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

a container for managing BuildInstructions More...

#include <BuildManager.hh>

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

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< core::Size,
core::Size
DependencyEdge
 
typedef utility::vector1
< DependencyEdge
DependencyEdges
 
typedef std::set< core::SizePositions
 
typedef std::map< core::Size,
core::Size
Original2Modified
 
typedef std::map< core::Size,
core::Size
Modified2Original
 
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 More...
 
 BuildManager (BuildManager const &rval)
 copy constructor More...
 
 ~BuildManager () override
 default destructor More...
 
BuildManageroperator= (BuildManager const &rval)
 copy assignment More...
 
virtual BuildManagerOP clone () const
 clone this object More...
 
virtual BuildManagerOP create () const
 create a new instance of this type of object More...
 
void reset_accounting ()
 reset all accounting info (intervals, positions, etc) to initial state More...
 
void add (BuildInstructionOP bi)
 add an instruction directly (no copy) More...
 
void clear ()
 clear all instructions More...
 
core::Size size () const
 current number of instructions More...
 
bool empty () const
 no instructions? More...
 
BIOPConstIterator begin () const
 const iterator pointing to the first instruction More...
 
BIOPConstIterator end () const
 const iterator pointing just beyond the last instruction More...
 
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' More...
 
core::Size n_dependencies () const
 the number of dependencies currently defined (i.e. # of edges in the dependency graph) More...
 
bool dependencies_exist () const
 have dependencies been defined? More...
 
core::Size clear_dependencies ()
 clear all dependencies More...
 
Original2Modified modify (Pose &pose)
 modify the pose using the instructions in this container More...
 
core::Size dummy_modify (core::Size const nres)
 a dry run of modify() with an all-ala helical Pose of the given length More...
 
bool compatibility_check () const
 check if instruction regions are compatible with each other More...
 
MoveMap movemap () const
 return the combined movemap from all instructions in this manager More...
 
MoveMapOP movemap_as_OP () const
 
SequenceMappingCOP sequence_mapping () const
 SequenceMapping consistent with the original -> modified mapping from the most recent modify() call. More...
 
Original2Modified const & original2modified () const
 return a map translating original residue -> modified residue for positions that existed within both the original Pose and modified Pose More...
 
Interval2Interval original2modified_intervals () const
 return a map translating original intervals to modified intervals More...
 
Original2Modified original2modified_interval_endpoints () const
 return a map translating original interval endpoints to modified interval endpoints More...
 
Interval2Interval modified2original_intervals () const
 return a map translating modified intervals to original intervals More...
 
Modified2Original modified2original_interval_endpoints () const
 return a map translating modified interval endpoints to original interval endpoints More...
 
std::set< Intervalintervals () const
 return all modified intervals More...
 
std::set< Intervalintervals_without_valid_original_equivalents () const
 return modified intervals that have no equivalent original interval in their BuildInstructions (original_interval_valid() = false) More...
 
std::set< Intervalintervals_containing_preexisting_positions () const
 return all intervals containing positions that were pre-existing in the original Pose prior to calling modify() More...
 
std::set< Intervalintervals_containing_new_positions () const
 return all intervals containing positions that are "new" and did not exist in the original Pose More...
 
std::set< Intervalintervals_containing_defined_positions () const
 return all intervals containing positions with defined conformation More...
 
std::set< Intervalintervals_containing_undefined_positions () const
 return all intervals containing positions with undefined conformation More...
 
std::set< Intervaloriginal_intervals_containing_kept_positions () const
 return all original intervals containing positions that will be kept by the BuildInstructions More...
 
std::set< Intervaloriginal_intervals_containing_deleted_positions () const
 return all original intervals containing positions that will be deleted by the BuildInstructions More...
 
Positions positions () const
 return all positions within the modified intervals More...
 
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() More...
 
Positions new_positions () const
 return a copy of the set of positions that are "new" and did not exist in the original Pose. More...
 
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. More...
 
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. More...
 
Positions union_of_intervals_containing_undefined_positions () const
 the positions representing the union of all intervals containing positions with undefined conformation More...
 
Positions original_kept_positions () const
 return the set of positions within the original intervals that will be kept by the BuildInstructions More...
 
Positions original_deleted_positions () const
 return set of positions within the original intervals that will be deleted by the BuildInstructions More...
 
Interval2Positions modified_i2p_preexisting () const
 return a map from modified intervals to the set of pre-existing positions inside them More...
 
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 More...
 
Interval2Positions modified_i2p_defined () const
 return a map from modified intervals to the set of positions inside them that have defined conformation More...
 
Interval2Positions modified_i2p_undefined () const
 return a map from modified intervals to the set of positions inside them that have undefined conformation More...
 
Interval2MoveMap modified_interval2movemap () const
 return a map from modified intervals to their individual movemaps More...
 
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 More...
 
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 More...
 

Private Types

typedef utility::VirtualBase Super
 

Private Member Functions

BIOPIterator find_instruction (BuildInstructionCOP u)
 find the given instruction More...
 
BIOPConstIterator find_instruction (BuildInstructionCOP u) const
 find the given instruction More...
 
DependencyEdges::iterator find_dependency (BuildInstructionCOP u, BuildInstructionCOP v)
 find the given dependency More...
 
DependencyEdges::const_iterator find_dependency (BuildInstructionCOP u, BuildInstructionCOP v) const
 find the given dependency More...
 
void reconstruct_dependencies (DependencyEdges const &dependency_list)
 clear the current dependency list and reconstruct the dependencies using the given list More...
 

Private Attributes

BuildInstructionOPs instructions_
 the list of BuildInstructions to apply More...
 
DependencyEdges instruction_dependencies_
 list recording BuildInstruction inter-dependencies by index into instructions_ array More...
 
Original2Modified original2modified_
 map translation old residue -> new residue for non-modified regions only More...
 
SequenceMappingOP seqmap_
 SequenceMapping consistent with the old -> new mapping from the most recent modify() call. More...
 
bool modify_was_successful_
 indicates modify() has been called and succeeded More...
 

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
typedef utility::VirtualBase protocols::forge::build::BuildManager::Super
private

Constructor & Destructor Documentation

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

default constructor

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

copy constructor

References add(), and reconstruct_dependencies().

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

default destructor

Member Function Documentation

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

const iterator pointing to the first instruction

References instructions_.

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

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

clear all instructions

References instruction_dependencies_, and instructions_.

Referenced by operator=().

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

clear all dependencies

Returns
number of dependencies dropped

References instruction_dependencies_, and instructions_.

Referenced by reconstruct_dependencies().

BuildManagerOP protocols::forge::build::BuildManager::clone ( ) const
virtual

clone this object

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

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(), find_instruction(), instruction_dependencies_, and instructions_.

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

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 modify_was_successful_.

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

have dependencies been defined?

References instruction_dependencies_.

BuildManager::Size protocols::forge::build::BuildManager::dummy_modify ( core::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 instructions_, core::pose::make_pose_from_sequence(), and modify().

Referenced by protocols::forge::remodel::RemodelMover::apply().

bool protocols::forge::build::BuildManager::empty ( ) const
inline

no instructions?

References instructions_.

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

BIOPConstIterator protocols::forge::build::BuildManager::end ( ) const
inline

const iterator pointing just beyond the last instruction

References instructions_.

Referenced by compatibility_check().

BuildManager::DependencyEdges::iterator protocols::forge::build::BuildManager::find_dependency ( BuildInstructionCOP  u,
BuildInstructionCOP  v 
)
private

find the given dependency

find the edge specifying the given dependency

Returns
iterator pointing to the DependencyEdge if found, otherwise the 'end' iterator

References instruction_dependencies_, and instructions_.

BuildManager::DependencyEdges::const_iterator protocols::forge::build::BuildManager::find_dependency ( BuildInstructionCOP  u,
BuildInstructionCOP  v 
) const
private

find the given dependency

Returns
const iterator pointing to the DependencyEdge if found, otherwise the 'end' const iterator

References instruction_dependencies_, and instructions_.

BuildManager::BIOPIterator protocols::forge::build::BuildManager::find_instruction ( BuildInstructionCOP  u)
private

find the given instruction

Returns
iterator pointing to the BuildInstructionOP if found, otherwise the 'end' iterator

References instructions_, and protocols::hybridization::u.

Referenced by create_directed_dependency().

BuildManager::BIOPConstIterator protocols::forge::build::BuildManager::find_instruction ( BuildInstructionCOP  u) const
private

find the given instruction

Returns
iterator pointing to the BuildInstructionCOP if found, otherwise the 'end' iterator

References instructions_, and protocols::hybridization::u.

std::set< Interval > protocols::forge::build::BuildManager::intervals ( ) const
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 protocols::forge::build::BuildInstruction::defined_positions(), protocols::forge::build::BuildInstruction::interval(), intervals(), and modify_was_successful_.

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 protocols::forge::build::BuildInstruction::interval(), intervals(), modify_was_successful_, 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 protocols::forge::build::BuildInstruction::interval(), intervals(), modify_was_successful_, and protocols::forge::build::BuildInstruction::preexisting_positions().

std::set< Interval > protocols::forge::build::BuildManager::intervals_containing_undefined_positions ( ) const
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 protocols::forge::build::BuildInstruction::interval(), intervals(), modify_was_successful_, 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 protocols::forge::build::BuildInstruction::interval(), protocols::forge::build::Interval::left, modify_was_successful_, 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 protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, 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 protocols::forge::build::BuildInstruction::defined_positions(), protocols::forge::build::BuildInstruction::interval(), and modify_was_successful_.

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 protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, 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 protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, 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 protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, 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 protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, and protocols::forge::build::BuildInstruction::movemap().

BuildManager::Original2Modified protocols::forge::build::BuildManager::modify ( Pose pose)

modify the pose using the instructions in this container

Parameters
[in,out]posethe Pose to modify
Returns
a map translating original residue -> modified residue for positions that existed within both the original Pose and modified Pose

References protocols::cluster::calibur::aa, core::chemical::aa_vrt, protocols::loops::Loops::add_loop(), core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::append_residue_by_jump(), core::conformation::Conformation::chains_from_termini(), protocols::forge::methods::closed_range(), compatibility_check(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::conformation::get_anchor_atomno(), instructions_, core::chemical::LOWER_TERMINUS_VARIANT, protocols::forge::methods::make_star_foldtree(), protocols::forge::build::BuildInstruction::modify(), protocols::forge::build::BuildInstruction::modify_was_successful(), modify_was_successful_, protocols::simple_filters::ne, protocols::forge::build::BuildInstruction::new_positions(), original2modified_, original2modified_interval_endpoints(), protocols::forge::build::BuildInstruction::original_deleted_positions(), protocols::make_rot_lib::PEPTIDE, reset_accounting(), core::pose::Pose::residue(), seqmap_, core::pose::Pose::size(), protocols::forge::build::TR(), core::chemical::UPPER_TERMINUS_VARIANT, and core::pose::virtual_type_for_pose().

Referenced by protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), and dummy_modify().

BuildManager::MoveMap protocols::forge::build::BuildManager::movemap ( ) const
BuildManager::MoveMapOP protocols::forge::build::BuildManager::movemap_as_OP ( ) const
core::Size protocols::forge::build::BuildManager::n_dependencies ( ) const
inline

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

References instruction_dependencies_.

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 modify_was_successful_.

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

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

References original2modified_.

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

BuildManager::Original2Modified protocols::forge::build::BuildManager::original2modified_interval_endpoints ( ) const
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 protocols::forge::build::BuildInstruction::interval(), modify_was_successful_, 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()
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 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 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 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 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()
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 protocols::forge::methods::insert_closed_range(), protocols::forge::build::Interval::left, modify_was_successful_, 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 modify_was_successful_.

void protocols::forge::build::BuildManager::reconstruct_dependencies ( DependencyEdges const &  dependency_list)
private

clear the current dependency list and reconstruct the dependencies using the given list

References clear_dependencies(), create_directed_dependency(), and instructions_.

Referenced by BuildManager(), and operator=().

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

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

References instructions_, modify_was_successful_, original2modified_, and seqmap_.

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
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 seqmap_.

core::Size protocols::forge::build::BuildManager::size ( ) const
inline
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 modify_was_successful_.

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

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

Member Data Documentation

DependencyEdges protocols::forge::build::BuildManager::instruction_dependencies_
private

list recording BuildInstruction inter-dependencies by index into instructions_ array

Remarks
For each pair "first,second" in the list, the instruction with index "first" must complete before the instruction with index "second" I.e. "second" depends on "first".

Referenced by clear(), clear_dependencies(), create_directed_dependency(), dependencies_exist(), find_dependency(), and n_dependencies().

BuildInstructionOPs protocols::forge::build::BuildManager::instructions_
private
bool protocols::forge::build::BuildManager::modify_was_successful_
private
Original2Modified protocols::forge::build::BuildManager::original2modified_
private

map translation old residue -> new residue for non-modified regions only

Remarks
only filled in after modify() called

Referenced by modify(), operator=(), original2modified(), and reset_accounting().

SequenceMappingOP protocols::forge::build::BuildManager::seqmap_
private

SequenceMapping consistent with the old -> new mapping from the most recent modify() call.

Referenced by modify(), operator=(), reset_accounting(), and sequence_mapping().


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