protocols::forge::build::SegmentRebuild Class Reference

instruction to rebuild a segment More...

#include <SegmentRebuild.hh>

Inheritance diagram for protocols::forge::build::SegmentRebuild:

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
	SegmentRebuild ()
	default constructor More...
	SegmentRebuild (Interval const &i, String const &ss, ResidueTypeSetCAP rts=core::chemical::ChemicalManager::get_instance() ->residue_type_set(core::chemical::FA_STANDARD), bool const keep_known_bb_torsions_at_junctions=false)
	sec.struct only constructor (poly-alanine for new region) More...
	SegmentRebuild (Interval const &i, String const &ss, String const &aa, ResidueTypeSetCAP rts=core::chemical::ChemicalManager::get_instance() ->residue_type_set(core::chemical::FA_STANDARD), bool const keep_known_bb_torsions_at_junctions=false)
	full constructor More...
	SegmentRebuild (SegmentRebuild const &rval)
	copy constructor More...
	~SegmentRebuild () override
	default destructor More...
SegmentRebuild &	operator= (SegmentRebuild const &rval)
	copy assignment More...
BuildInstructionOP	clone () const override
	clone this object More...
String const &	ss () const
	get secondary structure string More...
String const &	aa () const
	get annotated amino acid string More...
bool	keep_known_bb_torsions_at_junctions () const
	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? Default False. 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
Interval	interval_
	the working range of residues 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...
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? More...

Detailed Description

instruction to rebuild a segment

Remarks

Handles both cut based rebuilding (i.e. loops) and continuous rebuilding adjacent to the boundary of a chain, such as n-term/c-term extensions.

Member Typedef Documentation

LengthEvent

typedef Super::LengthEvent protocols::forge::build::SegmentRebuild::LengthEvent

MoveMap

typedef Super::MoveMap protocols::forge::build::SegmentRebuild::MoveMap

Pose

typedef Super::Pose protocols::forge::build::SegmentRebuild::Pose

Positions

typedef Super::Positions protocols::forge::build::SegmentRebuild::Positions

Real

typedef Super::Real protocols::forge::build::SegmentRebuild::Real

ResidueTypeSetCAP

typedef Super::ResidueTypeSetCAP protocols::forge::build::SegmentRebuild::ResidueTypeSetCAP

Size

typedef Super::Size protocols::forge::build::SegmentRebuild::Size

String

typedef Super::String protocols::forge::build::SegmentRebuild::String

Super

typedef BuildInstruction protocols::forge::build::SegmentRebuild::Super

private

Constructor & Destructor Documentation

SegmentRebuild() [1/4]

protocols::forge::build::SegmentRebuild::SegmentRebuild

(

)

default constructor

SegmentRebuild() [2/4]

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

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

Parameters

[in]	interval	rebuild this range of residues
[in]	ss	the secondary structure desired, also defines length of new build region
[in]	rts	the residue type set to use, default FA_STANDARD
[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.

Remarks

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

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

SegmentRebuild() [3/4]

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

full constructor

Parameters

[in]	interval	rebuild this range of residues
[in]	ss	the secondary structure desired, also defines length of new build region
[in]	aa	the annotated amino acid sequence desired, default is poly-alanine
[in]	rts	the residue type set to use, default FA_STANDARD
[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.

Remarks

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

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

SegmentRebuild() [4/4]

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

default

copy constructor

~SegmentRebuild()

protocols::forge::build::SegmentRebuild::~SegmentRebuild ( )

overridedefault

default destructor

Member Function Documentation

aa()

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

inline

get annotated amino acid string

References aa_.

clone()

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

overridevirtual

clone this object

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

creates_undefined_backbone()

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

inlineoverridevirtual

does this object create undefined backbone in the modified region?

Returns

true

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

defined_positions()

SegmentRebuild::Positions protocols::forge::build::SegmentRebuild::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::SegmentRebuild::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::SegmentRebuild::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 interval_.

Referenced by movemap(), and new_positions().

keep_known_bb_torsions_at_junctions()

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

inline

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? Default False.

References keep_known_bb_torsions_at_junctions_.

modify_impl()

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

overrideprotectedvirtual

do the actual work of modifying the Pose

There are two cases:

• internal rebuild where no residue of the segment is a terminus
• boundary rebuild where one residue of the segment is a terminus

In the case of an internal rebuild, the old segment will be removed and a new segment containing a random cutpoint will be inserted. The new jump will be created between (left-1) and (right+1) of the new segment.

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

References core::conformation::Residue::aa(), aa_, core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::conformation::Residue::atom_name(), protocols::forge::build::BuildInstruction::attach_to(), core::kinematics::FoldTree::begin(), core::conformation::Conformation::chain_endings(), core::pose::Pose::clear(), protocols::forge::methods::closest_larger_peptide_vertex(), protocols::forge::methods::closest_smaller_peptide_vertex(), core::pose::Pose::conformation(), protocols::sparta::contains(), core::conformation::Conformation::delete_chain_ending(), 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(), core::pose::Pose::fold_tree(), core::conformation::get_anchor_atomno(), protocols::forge::methods::grow_left_rtype(), protocols::forge::methods::grow_right_rtype(), core::conformation::idealize_position(), 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(), protocols::forge::methods::jumps_connected_to_position(), keep_known_bb_torsions_at_junctions_, protocols::forge::build::Interval::left, protocols::forge::build::BuildInstruction::length_obs_link(), protocols::mean_field::max(), protocols::mean_field::min(), core::kinematics::FoldTree::new_jump(), core::conformation::Conformation::num_chains(), core::pose::Pose::num_jump(), core::pose::Pose::omega(), protocols::forge::methods::order(), protocols::forge::build::BuildInstruction::original_interval(), core::pose::Pose::pdb_info(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::forge::methods::remove_cutpoint_variants(), 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::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), ss_, core::kinematics::Edge::start(), core::kinematics::Edge::start_atom(), core::kinematics::Edge::stop(), core::kinematics::Edge::stop_atom(), protocols::forge::methods::trans_omega(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

movemap()

SegmentRebuild::MoveMap protocols::forge::build::SegmentRebuild::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 core::id::BB, core::sequence::end, 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(), core::kinematics::MoveMap::set_bb(), and core::kinematics::MoveMap::set_chi().

new_positions()

SegmentRebuild::Positions protocols::forge::build::SegmentRebuild::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 modified interval – all positions are undefined.

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::SegmentRebuild::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::SegmentRebuild::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::SegmentRebuild::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=()

SegmentRebuild & protocols::forge::build::SegmentRebuild::operator=

(

SegmentRebuild const &

rval

)

copy assignment

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

original_deleted_positions()

SegmentRebuild::Positions protocols::forge::build::SegmentRebuild::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 original interval.

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

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

original_fixed_positions()

SegmentRebuild::Positions protocols::forge::build::SegmentRebuild::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. If SegmentRebuild has dependencies, the set of positions shrinks from the endpoints of [original_left - 1, original_right + 1] down to an empty set in the assumption that the user is requesting an advanced feature and knows what they're doing around the endpoints, e.g. rebuilding directly adjacent to a swapped out section.

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. If SegmentRebuild has dependencies, the set of positions shrinks from the endpoints of [original_left - 1, original_right + 1] down to an empty set in the assumption that the user is requesting an advanced feature and knows what they're doing around the endpoints, e.g. rebuilding directly adjacent to a swapped out section.

Returns

empty set if no fixed positions necessary

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

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

original_interval_valid()

bool protocols::forge::build::SegmentRebuild::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()

SegmentRebuild::Positions protocols::forge::build::SegmentRebuild::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()

SegmentRebuild::Positions protocols::forge::build::SegmentRebuild::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.

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

preexisting_positions()

SegmentRebuild::Positions protocols::forge::build::SegmentRebuild::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::SegmentRebuild::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::SegmentRebuild::ss ( ) const

inline

get secondary structure string

References ss_.

undefined_positions()

SegmentRebuild::Positions protocols::forge::build::SegmentRebuild::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 modified interval – 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::SegmentRebuild::aa_

private

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

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

interval_

Interval protocols::forge::build::SegmentRebuild::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::SegmentRebuild::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?

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 operator=().

ss_

String protocols::forge::build::SegmentRebuild::ss_

private

secondary structure string, also defines length of extension

Referenced by modify_impl(), operator=(), SegmentRebuild(), and ss().

---

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

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