Rosetta Protocols  2014.35
Public Member Functions | Private Types | Private Attributes | List of all members
protocols::abinitio::abscript::RigidChunkCM Class Reference

#include <RigidChunkCM.hh>

Public Member Functions

 RigidChunkCM ()
 RigidChunkCM (std::string const &label, loops::Loops const &rigid_core, core::pose::Pose const &template_pose)
virtual ~RigidChunkCM ()
virtual EnvClaims yield_claims (core::pose::Pose const &, basic::datacache::WriteableCacheableMapOP)
 Returns a list of claims for this mover. More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
virtual void initialize (Pose &pose)
 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 apply (core::pose::Pose &)
std::string const & label () const
void label (std::string const &label)
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
virtual moves::MoverOP clone () const
 Return a clone of the Mover object. More...
loops::Loops select_parts (loops::Loops const &rigid_core, core::Size random_grow_loops_by)
- Public Member Functions inherited from protocols::environment::ClaimingMover
 ClaimingMover ()
 ClaimingMover (ClaimingMover const &)
virtual ~ClaimingMover ()
virtual void yield_submovers (std::set< ClaimingMoverOP > &) 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...
virtual bool is_loop_closer () const
 indicate to the environment that this mover would like to close the loops after the environment closes. Perhaps this could be replaced by a claim type? More...
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
void set_type (std::string const &setting)
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...
void set_current_tag (std::string const &new_tag)
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 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...
void type (const std::string &type_in)
std::string get_type () const
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...
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 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...

Private Types

typedef ClaimingMover Parent

Private Attributes

std::string label_
EnvClaims claims_
loops::Loops rigid_core_
core::pose::PoseCOP template_

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::stringStrings
- 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::environment::ClaimingMover
virtual void 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). A conformation is provided for reference. 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...

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::abinitio::abscript::RigidChunkCM::RigidChunkCM ( )

Referenced by clone().

protocols::abinitio::abscript::RigidChunkCM::RigidChunkCM ( std::string const &  label,
loops::Loops const &  rigid_core,
core::pose::Pose const &  template_pose 
virtual protocols::abinitio::abscript::RigidChunkCM::~RigidChunkCM ( )

Member Function Documentation

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

References RigidChunkCM().

std::string protocols::abinitio::abscript::RigidChunkCM::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::abinitio::abscript::RigidChunkCM::initialize ( Pose conf)
std::string const& protocols::abinitio::abscript::RigidChunkCM::label ( ) const

References label_.

Referenced by parse_my_tag(), and yield_claims().

void protocols::abinitio::abscript::RigidChunkCM::label ( std::string const &  label)

References label(), and label_.

Referenced by label().

void protocols::abinitio::abscript::RigidChunkCM::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References core::chemical::FA_STANDARD, file, core::chemical::ChemicalManager::get_instance(), label(), option, core::import_pose::pose_from_pdb(), protocols::abinitio::abscript::read_rigid_core(), residue_type_set, rigid_core_, runtime_assert, select_parts(), and template_.

loops::Loops protocols::abinitio::abscript::RigidChunkCM::select_parts ( loops::Loops const &  rigid_core,
core::Size  random_grow_loops_by 
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::ClaimingMover.

References protocols::loops::Loops::begin(), protocols::environment::claims::DOES_NOT_CONTROL, protocols::loops::Loops::end(), protocols::environment::claims::EXCLUSIVE, core::pose::Pose::is_fullatom(), label(), protocols::environment::claims::MUST_CONTROL, rigid_core_, template_, utility::to_string(), and tr.

Member Data Documentation

EnvClaims protocols::abinitio::abscript::RigidChunkCM::claims_
std::string protocols::abinitio::abscript::RigidChunkCM::label_

Referenced by label().

loops::Loops protocols::abinitio::abscript::RigidChunkCM::rigid_core_
core::pose::PoseCOP protocols::abinitio::abscript::RigidChunkCM::template_

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