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protocols::forge::build::Bridge Class Reference

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

#include <Bridge.hh>

Inheritance diagram for protocols::forge::build::Bridge:
Inheritance graph
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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::SizePositions
 
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...
 
Bridgeoperator= (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...
 
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 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

Constructor & Destructor Documentation

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

default constructor

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

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

Parameters
[in]intervalbuild bridge using these two residues as anchor positions
[in]ssthe secondary structure desired, also defines length of new bridge, region between the anchor positions, can be empty
[in]rtsthe residue type set to use, default FA_STANDARD
Remarks
length of the one-letter aa must equal the length of ss
Parameters
[in]intervalbridge these two residues
[in]ssthe secondary structure desired, also defines length of new bridge, region between the anchor positions, can be empty
[in]rtsthe 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_.

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

full constructor

Parameters
[in]intervalbuild bridge using these two residues as anchor positions
[in]ssthe secondary structure desired, also defines length of new bridge, region between the anchor positions, can be empty
[in]aathe annotated amino acid sequence desired, default is poly-alanine
[in]rtsthe residue type set to use, default FA_STANDARD
Remarks
length of the one-letter aa must equal the length of ss
Parameters
[in]intervalbridge these two residues
[in]ssthe secondary structure desired, also defines length of new bridge, region between the anchor positions, can be empty
[in]aathe annotated amino acid sequence desired, default is poly-alanine
[in]rtsthe 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_.

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

copy constructor

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

default destructor

Member Function Documentation

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

clone this object

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

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.

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().

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 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().

void protocols::forge::build::Bridge::modify_impl ( Pose pose)
overrideprotectedvirtual
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().

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().

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.

void protocols::forge::build::Bridge::on_residue_delete ( LengthEvent const &  event)
overridevirtual
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.

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

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().

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.

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().

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().

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().

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().

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

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 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().

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: