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protocols::abinitio::abscript::RigidChunkCM Class Reference

#include <RigidChunkCM.hh>

Inheritance diagram for protocols::abinitio::abscript::RigidChunkCM:
Inheritance graph

Public Member Functions

 RigidChunkCM ()
 RigidChunkCM (core::select::residue_selector::ResidueSelectorCOP selector, core::pose::Pose const &template_pose)
 ~RigidChunkCM () override
EnvClaims yield_claims (core::pose::Pose const &, basic::datacache::WriteableCacheableMapOP) override
 Returns a list of claims for this mover. More...
void sim_selector (core::select::residue_selector::ResidueSelectorCOP selector)
core::select::residue_selector::ResidueSelectorCOP sim_selector () const
void templ_selector (core::select::residue_selector::ResidueSelectorCOP selector)
core::select::residue_selector::ResidueSelectorCOP templ_selector () const
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 (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...
loops::Loops select_parts (loops::Loops const &rigid_core, core::Size random_grow_loops_by)
core::pose::Pose const & templ () const
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
std::map< core::Size,
core::Size > const & 
sim_origin () const
std::map< core::Size,
core::Size > const & 
templ_target () const
- 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 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 Stringsinfo ()
 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...
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 ClientMover Parent

Private Member Functions

void configure (core::pose::Pose const &in_p, utility::vector1< bool > const selection)
void templ_target (std::map< core::Size, core::Size > const &in)
void sim_origin (std::map< core::Size, core::Size > const &in)

Private Attributes

EnvClaims claims_
core::pose::PoseCOP template_
core::select::residue_selector::ResidueSelectorCOP sim_selector_
core::select::residue_selector::ResidueSelectorCOP templ_selector_
std::string xml_name_
std::map< core::Size, core::Sizetempl_target_
std::map< core::Size, core::Sizesim_origin_

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

Constructor & Destructor Documentation

protocols::abinitio::abscript::RigidChunkCM::RigidChunkCM ( )
protocols::abinitio::abscript::RigidChunkCM::RigidChunkCM ( core::select::residue_selector::ResidueSelectorCOP  selector,
core::pose::Pose const &  template_pose 
protocols::abinitio::abscript::RigidChunkCM::~RigidChunkCM ( )

Member Function Documentation

void protocols::abinitio::abscript::RigidChunkCM::apply ( core::pose::Pose )

Main Method.

Implements protocols::moves::Mover.

moves::MoverOP protocols::abinitio::abscript::RigidChunkCM::clone ( ) const

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.

void protocols::abinitio::abscript::RigidChunkCM::configure ( core::pose::Pose const &  in_p,
utility::vector1< bool > const  selection 
std::string protocols::abinitio::abscript::RigidChunkCM::get_name ( ) const

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

Referenced by configure(), initialize(), parse_my_tag(), and yield_claims().

void protocols::abinitio::abscript::RigidChunkCM::initialize ( Pose conf)
std::string protocols::abinitio::abscript::RigidChunkCM::mover_name ( )
void protocols::abinitio::abscript::RigidChunkCM::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 

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::chemical::FA_STANDARD, get_name(), core::select::residue_selector::get_residue_selector(), protocols::rosetta_scripts::parse_mover_or_null(), core::import_pose::pose_from_file(), protocols::abinitio::abscript::read_rigid_core(), sim_selector(), templ_selector(), template_, tr(), and xml_name_.

void protocols::abinitio::abscript::RigidChunkCM::passport_updated ( )

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(), sim_origin_, and templ_target_.

void protocols::abinitio::abscript::RigidChunkCM::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
loops::Loops protocols::abinitio::abscript::RigidChunkCM::select_parts ( loops::Loops const &  rigid_core,
core::Size  random_grow_loops_by 
std::map< core::Size, core::Size > const& protocols::abinitio::abscript::RigidChunkCM::sim_origin ( ) const

References sim_origin_.

Referenced by configure(), and initialize().

void protocols::abinitio::abscript::RigidChunkCM::sim_origin ( std::map< core::Size, core::Size > const &  in)
void protocols::abinitio::abscript::RigidChunkCM::sim_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)
core::select::residue_selector::ResidueSelectorCOP protocols::abinitio::abscript::RigidChunkCM::sim_selector ( ) const

References sim_selector_.

Referenced by parse_my_tag(), and yield_claims().

core::pose::Pose const& protocols::abinitio::abscript::RigidChunkCM::templ ( ) const

References template_.

Referenced by configure(), and initialize().

void protocols::abinitio::abscript::RigidChunkCM::templ_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)
core::select::residue_selector::ResidueSelectorCOP protocols::abinitio::abscript::RigidChunkCM::templ_selector ( ) const

References templ_selector_.

Referenced by configure(), and parse_my_tag().

std::map< core::Size, core::Size > const& protocols::abinitio::abscript::RigidChunkCM::templ_target ( ) const

References templ_target_.

Referenced by configure().

void protocols::abinitio::abscript::RigidChunkCM::templ_target ( std::map< core::Size, core::Size > const &  in)
claims::EnvClaims protocols::abinitio::abscript::RigidChunkCM::yield_claims ( core::pose::Pose const &  ,

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, configure(), protocols::environment::claims::EXCLUSIVE, get_name(), protocols::moves::Mover::get_self_ptr(), protocols::mean_field::max(), protocols::mean_field::min(), core::pose::Pose::sequence(), sim_selector(), core::pose::Pose::size(), core::id::to_string(), and tr().

Member Data Documentation

EnvClaims protocols::abinitio::abscript::RigidChunkCM::claims_
std::map< core::Size, core::Size > protocols::abinitio::abscript::RigidChunkCM::sim_origin_

Referenced by passport_updated(), and sim_origin().

core::select::residue_selector::ResidueSelectorCOP protocols::abinitio::abscript::RigidChunkCM::sim_selector_

Referenced by sim_selector().

core::select::residue_selector::ResidueSelectorCOP protocols::abinitio::abscript::RigidChunkCM::templ_selector_

Referenced by templ_selector().

std::map< core::Size, core::Size > protocols::abinitio::abscript::RigidChunkCM::templ_target_

Referenced by passport_updated(), and templ_target().

core::pose::PoseCOP protocols::abinitio::abscript::RigidChunkCM::template_

Referenced by configure(), parse_my_tag(), and templ().

std::string protocols::abinitio::abscript::RigidChunkCM::xml_name_

Referenced by parse_my_tag().

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