insert an external segment flanked by new regions More...

#include <SegmentInsert.hh>

Inheritance diagram for protocols::forge::build::SegmentInsert:

Collaboration diagram for protocols::forge::build::SegmentInsert:

Public Types
typedef Super::Size	Size

typedef Super::Real	Real

typedef Super::ResidueTypeSetCAP	ResidueTypeSetCAP

typedef Super::LengthEvent	LengthEvent

typedef Super::MoveMap	MoveMap

typedef Super::Pose	Pose

typedef Super::Positions	Positions

typedef Super::String	String

Public Types inherited from protocols::forge::build::BuildInstruction
typedef core::Size	Size

typedef core::Real	Real

typedef core::chemical::ResidueTypeSet	ResidueTypeSet

typedef core::chemical::ResidueTypeSetCAP	ResidueTypeSetCAP

typedef core::conformation::signals::LengthEvent	LengthEvent

typedef core::kinematics::MoveMap	MoveMap

typedef core::pose::Pose	Pose

typedef utility::vector1 < BuildInstructionCAP >	BuildInstructionCAPs

typedef utility::signals::Link	Link

typedef std::set< Size >	Positions

typedef std::string	String

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

	SegmentInsert (Interval const &i, String const &ss, Pose const &insert, bool const keep_known_bb_torsions_at_junctions=false, SegmentInsertConnectionScheme::Enum connection_scheme=SegmentInsertConnectionScheme::RANDOM_SIDE)
	sec.struct only constructor (poly-ala for flanking regions) More...

	SegmentInsert (Interval const &i, String const &ss, String const &aa, Pose const &insert, bool const keep_known_bb_torsions_at_junctions=false, SegmentInsertConnectionScheme::Enum connection_scheme=SegmentInsertConnectionScheme::RANDOM_SIDE)
	sec.struct + aa constructor More...

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

virtual	~SegmentInsert ()
	default destructor More...

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

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

bool	performing_pure_insertion () const
	performing a pure insertion/extension? More...

bool	keep_known_bb_torsions_at_junctions () const
	Attempt to keep the phi at original_interval().left and the psi+omega at original_interval().right present from the original Pose in the modified Pose? Not applicable for pure insertions. Default False. More...

Pose const &	insert_pose () const
	the pose to insert More...

String const &	ss () const
	get secondary structure string (includes insertion point as '^') More...

String const &	aa () const
	get annotated amino acid string (includes insertion point as '^') More...

SegmentInsertConnectionScheme::Enum	insert_connection_scheme () const
	get the insert connection scheme – whether the insertion will be glued on the N-side, C-side, or if SegmentInsert will pick randomly between the two More...

Size	insertion_point_absolute_index () const
	get the absolute index of the insertion point with respect to the flanking regions (i.e. the index inside the ss string) More...

Size	insertion_start_residue () const
	get the residue at the start of the insertion relative to the modified interval (flanking positions are not part of the insertion!) More...

Size	insertion_end_residue () const
	get the residue at the end of the insertion relative to the modified interval (flanking positions are not part of the insertion!) More...

Size	flanking_left_nres () const
	get the number of flanking residues to the left of the insertion point More...

Size	flanking_right_nres () const
	get the number of flanking residues to the right of the insertion point More...

String	flanking_left_ss () const
	get the ss string of the flanking residues to the left of the insertion point More...

String	flanking_right_ss () const
	get the ss string of the flanking residues to the right of the insertion point More...

String	flanking_left_aa () const
	get the annotated aa string of the flanking residues to the left of the insertion point More...

String	flanking_right_aa () const
	get the annotated aa string of the flanking residues to the right of the insertion point More...

MoveMap const &	insert_pose_torsion_override_movemap () const
	a torsion (bb/chi) specific override movemap indexed wrt the insert Pose (residue indices may only be within the range [1, insert_pose.n_residue()] More...

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

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

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

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

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

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

virtual MoveMap	movemap () const
	return a copy of the MoveMap that defines the moveable/fixed positions/dofs for this instruction More...

void	insert_pose_torsion_override_movemap (MoveMap const &mm)
	set a torsion (bb/chi) specific override movemap indexed wrt the insert Pose (residue indices may only be within the range [1, insert_pose.n_residue()] More...

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

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

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

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

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

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

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

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

Public Member Functions inherited from protocols::forge::build::BuildInstruction
	BuildInstruction ()
	default constructor More...

	BuildInstruction (Interval const &i, ResidueTypeSetCAP rts=core::chemical::ChemicalManager::get_instance() ->residue_type_set(core::chemical::FA_STANDARD))
	interval constructor More...

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

virtual	~BuildInstruction ()
	default destructor More...

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

BuildInstructionState::Enum	modify (Pose &pose)
	modify this pose More...

BuildInstructionState::Enum	state () const
	return the state of this BuildInstruction More...

bool	ready () const
	Is the BuildInstruction's state at READY? More...

bool	waiting_on_dependencies () const
	Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES? More...

bool	modify_was_successful () const
	Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL? More...

void	attach_to (Pose &pose)
	attach to a Pose's conformation More...

void	detach_from ()
	detach from a Pose's conformation More...

void	on_length_change (LengthEvent const &event)
	update any indexing wrt length change to Pose/Conformation being watched More...

bool	detach_after_modify () const
	detach after modify()? More...

Interval const &	original_interval () const
	return original residue range of this instruction More...

ResidueTypeSet const &	residue_type_set () const
	the residue type set being used More...

bool	has_dependencies () const
	does this BuildInstruction have dependencies? More...

Size	n_dependencies () const
	the number of dependencies this BuildInstruction has More...

BuildInstructionCAPs const &	dependencies () const
	the list of instructions whose modify() must complete before the modify() for this instruction may be called successfully More...

void	detach_after_modify (bool const flag)
	set detach after modify() More...

void	reset_accounting ()
	reset intervals, positions, etc to initial state and drop observers. State set to READY. More...

virtual void	add_dependency_to (BuildInstructionCAP i)
	add an instruction to this BuildInstruction's dependency list More...

virtual bool	dependent_on (BuildInstructionCAP i) const
	is this instruction dependent upon the given instruction? More...

void	clear_dependencies ()
	clear the list of dependencies More...

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

Static Public Member Functions
static char	insertion_char ()
	the character representing the insertion point More...

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

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

virtual void	reset_accounting_impl ()
	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 ()
	init to be called during non-default constructors More...

Private Attributes
Interval	interval_
	the working range of residues More...

String	ss_
	secondary structure string defining the flanking regions and the insertion point More...

String	aa_
	annotated amino acid string including the insertion point More...

bool	keep_known_bb_torsions_at_junctions_
	Attempt to keep the omega at original_interval().left-1, the phi at original_interval().left and the psi+omega at original_interval().right present from the original Pose in the modified Pose? This should be false for pure insertions. More...

SegmentInsertConnectionScheme::Enum	insert_connection_scheme_
	connect insertion on its N-side, C-side, or decide randomly between the two (default RANDOM_SIDE) More...

Pose	insert_pose_
	insert this Pose More...

MoveMap	insert_pose_torsion_override_movemap_
	a torsion (bb/chi) specific override movemap indexed wrt the insert Pose (residue indices may only be within the range [1, insert_pose.n_residue()] More...

Detailed Description

insert an external segment flanked by new regions

Remarks: Similar to SegmentRebuild, but with the addition of a defined segment located in the modified region.

Definition at line 51 of file SegmentInsert.hh.

Member Typedef Documentation

typedef Super::LengthEvent protocols::forge::build::SegmentInsert::LengthEvent

Definition at line 67 of file SegmentInsert.hh.

typedef Super::MoveMap protocols::forge::build::SegmentInsert::MoveMap

Definition at line 68 of file SegmentInsert.hh.

typedef Super::Pose protocols::forge::build::SegmentInsert::Pose

Definition at line 69 of file SegmentInsert.hh.

typedef Super::Positions protocols::forge::build::SegmentInsert::Positions

Definition at line 71 of file SegmentInsert.hh.

typedef Super::Real protocols::forge::build::SegmentInsert::Real

Definition at line 64 of file SegmentInsert.hh.

typedef Super::ResidueTypeSetCAP protocols::forge::build::SegmentInsert::ResidueTypeSetCAP

Definition at line 66 of file SegmentInsert.hh.

typedef Super::Size protocols::forge::build::SegmentInsert::Size

Definition at line 63 of file SegmentInsert.hh.

typedef Super::String protocols::forge::build::SegmentInsert::String

Definition at line 72 of file SegmentInsert.hh.

typedef BuildInstruction protocols::forge::build::SegmentInsert::Super

private

Definition at line 57 of file SegmentInsert.hh.

Constructor & Destructor Documentation

protocols::forge::build::SegmentInsert::SegmentInsert ( )

default constructor

Definition at line 55 of file SegmentInsert.cc.

Referenced by clone().

protocols::forge::build::SegmentInsert::SegmentInsert	(	Interval const &	i,
		String const &	ss,
		Pose const &	insert,
		bool const	keep_known_bb_torsions_at_junctions = `false`,
		SegmentInsertConnectionScheme::Enum	connection_scheme = `SegmentInsertConnectionScheme::RANDOM_SIDE`
	)

sec.struct only constructor (poly-ala for flanking regions)

Parameters

[in]	interval	The interval between which the insert will span. To perform a pure insertion without replacing any residues within a region, use an interval with a zero as the left endpoint, e.g. [0, insert_after_this_residue]. If inserting before the first residue of the Pose then interval = [0,0]. If inserting after the last residue of the Pose then interval = [0, last_residue].
[in]	ss	The secondary structure specifying the flanking regions, with a character '^' specifying where the insert is to be placed.
[in]	insert	The Pose to insert.
[in]	keep_known_bb_torsions_at_junctions	Attempt to keep the omega at original_interval().left-1, the phi at original_interval().left, and the psi+omega at original_interval().right present from the original Pose in the modified Pose. This should be false for pure insertions.
[in]	connection_scheme	Connect insertion on its N-side, C-side, or decide randomly between the two (default RANDOM).

Definition at line 76 of file SegmentInsert.cc.

References aa_, init(), insertion_char(), keep_known_bb_torsions_at_junctions_, performing_pure_insertion(), ss_, and protocols::forge::build::TR().

protocols::forge::build::SegmentInsert::SegmentInsert	(	Interval const &	i,
		String const &	ss,
		String const &	aa,
		Pose const &	insert,
		bool const	keep_known_bb_torsions_at_junctions = `false`,
		SegmentInsertConnectionScheme::Enum	connection_scheme = `SegmentInsertConnectionScheme::RANDOM_SIDE`
	)

sec.struct + aa constructor

Parameters

[in]	interval	The interval between which the insert will span. To perform a pure insertion without replacing any residues within a region, use an interval with a zero as the left endpoint, e.g. [0, insert_after_this_residue]. If inserting before the first residue of the Pose then interval = [0,0]. If inserting after the last residue of the Pose then interval = [0, last_residue].
[in]	ss	The secondary structure specifying the flanking regions, with a character '^' specifying where the insert is to be placed.
[in]	aa	The annotated amino acid string specifying the flanking regions, with a character '^' specifying where the insert is to be placed.
[in]	insert	The Pose to insert.
[in]	keep_known_bb_torsions_at_junctions	Attempt to keep the omega at original_interval().left-1, the phi at original_interval().left, and the psi+omega at original_interval().right present from the original Pose in the modified Pose. This should be false for pure insertions.
[in]	connection_scheme	Connect insertion on its N-side, C-side, or decide randomly between the two (default RANDOM).

Remarks: length of the one-letter aa must equal the length of ss

Definition at line 129 of file SegmentInsert.cc.

References aa_, core::pose::annotated_to_oneletter_sequence(), init(), insertion_char(), keep_known_bb_torsions_at_junctions_, performing_pure_insertion(), ss_, and protocols::forge::build::TR().

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

copy constructor

Definition at line 174 of file SegmentInsert.cc.

protocols::forge::build::SegmentInsert::~SegmentInsert ( )

virtual

default destructor

Definition at line 186 of file SegmentInsert.cc.

Member Function Documentation

String const& protocols::forge::build::SegmentInsert::aa ( ) const

inline

get annotated amino acid string (includes insertion point as '^')

Definition at line 204 of file SegmentInsert.hh.

References aa_.

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

virtual

clone this object

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

Definition at line 207 of file SegmentInsert.cc.

References SegmentInsert().

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

inlinevirtual

does this object create undefined backbone in the modified region?

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

Definition at line 403 of file SegmentInsert.hh.

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

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.

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

Definition at line 315 of file SegmentInsert.cc.

References protocols::forge::methods::closed_range(), insertion_end_residue(), and insertion_start_residue().

virtual bool protocols::forge::build::SegmentInsert::dependencies_satisfied ( ) const

inlineprotectedvirtual

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

Returns: always True, this BuildInstruction has no dependencies

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

Definition at line 416 of file SegmentInsert.hh.

SegmentInsert::String protocols::forge::build::SegmentInsert::flanking_left_aa ( ) const

get the annotated aa string of the flanking residues to the left of the insertion point

Definition at line 272 of file SegmentInsert.cc.

References aa_, and insertion_char().

Referenced by modify_impl().

SegmentInsert::Size protocols::forge::build::SegmentInsert::flanking_left_nres ( ) const

get the number of flanking residues to the left of the insertion point

Definition at line 244 of file SegmentInsert.cc.

References insertion_char(), and ss_.

Referenced by modify_impl().

SegmentInsert::String protocols::forge::build::SegmentInsert::flanking_left_ss ( ) const

get the ss string of the flanking residues to the left of the insertion point

Definition at line 258 of file SegmentInsert.cc.

References insertion_char(), and ss_.

Referenced by modify_impl().

SegmentInsert::String protocols::forge::build::SegmentInsert::flanking_right_aa ( ) const

get the annotated aa string of the flanking residues to the right of the insertion point

Definition at line 279 of file SegmentInsert.cc.

References aa_, and insertion_char().

Referenced by modify_impl().

SegmentInsert::Size protocols::forge::build::SegmentInsert::flanking_right_nres ( ) const

get the number of flanking residues to the right of the insertion point

Definition at line 251 of file SegmentInsert.cc.

References insertion_char(), and ss_.

Referenced by modify_impl().

SegmentInsert::String protocols::forge::build::SegmentInsert::flanking_right_ss ( ) const

get the ss string of the flanking residues to the right of the insertion point

Definition at line 265 of file SegmentInsert.cc.

References insertion_char(), and ss_.

Referenced by modify_impl().

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

private

init to be called during non-default constructors

Definition at line 1196 of file SegmentInsert.cc.

References core::pose::Pose::conformation(), insert_pose_, core::conformation::Residue::is_lower_terminus(), core::pose::Pose::n_residue(), core::conformation::remove_lower_terminus_type_from_conformation_residue(), core::conformation::remove_upper_terminus_type_from_conformation_residue(), and core::pose::Pose::residue().

Referenced by SegmentInsert().

SegmentInsertConnectionScheme::Enum protocols::forge::build::SegmentInsert::insert_connection_scheme ( ) const

inline

get the insert connection scheme – whether the insertion will be glued on the N-side, C-side, or if SegmentInsert will pick randomly between the two

Definition at line 213 of file SegmentInsert.hh.

References insert_connection_scheme_.

Referenced by modify_impl().

SegmentInsert::Pose const & protocols::forge::build::SegmentInsert::insert_pose ( ) const

the pose to insert

Definition at line 213 of file SegmentInsert.cc.

References insert_pose_.

MoveMap const& protocols::forge::build::SegmentInsert::insert_pose_torsion_override_movemap ( ) const

inline

a torsion (bb/chi) specific override movemap indexed wrt the insert Pose (residue indices may only be within the range [1, insert_pose.n_residue()]

Remarks: When generating the movemap(), this torsion movemap will be enforced. Only explicit settings of TorsionType, MoveMapTorsionID, and TorsionID will be honored. Implicit false settings are ignored.

Definition at line 269 of file SegmentInsert.hh.

References insert_pose_torsion_override_movemap_.

Referenced by movemap().

void protocols::forge::build::SegmentInsert::insert_pose_torsion_override_movemap ( MoveMap const & mm)

set a torsion (bb/chi) specific override movemap indexed wrt the insert Pose (residue indices may only be within the range [1, insert_pose.n_residue()]

Remarks: When generating the movemap(), this torsion movemap will be enforced. Only explicit settings of TorsionType, MoveMapTorsionID, and TorsionID will be honored. Implicit false settings are ignored.

Definition at line 444 of file SegmentInsert.cc.

References core::id::BB, core::id::CHI, insert_pose_, insert_pose_torsion_override_movemap_, core::kinematics::MoveMap::movemap_torsion_id_begin(), core::kinematics::MoveMap::movemap_torsion_id_end(), core::pose::Pose::n_residue(), core::kinematics::MoveMap::torsion_id_begin(), core::kinematics::MoveMap::torsion_id_end(), core::kinematics::MoveMap::torsion_type_begin(), core::kinematics::MoveMap::torsion_type_end(), and protocols::forge::build::TR().

static char protocols::forge::build::SegmentInsert::insertion_char ( )

inlinestatic

the character representing the insertion point

Returns: '^'

Definition at line 168 of file SegmentInsert.hh.

Referenced by flanking_left_aa(), flanking_left_nres(), flanking_left_ss(), flanking_right_aa(), flanking_right_nres(), flanking_right_ss(), insertion_end_residue(), insertion_point_absolute_index(), insertion_start_residue(), and SegmentInsert().

SegmentInsert::Size protocols::forge::build::SegmentInsert::insertion_end_residue ( ) const

get the residue at the end of the insertion relative to the modified interval (flanking positions are not part of the insertion!)

Returns: the residue position, otherwise 0 if not found

Definition at line 237 of file SegmentInsert.cc.

References insert_pose_, insertion_char(), interval(), protocols::forge::build::Interval::left, core::pose::Pose::n_residue(), and ss_.

Referenced by defined_positions(), movemap(), and undefined_positions().

SegmentInsert::Size protocols::forge::build::SegmentInsert::insertion_point_absolute_index ( ) const

get the absolute index of the insertion point with respect to the flanking regions (i.e. the index inside the ss string)

Returns: the index, otherwise std::string::npos if not found

Definition at line 221 of file SegmentInsert.cc.

References insertion_char(), and ss_.

SegmentInsert::Size protocols::forge::build::SegmentInsert::insertion_start_residue ( ) const

get the residue at the start of the insertion relative to the modified interval (flanking positions are not part of the insertion!)

Returns: the residue position, otherwise 0 if not found

Definition at line 229 of file SegmentInsert.cc.

References insertion_char(), interval(), protocols::forge::build::Interval::left, and ss_.

Referenced by defined_positions(), movemap(), and undefined_positions().

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

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.

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

Definition at line 287 of file SegmentInsert.cc.

References interval_.

Referenced by insertion_end_residue(), insertion_start_residue(), movemap(), new_positions(), and undefined_positions().

bool protocols::forge::build::SegmentInsert::keep_known_bb_torsions_at_junctions ( ) const

inline

Attempt to keep the phi at original_interval().left and the psi+omega at original_interval().right present from the original Pose in the modified Pose? Not applicable for pure insertions. Default False.

Definition at line 186 of file SegmentInsert.hh.

References keep_known_bb_torsions_at_junctions_.

void protocols::forge::build::SegmentInsert::modify_impl ( Pose & pose)

protectedvirtual

do the actual work of modifying the Pose

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

Definition at line 593 of file SegmentInsert.cc.

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

virtual

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

Returns: TO BE FILLED IN

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

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

Definition at line 346 of file SegmentInsert.cc.

References core::id::BB, insert_pose_torsion_override_movemap(), insertion_end_residue(), insertion_start_residue(), interval(), keep_known_bb_torsions_at_junctions_, protocols::forge::build::Interval::left, core::id::omega_torsion(), core::id::phi_torsion(), core::id::psi_torsion(), protocols::forge::build::Interval::right, core::kinematics::MoveMap::set(), and core::kinematics::MoveMap::set_bb().

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

virtual

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

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

Definition at line 302 of file SegmentInsert.cc.

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

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

virtual

update indexing on residue append

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

Definition at line 503 of file SegmentInsert.cc.

References interval_, protocols::forge::build::Interval::left, core::conformation::signals::LengthEvent::position, and protocols::forge::build::Interval::right.

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

virtual

update indexing on residue delete

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

Definition at line 531 of file SegmentInsert.cc.

References interval_, protocols::forge::build::Interval::left, core::conformation::signals::LengthEvent::length_change, core::conformation::signals::LengthEvent::position, and protocols::forge::build::Interval::right.

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

virtual

update indexing on residue prepend

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

Definition at line 517 of file SegmentInsert.cc.

References interval_, protocols::forge::build::Interval::left, core::conformation::signals::LengthEvent::position, and protocols::forge::build::Interval::right.

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

copy assignment

Definition at line 190 of file SegmentInsert.cc.

References aa_, insert_connection_scheme_, insert_pose_, insert_pose_torsion_override_movemap_, interval_, protocols::forge::build::BuildInstruction::operator=(), and ss_.

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

virtual

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

Returns: A set containing all positions in the open interval (original.left, original.right)

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

Definition at line 561 of file SegmentInsert.cc.

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

Referenced by original_mutable_positions().

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

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

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

Definition at line 572 of file SegmentInsert.cc.

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

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

inlinevirtual

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

Returns: always false, original interval invalid

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

Definition at line 282 of file SegmentInsert.hh.

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

virtual

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.

Definition at line 552 of file SegmentInsert.cc.

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

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.

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

Definition at line 586 of file SegmentInsert.cc.

References original_deleted_positions().

bool protocols::forge::build::SegmentInsert::performing_pure_insertion ( ) const

inline

performing a pure insertion/extension?

Returns: True if SegmentInsert was initialized with an interval whose left endpoint == 0, False otherwise.

Definition at line 177 of file SegmentInsert.hh.

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

Referenced by modify_impl(), and SegmentInsert().

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

virtual

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, there are no pre-existing positions.

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

Definition at line 295 of file SegmentInsert.cc.

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

protectedvirtual

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

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

Definition at line 1190 of file SegmentInsert.cc.

References interval_, and protocols::forge::build::BuildInstruction::original_interval().

String const& protocols::forge::build::SegmentInsert::ss ( ) const

inline

get secondary structure string (includes insertion point as '^')

Definition at line 197 of file SegmentInsert.hh.

References ss_.

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

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.

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

Definition at line 327 of file SegmentInsert.cc.

References protocols::forge::methods::insert_closed_range(), insertion_end_residue(), insertion_start_residue(), interval(), protocols::forge::build::Interval::left, and protocols::forge::build::Interval::right.

Member Data Documentation

String protocols::forge::build::SegmentInsert::aa_

private

annotated amino acid string including the insertion point

Length of the one-letter version must be equal to length of ss. The insertion point must exist in the same spot as the insertion point in secondary structure string.

Definition at line 462 of file SegmentInsert.hh.

Referenced by aa(), flanking_left_aa(), flanking_right_aa(), operator=(), and SegmentInsert().

SegmentInsertConnectionScheme::Enum protocols::forge::build::SegmentInsert::insert_connection_scheme_

private

connect insertion on its N-side, C-side, or decide randomly between the two (default RANDOM_SIDE)

Definition at line 481 of file SegmentInsert.hh.

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

Pose protocols::forge::build::SegmentInsert::insert_pose_

private

insert this Pose

Definition at line 485 of file SegmentInsert.hh.

Referenced by init(), insert_pose(), insert_pose_torsion_override_movemap(), insertion_end_residue(), modify_impl(), and operator=().

MoveMap protocols::forge::build::SegmentInsert::insert_pose_torsion_override_movemap_

private

a torsion (bb/chi) specific override movemap indexed wrt the insert Pose (residue indices may only be within the range [1, insert_pose.n_residue()]

Remarks: When generating the movemap(), this torsion movemap will be enforced. Only explicit settings of TorsionType, MoveMapTorsionID, and TorsionID will be honored. Implicit false settings are ignored.

Definition at line 493 of file SegmentInsert.hh.

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

Interval protocols::forge::build::SegmentInsert::interval_

private

the working range of residues

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

Definition at line 447 of file SegmentInsert.hh.

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

bool protocols::forge::build::SegmentInsert::keep_known_bb_torsions_at_junctions_

private

Attempt to keep the omega at original_interval().left-1, the phi at original_interval().left and the psi+omega at original_interval().right present from the original Pose in the modified Pose? This should be false for pure insertions.

If True, during modify(), will (1) set the omega of interval_.left-1 in the newly modified Pose equal to the omega of the original Pose at original_interval().left-1, (2) set the phi of interval_.left in the newly modified Pose equal to the phi of the original Pose in original_interval().right, and (3) set the psi+omega of interval_.right in the newly modified Pose equal to the original psi+omega of original_interval().right. Default False.

Definition at line 476 of file SegmentInsert.hh.

Referenced by keep_known_bb_torsions_at_junctions(), modify_impl(), movemap(), and SegmentInsert().

String protocols::forge::build::SegmentInsert::ss_

private

secondary structure string defining the flanking regions and the insertion point

The insertion point is marked as '^'. For instance, "L^LLL" means one residue to the left of the insertion point and three residues to the right of the insertion point.

Definition at line 455 of file SegmentInsert.hh.

Referenced by flanking_left_nres(), flanking_left_ss(), flanking_right_nres(), flanking_right_ss(), insertion_end_residue(), insertion_point_absolute_index(), insertion_start_residue(), operator=(), SegmentInsert(), and ss().

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

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

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