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

a container for managing BuildInstructions More...

#include <BuildManager.hh>

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List of all members.

Public Types

typedef core::Size Size
typedef core::kinematics::MoveMap MoveMap
typedef core::kinematics::MoveMapOP MoveMapOP
typedef core::pose::Pose Pose
typedef core::id::SequenceMapping SequenceMapping
typedef core::id::SequenceMappingOP SequenceMappingOP
typedef
core::id::SequenceMappingCOP 
SequenceMappingCOP
typedef utility::vector1
< BuildInstructionOP
BuildInstructionOPs
typedef
BuildInstructionOPs::iterator 
BIOPIterator
typedef
BuildInstructionOPs::const_iterator 
BIOPConstIterator
typedef std::pair< Size, SizeDependencyEdge
typedef utility::vector1
< DependencyEdge
DependencyEdges
typedef std::set< SizePositions
typedef std::map< Size, SizeOriginal2Modified
typedef std::map< Size, SizeModified2Original
typedef std::map< Interval,
Positions
Interval2Positions
typedef std::map< Interval,
Interval
Interval2Interval
typedef std::map< Interval,
MoveMap
Interval2MoveMap
typedef std::string String

Public Member Functions

 BuildManager ()
 default constructor
 BuildManager (BuildManager const &rval)
 copy constructor
virtual ~BuildManager ()
 default destructor
BuildManageroperator= (BuildManager const &rval)
 copy assignment
virtual BuildManagerOP clone () const
 clone this object
virtual BuildManagerOP create () const
 create a new instance of this type of object
void reset_accounting ()
 reset all accounting info (intervals, positions, etc) to initial state
void add (BuildInstructionOP bi)
 add an instruction directly (no copy)
void clear ()
 clear all instructions
Size size () const
 current number of instructions
bool empty () const
 no instructions?
BIOPConstIterator begin () const
 const iterator pointing to the first instruction
BIOPConstIterator end () const
 const iterator pointing just beyond the last instruction
void create_directed_dependency (BuildInstructionOP u, BuildInstructionOP v)
 create a directed dependency: instruction 'u' must complete before instruction 'v' can complete, i.e. 'v' depends on 'u'
Size n_dependencies () const
 the number of dependencies currently defined (i.e. # of edges in the dependency graph)
bool dependencies_exist () const
 have dependencies been defined?
Size clear_dependencies ()
 clear all dependencies
Original2Modified modify (Pose &pose)
 modify the pose using the instructions in this container
Size dummy_modify (Size const nres)
 a dry run of modify() with an all-ala helical Pose of the given length
bool compatibility_check () const
 check if instruction regions are compatible with each other
MoveMap movemap () const
 return the combined movemap from all instructions in this manager
MoveMapOP movemap_as_OP () const
SequenceMappingCOP sequence_mapping () const
 SequenceMapping consistent with the original -> modified mapping from the most recent modify() call.
Original2Modified const & original2modified () const
 return a map translating original residue -> modified residue for positions that existed within both the original Pose and modified Pose
Interval2Interval original2modified_intervals () const
 return a map translating original intervals to modified intervals
Original2Modified original2modified_interval_endpoints () const
 return a map translating original interval endpoints to modified interval endpoints
Interval2Interval modified2original_intervals () const
 return a map translating modified intervals to original intervals
Modified2Original modified2original_interval_endpoints () const
 return a map translating modified interval endpoints to original interval endpoints
std::set< Intervalintervals () const
 return all modified intervals
std::set< Intervalintervals_without_valid_original_equivalents () const
 return modified intervals that have no equivalent original interval in their BuildInstructions (original_interval_valid() = false)
std::set< Intervalintervals_containing_preexisting_positions () const
 return all intervals containing positions that were pre-existing in the original Pose prior to calling modify()
std::set< Intervalintervals_containing_new_positions () const
 return all intervals containing positions that are "new" and did not exist in the original Pose
std::set< Intervalintervals_containing_defined_positions () const
 return all intervals containing positions with defined conformation
std::set< Intervalintervals_containing_undefined_positions () const
 return all intervals containing positions with undefined conformation
std::set< Intervaloriginal_intervals_containing_kept_positions () const
 return all original intervals containing positions that will be kept by the BuildInstructions
std::set< Intervaloriginal_intervals_containing_deleted_positions () const
 return all original intervals containing positions that will be deleted by the BuildInstructions
Positions positions () const
 return all positions within the modified intervals
Positions preexisting_positions () const
 return the set of positions within the new regions that were pre-existing in the original Pose prior to calling modify()
Positions new_positions () const
 return a copy of the set of positions that are "new" and did not exist in the original Pose.
Positions defined_positions () const
 return a copy of the set of positions within the newly modified regions that have a defined conformation. E.g. existing or copied residues.
Positions undefined_positions () const
 return a copy of the set of positions within the newly modified regions that have an undefined conformation. E.g. newly created residues.
Positions union_of_intervals_containing_undefined_positions () const
 the positions representing the union of all intervals containing positions with undefined conformation
Positions original_kept_positions () const
 return the set of positions within the original intervals that will be kept by the BuildInstructions
Positions original_deleted_positions () const
 return set of positions within the original intervals that will be deleted by the BuildInstructions
Interval2Positions modified_i2p_preexisting () const
 return a map from modified intervals to the set of pre-existing positions inside them
Interval2Positions modified_i2p_new () const
 return a map from modified intervals to the set of "new" positions inside them that were not present in the original Pose
Interval2Positions modified_i2p_defined () const
 return a map from modified intervals to the set of positions inside them that have defined conformation
Interval2Positions modified_i2p_undefined () const
 return a map from modified intervals to the set of positions inside them that have undefined conformation
Interval2MoveMap modified_interval2movemap () const
 return a map from modified intervals to their individual movemaps
Interval2Positions original_i2p_kept () const
 return a map from original intervals to the set of positions inside them that will be kept by the BuildInstructions
Interval2Positions original_i2p_deleted () const
 return a map from original intervals to the set of positions inside them that will be deleted by the BuildInstructions

Detailed Description

a container for managing BuildInstructions

Note:
Compatibility checks wrt dependencies currently do not exist. It remains to be seen how to handle this.

Member Typedef Documentation

typedef BuildInstructionOPs::const_iterator protocols::forge::build::BuildManager::BIOPConstIterator
typedef BuildInstructionOPs::iterator protocols::forge::build::BuildManager::BIOPIterator

Constructor & Destructor Documentation

protocols::forge::build::BuildManager::BuildManager ( )

default constructor

Referenced by clone(), and create().

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

copy constructor

References add(), begin(), and end().

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

default destructor


Member Function Documentation

void protocols::forge::build::BuildManager::add ( BuildInstructionOP  bi)
BIOPConstIterator protocols::forge::build::BuildManager::begin ( ) const [inline]
void protocols::forge::build::BuildManager::clear ( )

clear all instructions

Referenced by operator=().

BuildManager::Size protocols::forge::build::BuildManager::clear_dependencies ( )

clear all dependencies

Returns:
number of dependencies dropped
BuildManagerOP protocols::forge::build::BuildManager::clone ( ) const [virtual]

clone this object

References BuildManager().

bool protocols::forge::build::BuildManager::compatibility_check ( ) const

check if instruction regions are compatible with each other

Returns:
true if regions compatible, false if regions incompatible

References begin(), and end().

Referenced by modify().

BuildManagerOP protocols::forge::build::BuildManager::create ( ) const [virtual]

create a new instance of this type of object

References BuildManager().

void protocols::forge::build::BuildManager::create_directed_dependency ( BuildInstructionOP  u,
BuildInstructionOP  v 
)

create a directed dependency: instruction 'u' must complete before instruction 'v' can complete, i.e. 'v' depends on 'u'

References core::kinematics::distance().

Referenced by protocols::forge::components::BDR::create_directed_dependency(), and protocols::fldsgn::BluePrintBDR::create_directed_dependency().

BuildManager::Positions protocols::forge::build::BuildManager::defined_positions ( ) const

return a copy of the set of positions within the newly modified regions that have a defined conformation. E.g. existing or copied residues.

Returns:
If modify() has not been called will return an empty set.

References begin(), and end().

bool protocols::forge::build::BuildManager::dependencies_exist ( ) const [inline]

have dependencies been defined?

BuildManager::Size protocols::forge::build::BuildManager::dummy_modify ( Size const  nres)

a dry run of modify() with an all-ala helical Pose of the given length

Parameters:
[in]nresThe length of the dummy structure to use.
Returns:
The final length of the modified Pose.
Remarks:
Use this to do a fake run of modify() if you need any position or mapping information prior to actually calling modify().

References core::pose::make_pose_from_sequence(), and modify().

bool protocols::forge::build::BuildManager::empty ( ) const [inline]
BIOPConstIterator protocols::forge::build::BuildManager::end ( ) const [inline]
std::set< Interval > protocols::forge::build::BuildManager::intervals ( ) const

return all modified intervals

Remarks:
Since this encompasses everything this is typically not useful except for overall tracking purposes.
Returns:
If modify() has not been called will return an empty set.

References begin(), end(), and protocols::forge::build::BuildInstruction::interval().

Referenced by intervals_containing_defined_positions(), intervals_containing_new_positions(), intervals_containing_preexisting_positions(), intervals_containing_undefined_positions(), intervals_without_valid_original_equivalents(), original_intervals_containing_deleted_positions(), and original_intervals_containing_kept_positions().

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_defined_positions ( ) const

return all intervals containing positions with defined conformation

Returns:
If modify() has not been called will return an empty set.

References begin(), protocols::forge::build::BuildInstruction::defined_positions(), end(), protocols::forge::build::BuildInstruction::interval(), and intervals().

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_new_positions ( ) const

return all intervals containing positions that are "new" and did not exist in the original Pose

Returns:
If modify() has not been called will return an empty set.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), and protocols::forge::build::BuildInstruction::new_positions().

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_preexisting_positions ( ) const

return all intervals containing positions that were pre-existing in the original Pose prior to calling modify()

Returns:
If modify() has not been called will return an empty set.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), and protocols::forge::build::BuildInstruction::preexisting_positions().

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_undefined_positions ( ) const

return all intervals containing positions with undefined conformation

Remarks:
typically used to define intervals appropriate for loop modeling
Returns:
If modify() has not been called will return an empty set.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), and protocols::forge::build::BuildInstruction::undefined_positions().

Referenced by protocols::forge::components::VarLengthBuild::centroid_build().

std::set< Interval > protocols::forge::build::BuildManager::intervals_without_valid_original_equivalents ( ) const

return modified intervals that have no equivalent original interval in their BuildInstructions (original_interval_valid() = false)

Remarks:
This is for cases such as insertions where there is no equivalent original region.
Returns:
If modify() has not been called will return an empty set.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), intervals(), and protocols::forge::build::BuildInstruction::original_interval_valid().

BuildManager::Modified2Original protocols::forge::build::BuildManager::modified2original_interval_endpoints ( ) const

return a map translating modified interval endpoints to original interval endpoints

Remarks:
modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map
Returns:
map; empty if modify() has not yet been called
Remarks:
modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::Interval::left, protocols::forge::build::BuildInstruction::original_interval(), protocols::forge::build::BuildInstruction::original_interval_valid(), and protocols::forge::build::Interval::right.

BuildManager::Interval2Interval protocols::forge::build::BuildManager::modified2original_intervals ( ) const

return a map translating modified intervals to original intervals

Remarks:
modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map
Returns:
map; empty if modify() has not yet been called

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::BuildInstruction::original_interval(), and protocols::forge::build::BuildInstruction::original_interval_valid().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::modified_i2p_defined ( ) const

return a map from modified intervals to the set of positions inside them that have defined conformation

Returns:
If modify() has not been called will return an empty map.

References begin(), protocols::forge::build::BuildInstruction::defined_positions(), end(), and protocols::forge::build::BuildInstruction::interval().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::modified_i2p_new ( ) const

return a map from modified intervals to the set of "new" positions inside them that were not present in the original Pose

Returns:
If modify() has not been called will return an empty map.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), and protocols::forge::build::BuildInstruction::new_positions().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::modified_i2p_preexisting ( ) const

return a map from modified intervals to the set of pre-existing positions inside them

Returns:
If modify() has not been called will return an empty map.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), and protocols::forge::build::BuildInstruction::preexisting_positions().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::modified_i2p_undefined ( ) const

return a map from modified intervals to the set of positions inside them that have undefined conformation

Returns:
If modify() has not been called will return an empty map.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), and protocols::forge::build::BuildInstruction::undefined_positions().

BuildManager::Interval2MoveMap protocols::forge::build::BuildManager::modified_interval2movemap ( ) const

return a map from modified intervals to their individual movemaps

Returns:
If modify() has not been called will return an empty map.

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), and protocols::forge::build::BuildInstruction::movemap().

BuildManager::Original2Modified protocols::forge::build::BuildManager::modify ( Pose pose)
BuildManager::MoveMap protocols::forge::build::BuildManager::movemap ( ) const

return the combined movemap from all instructions in this manager

Returns:
If modify() has not been called will return an empty MoveMap.

References movemap_as_OP().

Referenced by protocols::forge::components::VarLengthBuild::centroid_build().

BuildManager::MoveMapOP protocols::forge::build::BuildManager::movemap_as_OP ( ) const

References begin(), and end().

Referenced by movemap().

Size protocols::forge::build::BuildManager::n_dependencies ( ) const [inline]

the number of dependencies currently defined (i.e. # of edges in the dependency graph)

BuildManager::Positions protocols::forge::build::BuildManager::new_positions ( ) const

return a copy of the set of positions that are "new" and did not exist in the original Pose.

Returns:
If modify() has not been called will return an empty set.

References begin(), and end().

Referenced by protocols::forge::components::VarLengthBuild::centroid_build().

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

copy assignment

References add(), begin(), clear(), and end().

BuildManager::Original2Modified const & protocols::forge::build::BuildManager::original2modified ( ) const

return a map translating original residue -> modified residue for positions that existed within both the original Pose and modified Pose

Returns:
map; empty if modify() has not yet been called

Referenced by protocols::forge::components::VarLengthBuild::apply(), and protocols::forge::components::VarLengthBuild::centroid_build().

BuildManager::Original2Modified protocols::forge::build::BuildManager::original2modified_interval_endpoints ( ) const

return a map translating original interval endpoints to modified interval endpoints

Remarks:
modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map
Returns:
map; empty if modify() has not yet been called

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::Interval::left, protocols::forge::build::BuildInstruction::original_interval(), protocols::forge::build::BuildInstruction::original_interval_valid(), and protocols::forge::build::Interval::right.

Referenced by modify().

BuildManager::Interval2Interval protocols::forge::build::BuildManager::original2modified_intervals ( ) const

return a map translating original intervals to modified intervals

Remarks:
modified intervals with no equivalent original interval (e.g. cases such as insertions) will not appear in this map
Returns:
map; empty if modify() has not yet been called
Remarks:
modified intervals with no equivalent original intervals (e.g. cases such as insertions) will not appear in this map
Returns:
map; empty if modify() has not yet been called

References begin(), end(), protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::BuildInstruction::original_interval(), and protocols::forge::build::BuildInstruction::original_interval_valid().

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

return set of positions within the original intervals that will be deleted by the BuildInstructions

Remarks:
returns valid data even without calling modify()

References begin(), and end().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::original_i2p_deleted ( ) const

return a map from original intervals to the set of positions inside them that will be deleted by the BuildInstructions

Remarks:
returns valid data even without calling modify()

References begin(), end(), protocols::forge::build::BuildInstruction::original_deleted_positions(), and protocols::forge::build::BuildInstruction::original_interval().

BuildManager::Interval2Positions protocols::forge::build::BuildManager::original_i2p_kept ( ) const

return a map from original intervals to the set of positions inside them that will be kept by the BuildInstructions

Remarks:
returns valid data even without calling modify()

References begin(), end(), protocols::forge::build::BuildInstruction::original_interval(), and protocols::forge::build::BuildInstruction::original_kept_positions().

std::set< Interval > protocols::forge::build::BuildManager::original_intervals_containing_deleted_positions ( ) const

return all original intervals containing positions that will be deleted by the BuildInstructions

Remarks:
returns valid data even without calling modify()

References begin(), end(), intervals(), protocols::forge::build::BuildInstruction::original_deleted_positions(), and protocols::forge::build::BuildInstruction::original_interval().

std::set< Interval > protocols::forge::build::BuildManager::original_intervals_containing_kept_positions ( ) const

return all original intervals containing positions that will be kept by the BuildInstructions

Remarks:
returns valid data even without calling modify()

References begin(), end(), intervals(), protocols::forge::build::BuildInstruction::original_interval(), and protocols::forge::build::BuildInstruction::original_kept_positions().

BuildManager::Positions protocols::forge::build::BuildManager::original_kept_positions ( ) const

return the set of positions within the original intervals that will be kept by the BuildInstructions

Remarks:
returns valid data even without calling modify()

References begin(), and end().

BuildManager::Positions protocols::forge::build::BuildManager::positions ( ) const

return all positions within the modified intervals

Remarks:
Since this encompasses everything this is typically not useful except for overall tracking purposes.
Returns:
If modify() has not been called will return an empty set.

References begin(), end(), protocols::forge::methods::insert_closed_range(), protocols::forge::build::Interval::left, and protocols::forge::build::Interval::right.

BuildManager::Positions protocols::forge::build::BuildManager::preexisting_positions ( ) const

return the set of positions within the new regions that were pre-existing in the original Pose prior to calling modify()

Returns:
If modify() has not been called will return an empty set.

References begin(), and end().

void protocols::forge::build::BuildManager::reset_accounting ( )

reset all accounting info (intervals, positions, etc) to initial state

Referenced by modify().

BuildManager::SequenceMappingCOP protocols::forge::build::BuildManager::sequence_mapping ( ) const

SequenceMapping consistent with the original -> modified mapping from the most recent modify() call.

returns a SequenceMapping of the sequence at index idx1 mapped to the sequence at idx2.

Returns:
valid Sequence mapping if modify() was called; otherwise returns NULL
Remarks:
This mapping contains the same information as original2modified() combined with original2modified_interval_endpoints().

References core::sequence::SequenceAlignment::length(), and core::sequence::SequenceAlignment::size().

Size protocols::forge::build::BuildManager::size ( ) const [inline]

current number of instructions

Referenced by protocols::fldsgn::BluePrintBDR::instruction_size().

BuildManager::Positions protocols::forge::build::BuildManager::undefined_positions ( ) const

return a copy of the set of positions within the newly modified regions that have an undefined conformation. E.g. newly created residues.

Returns:
If modify() has not been called will return an empty set.

References begin(), and end().

BuildManager::Positions protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions ( ) const

the positions representing the union of all intervals containing positions with undefined conformation

Remarks:
Useful as a reference for defining neighborhoods around loop modeled regions.
Returns:
If modify() has not been called will return an empty set.

References begin(), end(), protocols::forge::methods::insert_closed_range(), protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::Interval::left, protocols::forge::build::Interval::right, and protocols::forge::build::BuildInstruction::undefined_positions().

Referenced by protocols::forge::components::BDR::apply(), and protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover().


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