#include <BiasedFragmentMover.hh>
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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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
◆ FragSetCOP
◆ FrameMap
|
private |
◆ Probabilities
|
private |
Constructor & Destructor Documentation
◆ BiasedFragmentMover()
| 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().
◆ ~BiasedFragmentMover()
|
overridedefault |
Member Function Documentation
◆ apply()
|
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().
◆ get_name()
|
overridevirtual |
Returns the name of this mover.
Implements protocols::moves::Mover.
◆ initialize_library()
|
private |
Creates a position-indexable list of Frames.
@detail Creates a position-indexable Frame lookup
References fragments_, and frames_.
Referenced by BiasedFragmentMover().
◆ initialize_probabilities()
|
private |
Generates cdf from pdf.
@detail Computes cdf from pdf. cumulative() takes care of normalization.
Referenced by BiasedFragmentMover().
◆ random_position()
|
private |
◆ verify_probabilities_or_die()
|
private |
Verifies that the probability of selecting invalid positions is 0.
@detail 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
◆ cdf_
|
private |
CDF of residue sampling probabilities. Must remain in sync with pdf_.
Referenced by initialize_probabilities(), and random_position().
◆ fragments_
|
private |
Fragment library.
Referenced by BiasedFragmentMover(), initialize_library(), and verify_probabilities_or_die().
◆ frames_
|
private |
Position-indexable Frame lookup.
Referenced by apply(), and initialize_library().
◆ movable_
|
private |
Avoid creating a useless MoveMap for each call to Frame::apply().
Referenced by apply(), and BiasedFragmentMover().
◆ pdf_
|
private |
PDF of residue sampling probabilities. Must remain in sync with cdf_.
Referenced by initialize_probabilities(), and verify_probabilities_or_die().
◆ 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:
- src/protocols/nonlocal/BiasedFragmentMover.hh
- src/protocols/nonlocal/BiasedFragmentMover.cc
