#include <FragmentCM.hh>
Public Member Functions | |
| FragmentCM () | |
| FragmentCM (simple_moves::FragmentMoverOP, core::select::residue_selector::ResidueSelectorCOP=nullptr) | |
| virtual void | set_selector (core::select::residue_selector::ResidueSelectorCOP) |
| virtual void | set_mover (simple_moves::FragmentMoverOP mover) |
| ~FragmentCM () override | |
| 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... | |
| EnvClaims | yield_claims (core::pose::Pose const &, basic::datacache::WriteableCacheableMapOP) override |
| Returns a list of claims for this mover. More... | |
| void | initialize (Pose &pose) override |
| 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... | |
| void | apply (Pose &pose) override |
| Main Method. More... | |
| core::select::residue_selector::ResidueSelectorCOP const & | selector () const |
| bool | initialize () const |
| void | initialize (bool setting) |
| bool | yield_cut_bias () const |
| void | yield_cut_bias (bool setting) |
| 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 | 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 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 |
| 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... | |
| simple_moves::FragmentMoverOP | mover () const |
| 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... | |
| virtual void | broking_finished (EnvClaimBroker::BrokerResult const &) |
| hook that provides information about the final result of broking at the very end, though this BrokerResult construct. 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 protocols::environment::ClientMover | Parent |
| typedef environment::claims::EnvClaims | EnvClaims |
Private Attributes | |
| simple_moves::FragmentMoverOP | mover_ |
| core::select::residue_selector::ResidueSelectorCOP | selector_ |
| bool | bInitialize_ |
| bool | bYieldCutBias_ |
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
◆ Parent
|
private |
Constructor & Destructor Documentation
◆ FragmentCM() [1/2]
| protocols::abinitio::abscript::FragmentCM::FragmentCM | ( | ) |
◆ FragmentCM() [2/2]
| protocols::abinitio::abscript::FragmentCM::FragmentCM | ( | simple_moves::FragmentMoverOP | mover, |
| core::select::residue_selector::ResidueSelectorCOP | selector = nullptr |
||
| ) |
References get_name(), and protocols::moves::Mover::type().
◆ ~FragmentCM()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References core::pose::Pose::conformation(), and core::conformation::Conformation::is_protected().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Reimplemented in protocols::abinitio::abscript::FragmentJumpCM.
Referenced by FragmentCM(), and set_mover().
◆ initialize() [1/3]
|
inline |
References bInitialize_.
Referenced by protocols::abinitio::abscript::FragmentJumpCM::build_claims(), and protocols::abinitio::abscript::FragmentJumpCM::parse_my_tag().
◆ initialize() [2/3]
| void protocols::abinitio::abscript::FragmentCM::initialize | ( | bool | setting | ) |
◆ initialize() [3/3]
|
overridevirtual |
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.
Reimplemented from protocols::environment::ClientMover.
References core::pose::Pose::conformation().
◆ mover()
|
inlineprotected |
◆ mover_name()
|
static |
Referenced by protocols::abinitio::abscript::FragmentCMCreator::keyname().
◆ parse_my_tag()
|
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.
Reimplemented in protocols::abinitio::abscript::FragmentJumpCM.
References protocols::abinitio::abscript::determine_frag_size(), core::select::residue_selector::get_residue_selector(), and core::fragment::FragmentIO::read_data().
◆ 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 core::chemical::rdkit::get_name(), and tr().
◆ provide_xml_schema()
|
static |
◆ selector()
|
inline |
◆ set_mover()
|
virtual |
References get_name(), mover(), mover_, and protocols::moves::Mover::type().
Referenced by protocols::abinitio::abscript::FragmentJumpCM::setup_fragments().
◆ set_selector()
|
virtual |
References selector(), selector_, and protocols::environment::ClientMover::state_check().
Referenced by protocols::abinitio::abscript::FragmentJumpCM::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.
Reimplemented in protocols::abinitio::abscript::FragmentJumpCM.
References protocols::environment::claims::CAN_CONTROL, protocols::environment::claims::DOES_NOT_CONTROL, and core::chemical::rdkit::get_name().
◆ yield_cut_bias() [1/2]
|
inline |
References bYieldCutBias_.
◆ yield_cut_bias() [2/2]
| void protocols::abinitio::abscript::FragmentCM::yield_cut_bias | ( | bool | setting | ) |
Member Data Documentation
◆ bInitialize_
|
private |
Referenced by initialize().
◆ bYieldCutBias_
|
private |
Referenced by yield_cut_bias().
◆ mover_
|
private |
Referenced by mover(), and set_mover().
◆ selector_
|
private |
Referenced by selector(), and set_selector().
The documentation for this class was generated from the following files:
- src/protocols/abinitio/abscript/FragmentCM.hh
- src/protocols/abinitio/abscript/FragmentCM.cc
