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

#include <FragmentCM.hh>

Public Member Functions

 FragmentCM ()
 FragmentCM (simple_moves::FragmentMoverOP, core::pack::task::residue_selector::ResidueSelectorCOP=NULL)
virtual void set_selector (core::pack::task::residue_selector::ResidueSelectorCOP)
virtual void set_mover (simple_moves::FragmentMoverOP mover)
virtual ~FragmentCM ()
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 EnvClaims yield_claims (core::pose::Pose const &, basic::datacache::WriteableCacheableMapOP)
 Returns a list of claims for this mover. 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 (Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
const & 
selector () const
bool initialize () const
void initialize (bool setting)
bool yield_cut_bias () const
void yield_cut_bias (bool setting)
- 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)
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
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...
simple_moves::FragmentMoverOP mover () const
- Protected Member Functions inherited from protocols::environment::ClaimingMover
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


Private Attributes

simple_moves::FragmentMoverOP mover_
core::pack::task::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::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::FragmentCM::FragmentCM ( )
protocols::abinitio::abscript::FragmentCM::FragmentCM ( simple_moves::FragmentMoverOP  mover,
core::pack::task::residue_selector::ResidueSelectorCOP  selector = NULL 

References set_mover().

protocols::abinitio::abscript::FragmentCM::~FragmentCM ( )

Member Function Documentation

void protocols::abinitio::abscript::FragmentCM::apply ( Pose pose)
std::string protocols::abinitio::abscript::FragmentCM::get_name ( ) const

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

Implements protocols::moves::Mover.

Reimplemented in protocols::abinitio::abscript::FragmentJumpCM.

Referenced by set_mover().

void protocols::abinitio::abscript::FragmentCM::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.

Reimplemented from protocols::environment::ClaimingMover.

References core::pose::Pose::conformation().

bool protocols::abinitio::abscript::FragmentCM::initialize ( ) const
void protocols::abinitio::abscript::FragmentCM::initialize ( bool  setting)
simple_moves::FragmentMoverOP protocols::abinitio::abscript::FragmentCM::mover ( ) const
void protocols::abinitio::abscript::FragmentCM::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.

Reimplemented in protocols::abinitio::abscript::FragmentJumpCM.

References protocols::abinitio::abscript::determine_frag_size(), basic::datacache::DataMap::get(), initialize(), n_frags, option, core::fragment::FragmentIO::read_data(), and ss.

void protocols::abinitio::abscript::FragmentCM::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.

Reimplemented from protocols::environment::ClaimingMover.

core::pack::task::residue_selector::ResidueSelectorCOP const& protocols::abinitio::abscript::FragmentCM::selector ( ) const
void protocols::abinitio::abscript::FragmentCM::set_mover ( simple_moves::FragmentMoverOP  mover)
void protocols::abinitio::abscript::FragmentCM::set_selector ( core::pack::task::residue_selector::ResidueSelectorCOP  selector)
claims::EnvClaims protocols::abinitio::abscript::FragmentCM::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.

Reimplemented in protocols::abinitio::abscript::FragmentJumpCM.

References protocols::environment::claims::CAN_CONTROL, protocols::environment::claims::DOES_NOT_CONTROL, fragments, utility::vector1< T, class >::index(), initialize(), ss, and core::pose::Pose::total_residue().

bool protocols::abinitio::abscript::FragmentCM::yield_cut_bias ( ) const

References bYieldCutBias_.

void protocols::abinitio::abscript::FragmentCM::yield_cut_bias ( bool  setting)

Member Data Documentation

bool protocols::abinitio::abscript::FragmentCM::bInitialize_

Referenced by initialize().

bool protocols::abinitio::abscript::FragmentCM::bYieldCutBias_

Referenced by yield_cut_bias().

simple_moves::FragmentMoverOP protocols::abinitio::abscript::FragmentCM::mover_

Referenced by set_mover().

core::pack::task::residue_selector::ResidueSelectorCOP protocols::abinitio::abscript::FragmentCM::selector_

Referenced by selector(), and set_selector().

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