instruction to create a c-side extension More...

#include <GrowRight.hh>

Inheritance diagram for protocols::forge::build::GrowRight:

Public Types
typedef Super::Size	Size

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
	GrowRight ()
	default constructor More...

	GrowRight (core::Size const pos, String const &ss, String const &aa=String(), ResidueTypeSetCAP rts=core::chemical::ChemicalManager::get_instance() ->residue_type_set(core::chemical::FA_STANDARD))
	constructor More...

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

	~GrowRight () override
	default destructor More...

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

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

core::Size	pos () const
	grow right from this anchor position More...

String const &	ss () const
	get secondary structure string More...

String const &	aa () const
	get annotated amino acid string 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	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
core::Size	pos_
	make a c-side extension after this position More...

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

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

Detailed Description

instruction to create a c-side extension

Remarks: Use this for c-side insertions but typically not c-terminal extensions unless necessary. It does not automatically cover the additional residue on the left endpoint that needs to move during c-terminal extensions due to invalid psi torsion. For that case, use the SegmentRebuild class replacing the c-terminal residue with desired length+1.

Member Typedef Documentation

◆ LengthEvent

typedef Super::LengthEvent protocols::forge::build::GrowRight::LengthEvent

◆ MoveMap

typedef Super::MoveMap protocols::forge::build::GrowRight::MoveMap

◆ Pose

typedef Super::Pose protocols::forge::build::GrowRight::Pose

◆ Positions

typedef Super::Positions protocols::forge::build::GrowRight::Positions

◆ ResidueTypeSetCAP

typedef Super::ResidueTypeSetCAP protocols::forge::build::GrowRight::ResidueTypeSetCAP

◆ Size

typedef Super::Size protocols::forge::build::GrowRight::Size

◆ String

typedef Super::String protocols::forge::build::GrowRight::String

◆ Super

typedef BuildInstruction protocols::forge::build::GrowRight::Super

private

Constructor & Destructor Documentation

◆ GrowRight() [1/3]

protocols::forge::build::GrowRight::GrowRight ( )

default constructor

◆ GrowRight() [2/3]

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

constructor

Parameters

[in]	pos	grow a c-side extension after this position
[in]	ss	the secondary structure desired, also defines length of extension
[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]	pos	grow a c-side extension after to this position
[in]	ss	the secondary structure desired, also defines length of extension
[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_.

◆ GrowRight() [3/3]

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

default

copy constructor

◆ ~GrowRight()

protocols::forge::build::GrowRight::~GrowRight ( )

overridedefault

default destructor

Member Function Documentation

◆ aa()

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

inline

get annotated amino acid string

References aa_.

◆ clone()

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

overridevirtual

clone this object

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

◆ creates_undefined_backbone()

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

inlineoverridevirtual

does this object create undefined backbone in the modified region?

Returns: true

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

◆ defined_positions()

GrowRight::Positions protocols::forge::build::GrowRight::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: An empty set – no positions are defined.

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

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

◆ dependencies_satisfied()

bool protocols::forge::build::GrowRight::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::GrowRight::interval ( ) const

inlineoverridevirtual

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

Remarks: This can change if listening to Conformation LengthEvents

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

References pos_, and ss_.

Referenced by modify_impl(), and new_positions().

◆ modify_impl()

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

overrideprotectedvirtual

do the actual work of modifying the Pose

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

References aa_, protocols::forge::methods::grow_right_rtype(), interval(), protocols::forge::build::Interval::left, pos_, protocols::forge::build::BuildInstruction::residue_type_set(), core::pose::residue_types_from_sequence(), protocols::forge::build::Interval::right, core::pose::Pose::set_secstruct(), ss_, and protocols::forge::methods::trans_omega().

◆ movemap()

GrowRight::MoveMap protocols::forge::build::GrowRight::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 new_positions(), core::kinematics::MoveMap::set_bb(), and core::kinematics::MoveMap::set_chi().

◆ new_positions()

GrowRight::Positions protocols::forge::build::GrowRight::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 of positions spanning the entire region – all positions are new.

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 movemap(), and undefined_positions().

◆ on_residue_append()

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

overridevirtual

update indexing on residue append

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

References pos_, and core::conformation::signals::LengthEvent::position.

◆ on_residue_delete()

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

overridevirtual

update indexing on residue delete

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

References core::conformation::signals::LengthEvent::length_change, pos_, and core::conformation::signals::LengthEvent::position.

◆ on_residue_prepend()

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

overridevirtual

update indexing on residue prepend

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

References pos_, and core::conformation::signals::LengthEvent::position.

◆ operator=()

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

copy assignment

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

◆ original_deleted_positions()

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

overridevirtual

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

Returns: An empty set – no positions are deleted.

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

◆ original_fixed_positions()

GrowRight::Positions protocols::forge::build::GrowRight::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

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::GrowRight::original_interval_valid ( ) const

inlineoverridevirtual

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

Returns: false, stores invalid interval

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

◆ original_kept_positions()

GrowRight::Positions protocols::forge::build::GrowRight::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()

GrowRight::Positions protocols::forge::build::GrowRight::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.

Returns: empty set if no mutable positions

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

◆ pos()

core::Size protocols::forge::build::GrowRight::pos ( ) const

inline

grow right from this anchor position

Remarks: This can change if listening to Conformation LengthEvents. Use original_interval() to get the original anchor position.

References pos_.

◆ preexisting_positions()

GrowRight::Positions protocols::forge::build::GrowRight::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 – no positions are pre-existing.

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

◆ reset_accounting_impl()

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

overrideprotectedvirtual

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

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

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

◆ ss()

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

inline

get secondary structure string

References ss_.

◆ undefined_positions()

GrowRight::Positions protocols::forge::build::GrowRight::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 of positions spanning the entire region – all positions are undefined.

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::GrowRight::aa_

private

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

Referenced by aa(), GrowRight(), modify_impl(), and operator=().

◆ pos_

core::Size protocols::forge::build::GrowRight::pos_

private

make a c-side extension after this position

Remarks: this position 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=(), pos(), and reset_accounting_impl().

◆ ss_

String protocols::forge::build::GrowRight::ss_

private

secondary structure string, also defines length of extension

Referenced by GrowRight(), interval(), modify_impl(), operator=(), and ss().

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

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

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

◆ LengthEvent

◆ MoveMap

◆ Pose

◆ Positions

◆ ResidueTypeSetCAP

◆ Size

◆ String

◆ Super

Constructor & Destructor Documentation

◆ GrowRight() [1/3]

◆ GrowRight() [2/3]

◆ GrowRight() [3/3]

◆ ~GrowRight()

Member Function Documentation

◆ aa()

◆ 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()

◆ pos()

◆ preexisting_positions()

◆ reset_accounting_impl()

◆ ss()

◆ undefined_positions()

Member Data Documentation

◆ aa_

◆ pos_

◆ ss_