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

#include <AbscriptLoopCloserCM.hh>

Public Member Functions

 AbscriptLoopCloserCM ()
 
 AbscriptLoopCloserCM (core::fragment::FragSetCOP fragset, core::scoring::ScoreFunctionOP scorefxn)
 
virtual ~AbscriptLoopCloserCM ()
 
virtual EnvClaims yield_claims (core::pose::Pose const &, basic::datacache::WriteableCacheableMapOP)
 Returns a list of claims for this mover. More...
 
virtual void broking_finished (environment::EnvClaimBroker::BrokerResult const &)
 hook that provides information about the final result of broking at the very end, though this BrokerResult construct. More...
 
std::string const & label () const
 
void set_label (std::string const &label)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual void apply (core::pose::Pose &)
 
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...
 
- Public Member Functions inherited from protocols::environment::ClaimingMover
 ClaimingMover ()
 
 ClaimingMover (ClaimingMover const &)
 
virtual ~ClaimingMover ()
 
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< 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...
 

Protected Member Functions

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...
 
- Protected Member Functions inherited from protocols::environment::ClaimingMover
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 ClaimingMover Parent
 
typedef
environment::claims::EnvClaims 
EnvClaims
 

Private Member Functions

void attempt_idealize (core::pose::Pose &)
 
bool attempt_ccd (core::pose::Pose &)
 

Private Attributes

core::kinematics::FoldTreeOP final_ft_
 
core::fragment::FragSetCOP fragset_
 
core::kinematics::MoveMapOP movemap_
 
core::scoring::ScoreFunctionOP scorefxn_
 
std::string label_
 
bool bUpdateMM_
 

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
protocols::filters::Filters_map 
Filters_map
 
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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::abinitio::abscript::AbscriptLoopCloserCM::AbscriptLoopCloserCM ( )

Referenced by clone().

protocols::abinitio::abscript::AbscriptLoopCloserCM::AbscriptLoopCloserCM ( core::fragment::FragSetCOP  fragset,
core::scoring::ScoreFunctionOP  scorefxn 
)
virtual protocols::abinitio::abscript::AbscriptLoopCloserCM::~AbscriptLoopCloserCM ( )
inlinevirtual

Member Function Documentation

void protocols::abinitio::abscript::AbscriptLoopCloserCM::apply ( core::pose::Pose in_pose)
virtual
bool protocols::abinitio::abscript::AbscriptLoopCloserCM::attempt_ccd ( core::pose::Pose pose)
private
void protocols::abinitio::abscript::AbscriptLoopCloserCM::attempt_idealize ( core::pose::Pose pose)
private
void protocols::abinitio::abscript::AbscriptLoopCloserCM::broking_finished ( environment::EnvClaimBroker::BrokerResult const &  )
virtual

hook that provides information about the final result of broking at the very end, though this BrokerResult construct.

Reimplemented from protocols::environment::ClaimingMover.

References protocols::environment::EnvClaimBroker::BrokerResult::closer_ft, and final_ft_.

moves::MoverOP protocols::abinitio::abscript::AbscriptLoopCloserCM::clone ( ) const
virtual

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 AbscriptLoopCloserCM().

std::string protocols::abinitio::abscript::AbscriptLoopCloserCM::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

std::string const& protocols::abinitio::abscript::AbscriptLoopCloserCM::label ( ) const
inline

References label_.

Referenced by parse_my_tag(), set_label(), and yield_claims().

void protocols::abinitio::abscript::AbscriptLoopCloserCM::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 
)
virtual

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::scoring::atom_pair_constraint, jumps::chainbreak_weight_stage4, core::scoring::ScoreFunctionFactory::create_score_function(), fragset_, label(), core::scoring::linear_chainbreak, option, protocols::rosetta_scripts::parse_score_function(), scorefxn_, set_label(), and tr.

void protocols::abinitio::abscript::AbscriptLoopCloserCM::passport_updated ( )
protectedvirtual

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.

Reimplemented from protocols::environment::ClaimingMover.

References protocols::environment::ClaimingMover::has_passport(), movemap_, and protocols::environment::ClaimingMover::passport().

void protocols::abinitio::abscript::AbscriptLoopCloserCM::set_label ( std::string const &  label)
inline

References label(), and label_.

Referenced by parse_my_tag().

claims::EnvClaims protocols::abinitio::abscript::AbscriptLoopCloserCM::yield_claims ( core::pose::Pose const &  ,
basic::datacache::WriteableCacheableMapOP   
)
virtual

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::environment::claims::CAN_CONTROL, protocols::environment::claims::DOES_NOT_CONTROL, label(), and core::pose::Pose::total_residue().

Member Data Documentation

bool protocols::abinitio::abscript::AbscriptLoopCloserCM::bUpdateMM_
mutableprivate
core::kinematics::FoldTreeOP protocols::abinitio::abscript::AbscriptLoopCloserCM::final_ft_
private
core::fragment::FragSetCOP protocols::abinitio::abscript::AbscriptLoopCloserCM::fragset_
private

Referenced by attempt_ccd(), and parse_my_tag().

std::string protocols::abinitio::abscript::AbscriptLoopCloserCM::label_
private

Referenced by label(), and set_label().

core::kinematics::MoveMapOP protocols::abinitio::abscript::AbscriptLoopCloserCM::movemap_
mutableprivate
core::scoring::ScoreFunctionOP protocols::abinitio::abscript::AbscriptLoopCloserCM::scorefxn_
private

Referenced by attempt_ccd(), and parse_my_tag().


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