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protocols::nonlocal::SingleFragmentMover Class Reference

#include <SingleFragmentMover.hh>

Inheritance diagram for protocols::nonlocal::SingleFragmentMover:
Inheritance graph
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Public Types

typedef protocols::moves::Mover Mover
 
typedef protocols::moves::MoverOP MoverOP
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 SingleFragmentMover ()
 No-argument constructor required by RosettaScripts. The caller is responsible for initializing the instance. More...
 
 SingleFragmentMover (const FragSetOP &fragments, const MoveMapOP &movable)
 Creates a new SingleFragmentMover that selects uniformly from the available fragments at the selected insertion position. More...
 
 SingleFragmentMover (const FragSetOP &fragments, const MoveMapOP &movable, const PolicyOP &policy)
 Creates a new SingleFragmentMover that selects fragments at the selected insertion position using the given policy. More...
 
 ~SingleFragmentMover () override=default
 
void apply (Pose &pose) override
 Performs a single fragment insertion on <pose>, drawn from the set of fragments specified in the constructor. Respects the underlying kinematics of the system, as determined by the Pose's FoldTree and the user-specified MoveMap. Fragment insertions will only occur in allowable regions of the pose. No moves will span jumps in the FoldTree. More...
 
MoverOP clone () const override
 Returns the name of this mover. More...
 
MoverOP fresh_instance () const override
 Creates a new instance using the default constructor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Mover-specific parsing required by RosettaScripts. More...
 
bool valid () const
 Returns true if this instance is in a usable state, false otherwise. More...
 
void movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Types

typedef core::Real Real
 
typedef core::Size Size
 
typedef core::fragment::FragSetOP FragSetOP
 
typedef core::fragment::Frame Frame
 
typedef core::kinematics::FoldTree FoldTree
 
typedef
core::kinematics::FoldTreeOP 
FoldTreeOP
 
typedef core::kinematics::MoveMapOP MoveMapOP
 
typedef core::pose::Pose Pose
 
typedef boost::unordered_map
< core::Size, Frame
FrameMap
 
typedef utility::vector1< ChunkChunks
 

Private Member Functions

void initialize (const FragSetOP &fragments, const MoveMapOP &movable, const PolicyOP &policy)
 
void initialize_library ()
 Creates a position-indexable list of Frames. More...
 
void initialize_chunks (const FoldTree &tree, MoveMapOP const &movable)
 Creates a set of chunks by examining the stored MoveMap and FragSet in conjunction with <tree> More...
 
MoveMapOP movemap (core::pose::Pose const &pose)
 Get the movemap for this pose. More...
 
const Chunkrandom_chunk () const
 Returns a randomly chosen chunk with uniform probability. More...
 
bool to_centroid (Pose *pose) const
 If <pose> is fullatom, converts it to centroid and returns true. Otherwise, takes no action and returns false. More...
 

Private Attributes

FragSetOP fragments_
 The set of fragments to apply to the pose. More...
 
core::select::movemap::MoveMapFactoryCOP movemap_factory_
 Defines restrictions on which degrees of freedom in the system can be modified. More...
 
MoveMapOP movable_
 
PolicyOP policy_
 Selects the fragment to be inserted at <insertion_pos> given knowledge of the fragment library and the current state of the pose. More...
 
FoldTreeOP previous_tree_
 FoldTree used to initialize <chunks_> in a previous call to apply() More...
 
FrameMap library_
 Provides index-based access to the data contained in the FragSet. More...
 
Chunks chunks_
 Regions of sequence on which to perform fragment insertion. More...
 
utility::vector1< Realprobs_
 Probability of selecting chunk c_i. Proportional to chunk length. More...
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Member Typedef Documentation

typedef utility::vector1<Chunk> protocols::nonlocal::SingleFragmentMover::Chunks
private

Constructor & Destructor Documentation

protocols::nonlocal::SingleFragmentMover::SingleFragmentMover ( )

No-argument constructor required by RosettaScripts. The caller is responsible for initializing the instance.

protocols::nonlocal::SingleFragmentMover::SingleFragmentMover ( const FragSetOP fragments,
const MoveMapOP movable 
)

Creates a new SingleFragmentMover that selects uniformly from the available fragments at the selected insertion position.

References protocols::nonlocal::PolicyFactory::get_policy(), and initialize().

protocols::nonlocal::SingleFragmentMover::SingleFragmentMover ( const FragSetOP fragments,
const MoveMapOP movable,
const PolicyOP policy 
)

Creates a new SingleFragmentMover that selects fragments at the selected insertion position using the given policy.

References initialize().

protocols::nonlocal::SingleFragmentMover::~SingleFragmentMover ( )
overridedefault

Member Function Documentation

void protocols::nonlocal::SingleFragmentMover::apply ( Pose pose)
overridevirtual

Performs a single fragment insertion on <pose>, drawn from the set of fragments specified in the constructor. Respects the underlying kinematics of the system, as determined by the Pose's FoldTree and the user-specified MoveMap. Fragment insertions will only occur in allowable regions of the pose. No moves will span jumps in the FoldTree.

Assumptions:

  • <pose> has been instantiated (i.e. constructed from sequence or an alternate source) elsewhere
  • <pose>'s FoldTree is valid
  • <pose> is centroid-level (warning if full-atom)
  • The combination of FoldTree and MoveMap provide an unambiguous definition of what's movable and what's not

Implements protocols::moves::Mover.

References core::fragment::Frame::apply(), core::kinematics::FoldTree::check_fold_tree(), protocols::nonlocal::Chunk::choose(), chunks_, core::pose::Pose::fold_tree(), initialize_chunks(), library_, movemap(), policy_, previous_tree_, probs_, random_chunk(), core::pose::Pose::size(), to_centroid(), and valid().

protocols::moves::MoverOP protocols::nonlocal::SingleFragmentMover::clone ( ) const
overridevirtual

Returns the name of this mover.

Creates a new instance using the copy constructor

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::nonlocal::SingleFragmentMover::fresh_instance ( ) const
overridevirtual

Creates a new instance using the default constructor.

Reimplemented from protocols::moves::Mover.

std::string protocols::nonlocal::SingleFragmentMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

void protocols::nonlocal::SingleFragmentMover::initialize ( const FragSetOP fragments,
const MoveMapOP movable,
const PolicyOP policy 
)
private
void protocols::nonlocal::SingleFragmentMover::initialize_chunks ( const FoldTree tree,
MoveMapOP const &  movable 
)
private

Creates a set of chunks by examining the stored MoveMap and FragSet in conjunction with <tree>

References chunks_, fragments_, core::kinematics::FoldTree::is_cutpoint(), protocols::nonlocal::Chunk::is_movable(), core::chemical::element::N, probs_, core::chemical::rings::q, and core::simple_metrics::metrics::sum.

Referenced by apply().

void protocols::nonlocal::SingleFragmentMover::initialize_library ( )
private

Creates a position-indexable list of Frames.

References fragments_, and library_.

Referenced by initialize().

core::kinematics::MoveMapOP protocols::nonlocal::SingleFragmentMover::movemap ( core::pose::Pose const &  pose)
private

Get the movemap for this pose.

References movable_, and movemap_factory_.

Referenced by apply().

void protocols::nonlocal::SingleFragmentMover::movemap_factory ( core::select::movemap::MoveMapFactoryCOP  new_movemap_factory)
inline

References movemap_factory_.

Referenced by parse_my_tag().

std::string protocols::nonlocal::SingleFragmentMover::mover_name ( )
static
void protocols::nonlocal::SingleFragmentMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::nonlocal::SingleFragmentMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
const Chunk * protocols::nonlocal::SingleFragmentMover::random_chunk ( ) const
private

Returns a randomly chosen chunk with uniform probability.

References chunks_, and probs_.

Referenced by apply().

bool protocols::nonlocal::SingleFragmentMover::to_centroid ( Pose pose) const
private

If <pose> is fullatom, converts it to centroid and returns true. Otherwise, takes no action and returns false.

References core::chemical::CENTROID_t, core::pose::Pose::is_fullatom(), and core::util::switch_to_residue_type_set().

Referenced by apply().

bool protocols::nonlocal::SingleFragmentMover::valid ( ) const

Returns true if this instance is in a usable state, false otherwise.

References fragments_, movable_, movemap_factory_, and policy_.

Referenced by apply().

Member Data Documentation

Chunks protocols::nonlocal::SingleFragmentMover::chunks_
private

Regions of sequence on which to perform fragment insertion.

Referenced by apply(), initialize_chunks(), and random_chunk().

FragSetOP protocols::nonlocal::SingleFragmentMover::fragments_
private

The set of fragments to apply to the pose.

Referenced by initialize(), initialize_chunks(), initialize_library(), and valid().

FrameMap protocols::nonlocal::SingleFragmentMover::library_
private

Provides index-based access to the data contained in the FragSet.

Referenced by apply(), and initialize_library().

MoveMapOP protocols::nonlocal::SingleFragmentMover::movable_
private

Referenced by initialize(), movemap(), and valid().

core::select::movemap::MoveMapFactoryCOP protocols::nonlocal::SingleFragmentMover::movemap_factory_
private

Defines restrictions on which degrees of freedom in the system can be modified.

Referenced by movemap(), movemap_factory(), and valid().

PolicyOP protocols::nonlocal::SingleFragmentMover::policy_
private

Selects the fragment to be inserted at <insertion_pos> given knowledge of the fragment library and the current state of the pose.

Referenced by apply(), initialize(), and valid().

FoldTreeOP protocols::nonlocal::SingleFragmentMover::previous_tree_
private

FoldTree used to initialize <chunks_> in a previous call to apply()

Referenced by apply().

utility::vector1<Real> protocols::nonlocal::SingleFragmentMover::probs_
private

Probability of selecting chunk c_i. Proportional to chunk length.

Referenced by apply(), initialize_chunks(), and random_chunk().


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