connect two contiguous but disjoint sections of a Pose into one continuous section More...

#include <Bridge.hh>

Inheritance diagram for protocols::forge::build::Bridge:

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
	Bridge ()
	default constructor More...

	Bridge (Interval const &i, String const &ss, ResidueTypeSetCAP rts=core::chemical::ChemicalManager::get_instance() ->residue_type_set(core::chemical::FA_STANDARD))
	sec.struct only constructor (poly-alanine for new region) More...

	Bridge (Interval const &i, String const &ss, String const &aa, ResidueTypeSetCAP rts=core::chemical::ChemicalManager::get_instance() ->residue_type_set(core::chemical::FA_STANDARD))
	full constructor More...

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

	~Bridge () override
	default destructor More...

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

BuildInstructionOP	clone () const override
	clone this object 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 bridged region including the anchors 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	on_residue_append (LengthEvent const &event) override
	update indexing on residue append More...

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

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

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

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

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

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

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

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

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

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

	~BuildInstruction () override
	default destructor More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	modify_impl (Pose &pose) 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 Attributes
Interval	interval_
	the anchor positions of the bridge More...

String	ss_
	secondary structure string, also defines length of the bridge More...

String	aa_
	annotated amino acid string, length of the one-letter version must be equal to length of ss More...

Detailed Description

connect two contiguous but disjoint sections of a Pose into one continuous section

Anchor residues [i,j] to bridge must be adjacent to each other in the Pose (i+1 = j) and adjacent to a cutpoint. Both i and j will be idealized and marked as new moveable positions since the psi @ i and the phi @ j are undefined. Depending on the fold tree, this will cause a random swing either downstream or upstream of the bridge!

Member Typedef Documentation

◆ LengthEvent

typedef Super::LengthEvent protocols::forge::build::Bridge::LengthEvent

◆ MoveMap

typedef Super::MoveMap protocols::forge::build::Bridge::MoveMap

◆ Pose

typedef Super::Pose protocols::forge::build::Bridge::Pose

◆ Positions

typedef Super::Positions protocols::forge::build::Bridge::Positions

◆ Real

typedef Super::Real protocols::forge::build::Bridge::Real

◆ ResidueTypeSetCAP

typedef Super::ResidueTypeSetCAP protocols::forge::build::Bridge::ResidueTypeSetCAP

◆ Size

typedef Super::Size protocols::forge::build::Bridge::Size

◆ String

typedef Super::String protocols::forge::build::Bridge::String

◆ Super

typedef BuildInstruction protocols::forge::build::Bridge::Super

private

Constructor & Destructor Documentation

◆ Bridge() [1/4]

protocols::forge::build::Bridge::Bridge ( )

default constructor

◆ Bridge() [2/4]

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

sec.struct only constructor (poly-alanine for new region)

Parameters

[in]	interval	build bridge using these two residues as anchor positions
[in]	ss	the secondary structure desired, also defines length of new bridge, region between the anchor positions, can be empty
[in]	rts	the residue type set to use, default FA_STANDARD

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

Parameters

[in]	interval	bridge these two residues
[in]	ss	the secondary structure desired, also defines length of new bridge, region between the anchor positions, can be empty
[in]	rts	the residue type set to use, default FA_STANDARD

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

References aa_, core::pose::annotated_to_oneletter_sequence(), and ss_.

◆ Bridge() [3/4]

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

full constructor

Parameters

[in]	interval	build bridge using these two residues as anchor positions
[in]	ss	the secondary structure desired, also defines length of new bridge, region between the anchor positions, can be empty
[in]	aa	the annotated amino acid sequence desired, default is poly-alanine
[in]	rts	the residue type set to use, default FA_STANDARD

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

Parameters

[in]	interval	bridge these two residues
[in]	ss	the secondary structure desired, also defines length of new bridge, region between the anchor positions, can be empty
[in]	aa	the annotated amino acid sequence desired, default is poly-alanine
[in]	rts	the residue type set to use, default FA_STANDARD

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

References aa_, core::pose::annotated_to_oneletter_sequence(), and ss_.

◆ Bridge() [4/4]

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

default

copy constructor

◆ ~Bridge()

protocols::forge::build::Bridge::~Bridge ( )

overridedefault

default destructor

Member Function Documentation

◆ clone()

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

overridevirtual

clone this object

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

◆ creates_undefined_backbone()

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

inlineoverridevirtual

does this object create undefined backbone in the modified region?

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

◆ defined_positions()

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

overridevirtual

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

Returns: A set containing two positions – interval.left and interval.right.

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

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

References preexisting_positions().

◆ dependencies_satisfied()

bool protocols::forge::build::Bridge::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.

◆ interval()

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

inlineoverridevirtual

a copy of the working range of residues specifying the bridged region including the anchors

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

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

References interval_.

Referenced by movemap(), new_positions(), and preexisting_positions().

◆ modify_impl()

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

overrideprotectedvirtual

do the actual work of modifying the Pose

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

References aa_, core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), protocols::ligand_docking::grow(), core::conformation::idealize_position(), interval_, core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), protocols::forge::build::Interval::left, protocols::forge::methods::remove_cutpoint(), core::util::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), protocols::forge::build::BuildInstruction::residue_type_set(), protocols::forge::build::Interval::right, core::pose::Pose::set_omega(), core::pose::Pose::size(), and ss_.

◆ movemap()

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

overridevirtual

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

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

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

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

References interval(), protocols::forge::build::Interval::left, protocols::forge::build::Interval::right, core::kinematics::MoveMap::set_bb(), and core::kinematics::MoveMap::set_chi().

◆ new_positions()

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

overridevirtual

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

Returns: A set containing positions spanning [interval.left+1, interval.right-1].

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

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

Referenced by undefined_positions().

◆ on_residue_append()

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

overridevirtual

update indexing on residue append

Remarks: left and right endpoints of the interval can travel independently

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::Bridge::on_residue_delete ( LengthEvent const & event )

overridevirtual

update indexing on residue delete

Remarks: Left and right endpoints of the interval can travel independently.

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::Bridge::on_residue_prepend ( LengthEvent const & event )

overridevirtual

update indexing on residue prepend

Remarks: left and right endpoints of the interval can travel independently

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

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

◆ operator=()

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

copy assignment

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

◆ original_deleted_positions()

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

overridevirtual

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

Returns: A set containing the positions in [original.left+1, original.right-1].

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

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

◆ original_fixed_positions()

Bridge::Positions protocols::forge::build::Bridge::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::Bridge::original_interval_valid ( ) const

inlineoverridevirtual

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

Returns: true, stores valid interval

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

◆ original_kept_positions()

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

overridevirtual

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

Returns: A set containing the endpoints of the original interval.

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

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

◆ original_mutable_positions()

Bridge::Positions protocols::forge::build::Bridge::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.; Used for ensuring build regions for instructions do not overlap and so that jumps may be placed correctly.

Returns: empty set if no mutable positions

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

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

◆ preexisting_positions()

Bridge::Positions protocols::forge::build::Bridge::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: A set containing two positions – interval.left and interval.right.

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

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

Referenced by defined_positions().

◆ reset_accounting_impl()

void protocols::forge::build::Bridge::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().

◆ undefined_positions()

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

overridevirtual

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

Returns: A set containing positions spanning [interval.left+1, interval.right-1].

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

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

References new_positions().

Member Data Documentation

◆ aa_

String protocols::forge::build::Bridge::aa_

private

annotated amino acid string, length of the one-letter version must be equal to length of ss

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

◆ interval_

Interval protocols::forge::build::Bridge::interval_

private

the anchor positions of the bridge

Remarks: this 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().

◆ ss_

String protocols::forge::build::Bridge::ss_

private

secondary structure string, also defines length of the bridge

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

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

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

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

◆ LengthEvent

◆ MoveMap

◆ Pose

◆ Positions

◆ Real

◆ ResidueTypeSetCAP

◆ Size

◆ String

◆ Super

Constructor & Destructor Documentation

◆ Bridge() [1/4]

◆ Bridge() [2/4]

◆ Bridge() [3/4]

◆ Bridge() [4/4]

◆ ~Bridge()

Member Function Documentation

◆ clone()

◆ creates_undefined_backbone()

◆ defined_positions()

◆ dependencies_satisfied()

◆ interval()

◆ modify_impl()

◆ movemap()

◆ new_positions()

◆ on_residue_append()

◆ on_residue_delete()

◆ on_residue_prepend()

◆ operator=()

◆ original_deleted_positions()

◆ original_fixed_positions()

◆ original_interval_valid()

◆ original_kept_positions()

◆ original_mutable_positions()

◆ preexisting_positions()

◆ reset_accounting_impl()

◆ undefined_positions()

Member Data Documentation

◆ aa_

◆ interval_

◆ ss_