protocols::forge::build::SegmentInsert Class Reference

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

#include <SegmentInsert.hh>

Inheritance 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::chemical::ResidueTypeSetCOP	ResidueTypeSetCOP
typedef core::conformation::signals::LengthEvent	LengthEvent
typedef core::kinematics::MoveMap	MoveMap
typedef core::pose::Pose	Pose
typedef utility::vector1< BuildInstructionCAP >	BuildInstructionCAPs
typedef utility::signals::Link	Link
typedef std::set< core::Size >	Positions
typedef std::string	String

Public Member Functions
	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=protocols::forge::build::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=protocols::forge::build::SegmentInsertConnectionScheme::RANDOM_SIDE)
	sec.struct + aa constructor More...
	SegmentInsert (SegmentInsert const &rval)
	copy constructor More...
	~SegmentInsert () override
	default destructor More...
SegmentInsert &	operator= (SegmentInsert const &rval)
	copy assignment More...
BuildInstructionOP	clone () const override
	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...
core::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...
core::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...
core::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...
core::Size	flanking_left_nres () const
	get the number of flanking residues to the left of the insertion point More...
core::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.size()] More...
bool	original_interval_valid () const override
	is the original interval storing valid information, or is empty or being used for something else? More...
Interval	interval () const override
	a copy of the working range of residues specifying the modified region More...
Positions	preexisting_positions () const override
	return a copy of the set of positions within the new region that were pre-existing in the original Pose prior to modify() More...
Positions	new_positions () const override
	return a copy of the set of positions that are "new" and did not exist in the original Pose. More...
Positions	defined_positions () const override
	return a copy of the set of positions within the newly modified region that has a defined conformation. E.g. existing or copied residues. More...
Positions	undefined_positions () const override
	return a copy of the set of positions within the newly modified region that has an undefined conformation. E.g. newly created residues. More...
MoveMap	movemap () const override
	return a copy of the MoveMap that defines the moveable/fixed positions/dofs for this instruction More...
void	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.size()] More...
void	on_residue_append (LengthEvent const &event) override
	update indexing on residue append More...
void	on_residue_prepend (LengthEvent const &event) override
	update indexing on residue prepend More...
void	on_residue_delete (LengthEvent const &event) override
	update indexing on residue delete More...
Positions	original_kept_positions () const override
	return the set of positions within the original interval that will be kept in this BuildInstruction More...
Positions	original_deleted_positions () const override
	return set of positions within the original interval that will be deleted in this BuildInstruction More...
Positions	original_fixed_positions () const override
	return set of any fixed positions necessary with respect to the original interval and original Pose numbering More...
Positions	original_mutable_positions () const override
	return set of any mutable positions necessary with respect to the original interval and original Pose numbering More...
bool	creates_undefined_backbone () const override
	does this object create undefined backbone in the modified region? More...
Public Member Functions inherited from protocols::forge::build::BuildInstruction
	BuildInstruction ()
	default constructor More...
	BuildInstruction (Interval const &i, ResidueTypeSetCAP rts=core::chemical::ChemicalManager::get_instance() ->residue_type_set(core::chemical::FA_STANDARD))
	interval constructor More...
	BuildInstruction (BuildInstruction const &rval)
	copy constructor More...
	~BuildInstruction () override
	default destructor More...
BuildInstruction &	operator= (BuildInstruction const &rval)
	copy assignment More...
BuildInstructionState::Enum	modify (Pose &pose)
	modify this pose More...
BuildInstructionState::Enum	state () const
	return the state of this BuildInstruction More...
bool	ready () const
	Is the BuildInstruction's state at READY? More...
bool	waiting_on_dependencies () const
	Is the BuildInstruction's state at WAITING_ON_DEPENDENCIES? More...
bool	modify_was_successful () const
	Is the BuildInstruction's state at MODIFY_WAS_SUCCESSFUL? More...
void	attach_to (Pose &pose)
	attach to a Pose's conformation More...
void	detach_from ()
	detach from a Pose's conformation More...
void	on_length_change (LengthEvent const &event)
	update any indexing wrt length change to Pose/Conformation being watched More...
bool	detach_after_modify () const
	detach after modify()? More...
Interval const &	original_interval () const
	return original residue range of this instruction More...
ResidueTypeSet const &	residue_type_set () const
	the residue type set being used More...
bool	has_dependencies () const
	does this BuildInstruction have dependencies? More...
core::Size	n_dependencies () const
	the number of dependencies this BuildInstruction has More...
BuildInstructionCAPs const &	dependencies () const
	the list of instructions whose modify() must complete before the modify() for this instruction may be called successfully More...
void	detach_after_modify (bool const flag)
	set detach after modify() More...
void	reset_accounting ()
	reset intervals, positions, etc to initial state and drop observers. State set to READY. More...
virtual void	add_dependency_to (BuildInstructionCAP i)
	add an instruction to this BuildInstruction's dependency list More...
virtual bool	dependent_on (BuildInstructionCAP i) const
	is this instruction dependent upon the given instruction? More...
void	clear_dependencies ()
	clear the list of dependencies More...
virtual bool	compatible_with (BuildInstruction const &rval) const
	compares fixed and mutable positions to determine compatibility with another instruction More...

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

Protected Member Functions
bool	dependencies_satisfied () const override
	are dependencies satisfied so that modify_impl() can complete successfully? More...
void	modify_impl (Pose &pose) override
	do the actual work of modifying the Pose More...
void	reset_accounting_impl () override
	do the actual reset of intervals, positions, etc to initial state More...
Protected Member Functions inherited from protocols::forge::build::BuildInstruction
Link const &	length_obs_link () const
	access to the Conformation length observer link More...
void	state (BuildInstructionState::Enum const s)
	set the BuildInstruction's current state More...

Private Types
typedef BuildInstruction	Super

Private Member Functions
void	init ()
	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.size()] 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.

Member Typedef Documentation

LengthEvent

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

MoveMap

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

Pose

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

Positions

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

Real

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

ResidueTypeSetCAP

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

Size

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

String

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

Super

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

private

Constructor & Destructor Documentation

SegmentInsert() [1/4]

protocols::forge::build::SegmentInsert::SegmentInsert

(

)

default constructor

SegmentInsert() [2/4]

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 = protocols::forge::build::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).

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

SegmentInsert() [3/4]

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 = protocols::forge::build::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

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

SegmentInsert() [4/4]

protocols::forge::build::SegmentInsert::SegmentInsert

(

SegmentInsert const &

rval

)

copy constructor

~SegmentInsert()

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

overridedefault

default destructor

Member Function Documentation

aa()

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

inline

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

References aa_.

Referenced by SegmentInsert().

clone()

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

overridevirtual

clone this object

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

creates_undefined_backbone()

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

inlineoverridevirtual

does this object create undefined backbone in the modified region?

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

defined_positions()

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

overridevirtual

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

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

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

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

dependencies_satisfied()

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

inlineoverrideprotectedvirtual

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

Returns

always True, this BuildInstruction has no dependencies

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

flanking_left_aa()

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

References aa_, and insertion_char().

Referenced by modify_impl().

flanking_left_nres()

SegmentInsert::Size protocols::forge::build::SegmentInsert::flanking_left_nres

(

)

const

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

References insertion_char(), and ss_.

Referenced by modify_impl().

flanking_left_ss()

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

References insertion_char(), and ss_.

Referenced by modify_impl().

flanking_right_aa()

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

References aa_, and insertion_char().

Referenced by modify_impl().

flanking_right_nres()

SegmentInsert::Size protocols::forge::build::SegmentInsert::flanking_right_nres

(

)

const

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

References insertion_char(), and ss_.

Referenced by modify_impl().

flanking_right_ss()

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

References insertion_char(), and ss_.

Referenced by modify_impl().

init()

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

private

init to be called during non-default constructors

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

Referenced by SegmentInsert().

insert_connection_scheme()

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

References insert_connection_scheme_.

Referenced by modify_impl().

insert_pose()

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

(

)

const

the pose to insert

References insert_pose_.

insert_pose_torsion_override_movemap() [1/2]

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.size()]

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.

References insert_pose_torsion_override_movemap_.

Referenced by movemap().

insert_pose_torsion_override_movemap() [2/2]

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.size()]

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.

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::size(), 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().

insertion_char()

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

inlinestatic

the character representing the insertion point

Returns

'^'

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(), protocols::forge::remodel::RemodelMover::process_insert_design_string(), and SegmentInsert().

insertion_end_residue()

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

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

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

insertion_point_absolute_index()

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

References insertion_char(), and ss_.

insertion_start_residue()

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

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

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

interval()

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

overridevirtual

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.

References interval_.

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

keep_known_bb_torsions_at_junctions()

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.

References keep_known_bb_torsions_at_junctions_.

modify_impl()

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

overrideprotectedvirtual

do the actual work of modifying the Pose

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

References core::kinematics::FoldTree::add_edge(), core::conformation::Residue::atom_name(), core::kinematics::FoldTree::begin(), core::pose::Pose::begin(), core::chemical::element::C, protocols::forge::build::SegmentInsertConnectionScheme::C, core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::kinematics::FoldTree::delete_edge(), core::conformation::Conformation::delete_residue_range_slow(), core::kinematics::dir_jump, core::kinematics::FoldTree::end(), protocols::forge::methods::find_connecting_jump(), protocols::forge::methods::find_cutpoint(), flanking_left_aa(), flanking_left_nres(), flanking_left_ss(), flanking_right_aa(), flanking_right_nres(), flanking_right_ss(), core::pose::Pose::fold_tree(), core::conformation::get_anchor_atomno(), protocols::forge::methods::grow_left_r(), protocols::forge::methods::grow_left_rtype(), protocols::forge::methods::grow_right_r(), protocols::forge::methods::grow_right_rtype(), core::conformation::idealize_position(), insert_connection_scheme(), insert_connection_scheme_, core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), insert_pose_, interval_, core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::kinematics::FoldTree::jump_edge(), protocols::forge::methods::jumps_and_cuts_from_pose(), keep_known_bb_torsions_at_junctions_, protocols::forge::build::Interval::left, protocols::forge::build::Interval::length(), protocols::mean_field::max(), protocols::mean_field::min(), core::chemical::element::N, protocols::forge::build::SegmentInsertConnectionScheme::N, core::kinematics::FoldTree::new_jump(), core::pose::Pose::num_jump(), core::pose::Pose::omega(), protocols::forge::methods::order(), protocols::forge::build::BuildInstruction::original_interval(), core::pose::Pose::pdb_info(), performing_pure_insertion(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::forge::build::SegmentInsertConnectionScheme::RANDOM_SIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), protocols::forge::build::BuildInstruction::residue_type_set(), core::pose::residue_types_from_sequence(), core::scoring::rg, protocols::forge::build::Interval::right, core::kinematics::FoldTree::root(), core::pose::Pose::secstruct(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), core::kinematics::FoldTree::slide_cutpoint(), core::kinematics::Edge::start(), core::kinematics::Edge::start_atom(), core::kinematics::Edge::stop(), core::kinematics::Edge::stop_atom(), protocols::forge::build::TR(), protocols::forge::methods::trans_omega(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

movemap()

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

overridevirtual

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.

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::id::TorsionID::rsd(), core::kinematics::MoveMap::set(), and core::kinematics::MoveMap::set_bb().

new_positions()

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

overridevirtual

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

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

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

on_residue_append()

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

overridevirtual

update indexing on residue append

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

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

on_residue_delete()

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

overridevirtual

update indexing on residue delete

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

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

on_residue_prepend()

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

overridevirtual

update indexing on residue prepend

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

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

operator=()

SegmentInsert & protocols::forge::build::SegmentInsert::operator=

(

SegmentInsert const &

rval

)

copy assignment

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

original_deleted_positions()

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

overridevirtual

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.

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

Referenced by original_mutable_positions().

original_fixed_positions()

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

overridevirtual

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

Remarks

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

Returns

empty set if no fixed positions necessary

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

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

original_interval_valid()

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

inlineoverridevirtual

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.

original_kept_positions()

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

overridevirtual

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

Returns

An empty set – no positions are kept.

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

original_mutable_positions()

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

overridevirtual

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

Remarks

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

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

References original_deleted_positions().

performing_pure_insertion()

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.

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

Referenced by modify_impl(), and SegmentInsert().

preexisting_positions()

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

overridevirtual

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

Returns

An empty set, there are no pre-existing positions.

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

reset_accounting_impl()

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

overrideprotectedvirtual

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

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

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

ss()

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

inline

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

References ss_.

Referenced by SegmentInsert().

undefined_positions()

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

overridevirtual

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

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

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

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

aa_

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.

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

insert_connection_scheme_

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)

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

insert_pose_

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

private

insert this Pose

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

insert_pose_torsion_override_movemap_

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.size()]

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.

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

interval_

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

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

keep_known_bb_torsions_at_junctions_

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.

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

ss_

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.

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().

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

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