Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Protected Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
protocols::forge::build::SegmentSwap Class Reference

instruction to swap a segment with an external segment More...

#include <SegmentSwap.hh>

Inheritance diagram for protocols::forge::build::SegmentSwap:
Inheritance graph
[legend]

Public Types

typedef Super::Size Size
 
typedef Super::ResidueTypeSetCAP ResidueTypeSetCAP
 
typedef Super::LengthEvent LengthEvent
 
typedef Super::Pose Pose
 
typedef Super::Positions Positions
 
typedef Super::String String
 
typedef core::kinematics::MoveMap MoveMap
 
- 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::SizePositions
 
typedef std::string String
 

Public Member Functions

 SegmentSwap ()
 default constructor More...
 
 SegmentSwap (Interval const &i, MoveMap const &swap_in_movemap, Pose const &swap_in)
 constructor More...
 
 SegmentSwap (SegmentSwap const &rval)
 copy constructor More...
 
 ~SegmentSwap () override
 default destructor More...
 
SegmentSwapoperator= (SegmentSwap const &rval)
 copy assignment More...
 
BuildInstructionOP clone () const override
 clone this object More...
 
MoveMap const & swap_in_movemap () const
 fixed backbone residues in this movemap will be used for new jumps More...
 
Pose const & swap_in () const
 the pose to swap in 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 swapped 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...
 
BuildInstructionoperator= (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 Member Functions

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

Private Attributes

Interval interval_
 range of residues to swap out More...
 
MoveMap swap_in_movemap_
 fixed backbone residues in this movemap will be used for new jumps More...
 
Pose swap_in_
 swap in this Pose More...
 

Detailed Description

instruction to swap a segment with an external segment

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::forge::build::SegmentSwap::SegmentSwap ( )

default constructor

protocols::forge::build::SegmentSwap::SegmentSwap ( Interval const &  i,
MoveMap const &  swap_in_movemap,
Pose const &  swap_in 
)

constructor

Parameters
[in]intervalswap out this range of residues
[in]move_mapfixed backbone residues in this movemap will be used for new jumps
[in]swap_inswap in this pose
[in]intervalswap out this range of residues
[in]move_mapfixed backbone residues in this movemap will be used for new jumps
[in]swap_inswap in this pose
Remarks
Procedure will attempt to honor the movemap as much as it can. The caveat is that sequences of calls to some FoldTree routines may shift the jumps internally in a way that is not easily predictable. If the procedure cannot find an allowed residue for a jump, it will make a jump to the (lower) median residue in the disconnected fold tree interval.

References init().

protocols::forge::build::SegmentSwap::SegmentSwap ( SegmentSwap const &  rval)
default

copy constructor

protocols::forge::build::SegmentSwap::~SegmentSwap ( )
overridedefault

default destructor

Member Function Documentation

BuildInstructionOP protocols::forge::build::SegmentSwap::clone ( ) const
overridevirtual

clone this object

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

bool protocols::forge::build::SegmentSwap::creates_undefined_backbone ( ) const
inlineoverridevirtual

does this object create undefined backbone in the modified region?

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

SegmentSwap::Positions protocols::forge::build::SegmentSwap::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 of positions spanning the interval – all positions are are defined.

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

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

References new_positions().

bool protocols::forge::build::SegmentSwap::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.

void protocols::forge::build::SegmentSwap::init ( void  )
private
Interval protocols::forge::build::SegmentSwap::interval ( ) const
overridevirtual

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

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

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

References interval_.

Referenced by new_positions().

void protocols::forge::build::SegmentSwap::modify_impl ( Pose pose)
overrideprotectedvirtual
SegmentSwap::MoveMap protocols::forge::build::SegmentSwap::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 set to false at the MoveMapTorsionID level

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

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

References new_positions(), and core::kinematics::MoveMap::set_bb().

SegmentSwap::Positions protocols::forge::build::SegmentSwap::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 interval – all positions are are defined.

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 defined_positions(), and movemap().

void protocols::forge::build::SegmentSwap::on_residue_append ( LengthEvent const &  event)
overridevirtual
void protocols::forge::build::SegmentSwap::on_residue_delete ( LengthEvent const &  event)
overridevirtual
void protocols::forge::build::SegmentSwap::on_residue_prepend ( LengthEvent const &  event)
overridevirtual
SegmentSwap & protocols::forge::build::SegmentSwap::operator= ( SegmentSwap const &  rval)
SegmentSwap::Positions protocols::forge::build::SegmentSwap::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.

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

SegmentSwap::Positions protocols::forge::build::SegmentSwap::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.

bool protocols::forge::build::SegmentSwap::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.

SegmentSwap::Positions protocols::forge::build::SegmentSwap::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.

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

SegmentSwap::Positions protocols::forge::build::SegmentSwap::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.

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

SegmentSwap::Pose const & protocols::forge::build::SegmentSwap::swap_in ( ) const

the pose to swap in

References swap_in_.

SegmentSwap::MoveMap const & protocols::forge::build::SegmentSwap::swap_in_movemap ( ) const

fixed backbone residues in this movemap will be used for new jumps

Remarks
Procedure will attempt to honor this movemap as much as it can. The caveat is that sequences of calls to some FoldTree routines may shift the jumps internally in a way that is not easily predictable. If the procedure cannot find an allowed residue for a jump, it will make a jump to the (lower) median residue in the disconnected fold tree interval.

References swap_in_movemap_.

SegmentSwap::Positions protocols::forge::build::SegmentSwap::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
An empty set – no undefined positions.

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

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

Member Data Documentation

Interval protocols::forge::build::SegmentSwap::interval_
private

range of residues to swap out

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().

Pose protocols::forge::build::SegmentSwap::swap_in_
private

swap in this Pose

Referenced by init(), modify_impl(), operator=(), and swap_in().

MoveMap protocols::forge::build::SegmentSwap::swap_in_movemap_
private

fixed backbone residues in this movemap will be used for new jumps

Remarks
Procedure will attempt to honor this movemap as much as it can. The caveat is that sequences of calls to some FoldTree routines may shift the jumps internally in a way that is not easily predictable. If the procedure cannot find an allowed residue for a jump, it will make a jump to the (lower) median residue in the disconnected fold tree interval.

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


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