#include <AbscriptLoopCloserCM.hh>
Public Member Functions | |
| AbscriptLoopCloserCM () | |
| AbscriptLoopCloserCM (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn) | |
| ~AbscriptLoopCloserCM () override | |
| EnvClaims | yield_claims (core::pose::Pose const &, basic::datacache::WriteableCacheableMapOP) override |
| Returns a list of claims for this mover. More... | |
| void | broking_finished (environment::EnvClaimBroker::BrokerResult const &) override |
| hook that provides information about the final result of broking at the very end, though this BrokerResult construct. More... | |
| core::select::residue_selector::ResidueSelectorCOP | selector () const |
| void | set_selector (core::select::residue_selector::ResidueSelectorCOP selector) |
| void | apply (core::pose::Pose &) override |
| Main Method. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| moves::MoverOP | clone () const override |
| Return a clone of the Mover object. More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
 Public Member Functions inherited from protocols::environment::ClientMover | |
| ClientMover () | |
| ClientMover (ClientMover const &) | |
| ~ClientMover () override | |
| virtual void | initialize (Pose &conf) |
| this method is called by the broking system in response to a successful initialization claim by this mover. The passport will prevent any unauthorized changes. More... | |
| virtual void | yield_submovers (std::set< ClientMoverOP > &) const |
| this method is used to make sure any movers contained in this mover (that want to make claims) also get registered with the environment. 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... | |
| 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 |
| 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... | |
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... | |
Protected Member Functions | |
| void | passport_updated () override |
| hook that is called each time the passport status is updated (presumably because there's a new subenvironment, or the sub- environment has expired). More... | |
| Protected Member Functions inherited from protocols::environment::ClientMover | |
| void | sandboxed_copy (core::pose::Pose const &sandbox_pose, core::pose::Pose &true_pose) const |
| convience method that copies all changes from an unprotected pose to a protected pose. More... | |
| EnvironmentCAP | active_environment () const |
| return a pointer the active environment More... | |
| core::environment::DofPassportCOP | passport () const |
| read-only access to the top passport in the passport stack. More... | |
| bool | has_passport () const |
| bool | state_check (std::string const &method_name, bool test) const |
| convienence method for failing a state-set call after brokering. 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... | |
Private Types | |
| typedef ClientMover | Parent |
| typedef environment::claims::EnvClaims | EnvClaims |
Private Member Functions | |
| void | attempt_idealize (core::pose::Pose &) |
| bool | attempt_ccd (core::pose::Pose &) |
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 |
Member Typedef Documentation
◆ EnvClaims
|
private |
◆ Parent
Constructor & Destructor Documentation
◆ AbscriptLoopCloserCM() [1/2]
| protocols::abinitio::abscript::AbscriptLoopCloserCM::AbscriptLoopCloserCM | ( | ) |
◆ AbscriptLoopCloserCM() [2/2]
| protocols::abinitio::abscript::AbscriptLoopCloserCM::AbscriptLoopCloserCM | ( | core::fragment::FragSetCOP | fragset, |
| core::scoring::ScoreFunctionOP | scorefxn | ||
| ) |
◆ ~AbscriptLoopCloserCM()
|
inlineoverride |
Member Function Documentation
◆ apply()
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overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References protocols::abinitio::abscript::angle_cpy(), attempt_ccd(), attempt_idealize(), core::id::BB, core::pose::Pose::conformation(), protocols::moves::FAIL_DO_NOT_RETRY, final_ft_, core::pose::Pose::fold_tree(), get_name(), movemap_, core::conformation::Residue::name3(), core::id::omega_torsion(), protocols::environment::ClientMover::passport(), core::id::phi_torsion(), core::id::psi_torsion(), core::pose::Pose::residue(), protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_new_conformation(), core::pose::Pose::size(), and tr().
◆ attempt_ccd()
|
private |
References protocols::jumping::close_chainbreaks(), protocols::moves::FAIL_DO_NOT_RETRY, final_ft_, fragset_, protocols::moves::Mover::get_current_tag(), get_name(), protocols::mean_field::min(), movemap_, scorefxn_, protocols::moves::Mover::set_current_tag(), protocols::moves::Mover::set_last_move_status(), and tr().
Referenced by apply().
◆ attempt_idealize()
|
private |
References final_ft_, core::pose::Pose::fold_tree(), get_name(), movemap_, core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::size(), and tr().
Referenced by apply().
◆ broking_finished()
|
overridevirtual |
hook that provides information about the final result of broking at the very end, though this BrokerResult construct.
Reimplemented from protocols::environment::ClientMover.
References protocols::environment::EnvClaimBroker::BrokerResult::closer_ft, and final_ft_.
◆ clone()
|
overridevirtual |
Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. 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.
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
Referenced by apply(), attempt_ccd(), and attempt_idealize().
◆ mover_name()
|
static |
◆ parse_my_tag()
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overridevirtual |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References core::scoring::atom_pair_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), fragset_, core::select::residue_selector::get_residue_selector(), core::scoring::linear_chainbreak, core::scoring::parse_score_function(), core::fragment::FragmentIO::read_data(), scorefxn_, set_selector(), and tr().
◆ passport_updated()
|
overrideprotectedvirtual |
hook that is called each time the passport status is updated (presumably because there's a new subenvironment, or the sub- environment has expired).
Reimplemented from protocols::environment::ClientMover.
References protocols::environment::ClientMover::has_passport(), movemap_, and protocols::environment::ClientMover::passport().
◆ provide_xml_schema()
|
static |
References core::select::residue_selector::attributes_for_parse_residue_selector(), core::scoring::attributes_for_parse_score_function(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::abinitio::abscript::AbscriptLoopCloserCMCreator::provide_xml_schema().
◆ selector()
|
inline |
References selector_.
Referenced by set_selector(), and yield_claims().
◆ set_selector()
|
inline |
References selector(), and selector_.
Referenced by parse_my_tag().
◆ yield_claims()
|
overridevirtual |
Returns a list of claims for this mover.
The pose passed as an argument is used for reference informational purposes only (for example, you want to know the sequence) or access the pose cache. Any changes to the conformation will get overwritten!
Implements protocols::environment::ClientMover.
References protocols::environment::claims::CAN_CONTROL, protocols::environment::claims::DOES_NOT_CONTROL, protocols::moves::Mover::get_self_ptr(), and selector().
Member Data Documentation
◆ final_ft_
|
private |
Referenced by apply(), attempt_ccd(), attempt_idealize(), and broking_finished().
◆ fragset_
|
private |
Referenced by attempt_ccd(), and parse_my_tag().
◆ movemap_
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mutableprivate |
Referenced by apply(), attempt_ccd(), attempt_idealize(), and passport_updated().
◆ scorefxn_
|
private |
Referenced by attempt_ccd(), and parse_my_tag().
◆ selector_
|
private |
Referenced by selector(), and set_selector().
The documentation for this class was generated from the following files:
- src/protocols/abinitio/abscript/AbscriptLoopCloserCM.hh
- src/protocols/abinitio/abscript/AbscriptLoopCloserCM.cc
