Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
protocols::forge::build::Bridge Class Reference

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

#include <Bridge.hh>

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List of all members.

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 Member Functions

 Bridge ()
 default constructor
 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)
 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
 Bridge (Bridge const &rval)
 copy constructor
virtual ~Bridge ()
 default destructor
Bridgeoperator= (Bridge const &rval)
 copy assignment
virtual BuildInstructionOP clone () const
 clone this object
virtual bool original_interval_valid () const
 is the original interval storing valid information, or is empty or being used for something else?
virtual Interval interval () const
 a copy of the working range of residues specifying the bridged region including the anchors
virtual Positions preexisting_positions () const
 return a copy of the set of positions within the new region that were pre-existing in the original Pose prior to modify()
virtual Positions new_positions () const
 return a copy of the set of positions that are "new" and did not exist in the original Pose.
virtual Positions defined_positions () const
 return a copy of the set of positions within the newly modified region that has a defined conformation. E.g. existing or copied residues.
virtual Positions undefined_positions () const
 return a copy of the set of positions within the newly modified region that has an undefined conformation. E.g. newly created residues.
virtual MoveMap movemap () const
 return a copy of the MoveMap that defines the moveable/fixed positions/dofs for this instruction
virtual void on_residue_append (LengthEvent const &event)
 update indexing on residue append
virtual void on_residue_prepend (LengthEvent const &event)
 update indexing on residue prepend
virtual void on_residue_delete (LengthEvent const &event)
 update indexing on residue delete
virtual Positions original_kept_positions () const
 return the set of positions within the original interval that will be kept in this BuildInstruction
virtual Positions original_deleted_positions () const
 return set of positions within the original interval that will be deleted in this BuildInstruction
virtual Positions original_fixed_positions () const
 return set of any fixed positions necessary with respect to the original interval and original Pose numbering
virtual Positions original_mutable_positions () const
 return set of any mutable positions necessary with respect to the original interval and original Pose numbering
virtual bool creates_undefined_backbone () const
 does this object create undefined backbone in the modified region?

Protected Member Functions

virtual bool dependencies_satisfied () const
 are dependencies satisfied so that modify_impl() can complete successfully?
virtual void modify_impl (Pose &pose)
 do the actual work of modifying the Pose
virtual void reset_accounting_impl ()
 do the actual reset of intervals, positions, etc to initial state

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

Referenced by clone().

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]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 core::pose::annotated_to_oneletter_sequence().

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]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 core::pose::annotated_to_oneletter_sequence().

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

copy constructor

protocols::forge::build::Bridge::~Bridge ( ) [virtual]

default destructor


Member Function Documentation

BuildInstructionOP protocols::forge::build::Bridge::clone ( ) const [virtual]

clone this object

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

References Bridge().

virtual bool protocols::forge::build::Bridge::creates_undefined_backbone ( ) const [inline, virtual]

does this object create undefined backbone in the modified region?

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

Bridge::Positions protocols::forge::build::Bridge::defined_positions ( ) const [virtual]

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().

virtual bool protocols::forge::build::Bridge::dependencies_satisfied ( ) const [inline, protected, virtual]

are dependencies satisfied so that modify_impl() can complete successfully?

Returns:
always True, this BuildInstruction has no dependencies

Reimplemented from protocols::forge::build::BuildInstruction.

virtual Interval protocols::forge::build::Bridge::interval ( ) const [inline, virtual]

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.

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

void protocols::forge::build::Bridge::modify_impl ( Pose pose) [protected, virtual]
Bridge::MoveMap protocols::forge::build::Bridge::movemap ( ) const [virtual]

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 [virtual]

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) [virtual]

update indexing on residue append

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

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

References 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) [virtual]
void protocols::forge::build::Bridge::on_residue_prepend ( LengthEvent const &  event) [virtual]

update indexing on residue prepend

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

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

References 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 [virtual]

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 [virtual]

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().

virtual bool protocols::forge::build::Bridge::original_interval_valid ( ) const [inline, virtual]

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 [virtual]

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 [virtual]

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 [virtual]

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 ( ) [protected, virtual]

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

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

References protocols::forge::build::BuildInstruction::original_interval().

Bridge::Positions protocols::forge::build::Bridge::undefined_positions ( ) const [virtual]

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().


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