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protocols::nonlocal::BiasedFragmentMover Class Reference

#include <BiasedFragmentMover.hh>

Inheritance diagram for protocols::nonlocal::BiasedFragmentMover:
Inheritance graph
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Public Member Functions

 BiasedFragmentMover (PolicyOP const &policy, Probabilities const &probs)
 Creates a new BiasedFragmentMover that selects uniformly from the available fragments at the selected insertion position. More...
 
 ~BiasedFragmentMover () override=default
 
void apply (core::pose::Pose &pose) override
 Inserts a single fragment into pose. More...
 
std::string get_name () const override
 Returns the name of this mover. 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Private Types

typedef boost::unordered_map
< unsigned,
core::fragment::Frame
FrameMap
 
typedef core::fragment::FragSetCOP FragSetCOP
 
typedef utility::vector1
< core::Real
Probabilities
 

Private Member Functions

void initialize_library ()
 Creates a position-indexable list of Frames. More...
 
void initialize_probabilities ()
 Generates cdf from pdf. More...
 
void verify_probabilities_or_die (const core::kinematics::FoldTree &tree) const
 Verifies that the probability of selecting invalid positions is 0. More...
 
unsigned random_position () const
 Returns a randomly chosen position according to the input probabilities. More...
 

Private Attributes

core::kinematics::MoveMap movable_
 Avoid creating a useless MoveMap for each call to Frame::apply(). More...
 
FragSetCOP fragments_
 Fragment library. More...
 
FrameMap frames_
 Position-indexable Frame lookup. More...
 
PolicyOP policy_
 Guidance for selecting the fragment to be inserted at a given position. More...
 
Probabilities pdf_
 PDF of residue sampling probabilities. Must remain in sync with cdf_. More...
 
Probabilities cdf_
 CDF of residue sampling probabilities. Must remain in sync with pdf_. More...
 

Additional Inherited Members

- 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
 
- 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...
 
- 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 boost::unordered_map<unsigned, core::fragment::Frame> protocols::nonlocal::BiasedFragmentMover::FrameMap
private

Constructor & Destructor Documentation

protocols::nonlocal::BiasedFragmentMover::BiasedFragmentMover ( PolicyOP const &  policy,
Probabilities const &  probs 
)

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

References fragments_, initialize_library(), initialize_probabilities(), movable_, and core::kinematics::MoveMap::set_bb().

protocols::nonlocal::BiasedFragmentMover::~BiasedFragmentMover ( )
overridedefault

Member Function Documentation

void protocols::nonlocal::BiasedFragmentMover::apply ( core::pose::Pose pose)
overridevirtual

Inserts a single fragment into pose.

Insertion position is chosen in a biased manner using the per-residue probabilities provided in the constructor. The decision on which fragment to insert from the fragment library is delegated to the policy specified in the constructor.

Respects the underlying kinematics of the system.

Implements protocols::moves::Mover.

References core::fragment::Frame::apply(), core::pose::Pose::fold_tree(), frames_, movable_, policy_, random_position(), and verify_probabilities_or_die().

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

Returns the name of this mover.

Implements protocols::moves::Mover.

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

Creates a position-indexable list of Frames.

Creates a position-indexable Frame lookup

References fragments_, and frames_.

Referenced by BiasedFragmentMover().

void protocols::nonlocal::BiasedFragmentMover::initialize_probabilities ( )
private

Generates cdf from pdf.

Computes cdf from pdf. cumulative() takes care of normalization.

References cdf_, and pdf_.

Referenced by BiasedFragmentMover().

unsigned protocols::nonlocal::BiasedFragmentMover::random_position ( ) const
private

Returns a randomly chosen position according to the input probabilities.

Selects the insertion position in a weighted random fashion using binary search on the cdf

References cdf_.

Referenced by apply().

void protocols::nonlocal::BiasedFragmentMover::verify_probabilities_or_die ( const core::kinematics::FoldTree tree) const
private

Verifies that the probability of selecting invalid positions is 0.

Verifies that the probability of selecting invalid positions is 0

References core::kinematics::FoldTree::cutpoint(), fragments_, core::kinematics::FoldTree::num_cutpoint(), pdf_, and protocols::kinmatch::str().

Referenced by apply().

Member Data Documentation

Probabilities protocols::nonlocal::BiasedFragmentMover::cdf_
private

CDF of residue sampling probabilities. Must remain in sync with pdf_.

Referenced by initialize_probabilities(), and random_position().

FragSetCOP protocols::nonlocal::BiasedFragmentMover::fragments_
private
FrameMap protocols::nonlocal::BiasedFragmentMover::frames_
private

Position-indexable Frame lookup.

Referenced by apply(), and initialize_library().

core::kinematics::MoveMap protocols::nonlocal::BiasedFragmentMover::movable_
private

Avoid creating a useless MoveMap for each call to Frame::apply().

Referenced by apply(), and BiasedFragmentMover().

Probabilities protocols::nonlocal::BiasedFragmentMover::pdf_
private

PDF of residue sampling probabilities. Must remain in sync with cdf_.

Referenced by initialize_probabilities(), and verify_probabilities_or_die().

PolicyOP protocols::nonlocal::BiasedFragmentMover::policy_
private

Guidance for selecting the fragment to be inserted at a given position.

Referenced by apply().


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