FloppyTail mover. More...
#include <FloppyTailMover.hh>
Public Member Functions | |
| FloppyTailMover () | |
| ctor with no arguments More... | |
| FloppyTailMover (FloppyTailMover const &rhs) | |
| copy ctor More... | |
| FloppyTailMover & | operator= (FloppyTailMover const &rhs) |
| assignment operator More... | |
| ~FloppyTailMover () override | |
| virtual void | set_movemap (core::kinematics::MoveMapOP const movemap) |
| set the movemap instead of initializing it from cmd-line More... | |
| virtual void | set_fa_scorefxn (core::scoring::ScoreFunctionOP const fa_scorefxn) |
| virtual void | set_cen_scorefxn (core::scoring::ScoreFunctionOP const cen_scorefunction) |
| void | apply (core::pose::Pose &pose) override |
| Main Method. More... | |
| virtual void | low_res (core::pose::Pose &pose) |
| virtual void | high_res (core::pose::Pose &pose) |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Generates a new Mover object freshly created with the default ctor. More... | |
| bool | reinitialize_for_each_job () const override |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| bool | reinitialize_for_new_input () const override |
| 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... | |
 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... | |
| 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 Member Functions | |
| virtual void | init_on_new_input (core::pose::Pose const &pose) |
| init_on_new_input system allows for initializing these details the first time apply() is called. The job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply()). More... | |
Private Attributes | |
| core::Size | start_ |
| core::Size | stop_ |
| bool | init_for_input_yet_ |
| core::scoring::ScoreFunctionOP | centroid_scorefunction_ |
| core::scoring::ScoreFunctionOP | fullatom_scorefunction_ |
| core::pack::task::TaskFactoryOP | task_factory_ |
| core::kinematics::MoveMapOP | movemap_ |
| core::kinematics::MoveMapOP | movemap_lesstail_ |
| core::kinematics::FoldTreeOP | foldtree_ |
| stored so that it can be generated in the init_on_new_input function More... | |
| core::fragment::ConstantLengthFragSetOP | fragset3mer_ |
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... | |
Detailed Description
FloppyTail mover.
Constructor & Destructor Documentation
◆ FloppyTailMover() [1/2]
| protocols::floppy_tail::FloppyTailMover::FloppyTailMover | ( | ) |
ctor with no arguments
References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), core::scoring::cbeta, core::scoring::cenpack, centroid_scorefunction_, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::env, core::scoring::fa_pair, fragset3mer_, fullatom_scorefunction_, core::scoring::get_score_function(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::pair, core::scoring::rama, protocols::TR(), protocols::moves::Mover::type(), and core::scoring::vdw.
◆ FloppyTailMover() [2/2]
| protocols::floppy_tail::FloppyTailMover::FloppyTailMover | ( | FloppyTailMover const & | rhs | ) |
copy ctor
◆ ~FloppyTailMover()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), protocols::moves::AddPyMOLObserver(), protocols::floppy_tail::create_extra_output(), core::pose::Pose::fold_tree(), foldtree_, fullatom_scorefunction_, high_res(), init_for_input_yet_, init_on_new_input(), low_res(), movemap_, movemap_lesstail_, protocols::moves::MS_SUCCESS, protocols::moves::Mover::set_last_move_status(), core::kinematics::simple_visualize_fold_tree_and_movemap(), core::pose::Pose::size(), stop_, and protocols::TR().
◆ fresh_instance()
|
inlineoverridevirtual |
Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
inlineoverridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ high_res()
|
virtual |
References fullatom_scorefunction_, core::pose::symmetry::is_symmetric(), movemap_, movemap_lesstail_, task_factory_, and protocols::TR().
Referenced by apply().
◆ init_on_new_input()
|
privatevirtual |
init_on_new_input system allows for initializing these details the first time apply() is called. The job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply()).
init_on_new_input system allows for initializing these details the first time apply() is called. the job distributor will reinitialize the whole mover when the input changes (a freshly constructed mover, which will re-run this on first apply().
References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), foldtree_, core::pose::symmetry::get_nres_asymmetric_unit(), init_for_input_yet_, core::pose::metrics::CalculatorFactory::Instance(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_terminus(), core::kinematics::linearize_fold_tree(), core::pose::symmetry::make_symmetric_movemap(), movemap_, movemap_lesstail_, core::conformation::Conformation::num_chains(), core::pose::Pose::pdb_info(), core::pose::metrics::CalculatorFactory::register_calculator(), core::pose::metrics::CalculatorFactory::remove_calculator(), core::pose::Pose::residue(), core::conformation::symmetry::residue_center_of_mass(), core::pose::Pose::size(), start_, stop_, task_factory_, and protocols::TR().
Referenced by apply().
◆ low_res()
|
virtual |
References core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::moves::PDBDumpMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID, centroid_scorefunction_, core::pack::interaction_graph::debug, fragset3mer_, movemap_, protocols::jd2::output_intermediate_pose(), core::pose::Pose::remove_constraints(), and protocols::TR().
Referenced by apply().
◆ operator=()
| FloppyTailMover & protocols::floppy_tail::FloppyTailMover::operator= | ( | FloppyTailMover const & | rhs | ) |
assignment operator
References centroid_scorefunction_, foldtree_, fragset3mer_, fullatom_scorefunction_, init_for_input_yet_, movemap_, movemap_lesstail_, start_, stop_, and task_factory_.
◆ reinitialize_for_each_job()
|
inlineoverridevirtual |
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.
Movers default to not regenerating
Reimplemented from protocols::moves::Mover.
◆ reinitialize_for_new_input()
|
inlineoverridevirtual |
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).
Movers default to not regenerating
Reimplemented from protocols::moves::Mover.
◆ set_cen_scorefxn()
|
virtual |
References centroid_scorefunction_.
◆ set_fa_scorefxn()
|
virtual |
References fullatom_scorefunction_.
◆ set_movemap()
|
virtual |
set the movemap instead of initializing it from cmd-line
References movemap_.
Member Data Documentation
◆ centroid_scorefunction_
|
private |
Referenced by FloppyTailMover(), low_res(), operator=(), and set_cen_scorefxn().
◆ foldtree_
|
private |
stored so that it can be generated in the init_on_new_input function
Referenced by apply(), init_on_new_input(), and operator=().
◆ fragset3mer_
|
private |
Referenced by FloppyTailMover(), low_res(), and operator=().
◆ fullatom_scorefunction_
|
private |
Referenced by apply(), FloppyTailMover(), high_res(), operator=(), and set_fa_scorefxn().
◆ init_for_input_yet_
|
private |
Referenced by apply(), init_on_new_input(), and operator=().
◆ movemap_
|
private |
Referenced by apply(), high_res(), init_on_new_input(), low_res(), operator=(), and set_movemap().
◆ movemap_lesstail_
|
private |
Referenced by apply(), high_res(), init_on_new_input(), and operator=().
◆ start_
|
private |
Referenced by init_on_new_input(), and operator=().
◆ stop_
|
private |
Referenced by apply(), init_on_new_input(), and operator=().
◆ task_factory_
|
private |
Referenced by high_res(), init_on_new_input(), and operator=().
The documentation for this class was generated from the following files:
- src/protocols/floppy_tail/FloppyTailMover.hh
- src/protocols/floppy_tail/FloppyTailMover.cc
