge::build::BuildInstruction::original_interval(), and protocols::forge::build::BuildInstruction::original_interval_valid().

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

return set of positions within the original intervals that will be deleted by the BuildInstructions

Remarks: returns valid data even without calling modify()

Definition at line 888 of file BuildManager.cc.

References begin(), and end().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::original_i2p_deleted ( ) const

return a map from original intervals to the set of positions inside them that will be deleted by the BuildInstructions

Remarks: returns valid data even without calling modify()

Definition at line 1012 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::original_deleted_positions(), and protocols::forge::build::BuildInstruction::original_interval().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::original_i2p_kept ( ) const

return a map from original intervals to the set of positions inside them that will be kept by the BuildInstructions

Remarks: returns valid data even without calling modify()

Definition at line 997 of file BuildManager.cc.

References begin(), end(), protocols::forge::build::BuildInstruction::original_interval(), and protocols::forge::build::BuildInstruction::original_kept_positions().

std::set< Interval > protocols::forge::build::BuildManager::original_intervals_containing_deleted_positions ( ) const

return all original intervals containing positions that will be deleted by the BuildInstructions

Remarks: returns valid data even without calling modify()

Definition at line 731 of file BuildManager.cc.

References begin(), end(), intervals(), protocols::forge::build::BuildInstruction::original_deleted_positions(), and protocols::forge::build::BuildInstruction::original_interval().

std::set< Interval > protocols::forge::build::BuildManager::original_intervals_containing_kept_positions ( ) const

return all original intervals containing positions that will be kept by the BuildInstructions

Remarks: returns valid data even without calling modify()

Definition at line 714 of file BuildManager.cc.

References begin(), end(), intervals(), protocols::forge::build::BuildInstruction::original_interval(), and protocols::forge::build::BuildInstruction::original_kept_positions().

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

return the set of positions within the original intervals that will be kept by the BuildInstructions

Remarks: returns valid data even without calling modify()

Definition at line 873 of file BuildManager.cc.

References begin(), and end().

BuildManager::Positions protocols::forge::build::BuildManager::positions ( ) const

return all positions within the modified intervals

Remarks: Since this encompasses everything this is typically not useful except for overall tracking purposes.

Returns: If modify() has not been called will return an empty set.

Definition at line 749 of file BuildManager.cc.

References begin(), end(), protocols::forge::methods::insert_closed_range(), protocols::forge::build::Interval::left, modify_was_successful_, and protocols::forge::build::Interval::right.

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

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

Returns: If modify() has not been called will return an empty set.

Definition at line 770 of file BuildManager.cc.

References begin(), end(), and modify_was_successful_.

void protocols::forge::build::BuildManager::reconstruct_dependencies ( DependencyEdges const & dependency_list)

private

clear the current dependency list and reconstruct the dependencies using the given list

Definition at line 1070 of file BuildManager.cc.

References clear_dependencies(), create_directed_dependency(), and instructions_.

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

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

reset all accounting info (intervals, positions, etc) to initial state

Definition at line 135 of file BuildManager.cc.

References instructions_, modify_was_successful_, original2modified_, and seqmap_.

Referenced by modify().

BuildManager::SequenceMappingCOP protocols::forge::build::BuildManager::sequence_mapping ( ) const

SequenceMapping consistent with the original -> modified mapping from the most recent modify() call.

Returns: valid Sequence mapping if modify() was called; otherwise returns NULL

Remarks: This mapping contains the same information as original2modified() combined with original2modified_interval_endpoints().

Definition at line 470 of file BuildManager.cc.

References seqmap_.

Size protocols::forge::build::BuildManager::size ( ) const

inline

current number of instructions

Definition at line 148 of file BuildManager.hh.

References instructions_.

Referenced by protocols::fldsgn::BluePrintBDR::instruction_size().

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

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

Returns: If modify() has not been called will return an empty set.

Definition at line 827 of file BuildManager.cc.

References begin(), end(), and modify_was_successful_.

BuildManager::Positions protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions ( ) const

the positions representing the union of all intervals containing positions with undefined conformation

Remarks: Useful as a reference for defining neighborhoods around loop modeled regions.

Returns: If modify() has not been called will return an empty set.

Definition at line 848 of file BuildManager.cc.

References begin(), end(), protocols::forge::methods::insert_closed_range(), protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::Interval::left, modify_was_successful_, protocols::forge::build::Interval::right, and protocols::forge::build::BuildInstruction::undefined_positions().

Referenced by protocols::forge::components::BDR::apply(), protocols::forge::remodel::RemodelMover::apply(), and protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover().

Member Data Documentation

DependencyEdges protocols::forge::build::BuildManager::instruction_dependencies_

private

list recording BuildInstruction inter-dependencies by index into instructions_ array

Remarks: For each pair "first,second" in the list, the instruction with index "first" must complete before the instruction with index "second" I.e. "second" depends on "first".

Definition at line 491 of file BuildManager.hh.

Referenced by BuildManager(), clear(), clear_dependencies(), create_directed_dependency(), dependencies_exist(), find_dependency(), n_dependencies(), and operator=().