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

#include <FragmentJumpCM.hh>

Public Member Functions

 FragmentJumpCM ()
 
 FragmentJumpCM (std::string const &topol_filename, core::pack::task::residue_selector::ResidueSelectorCOP selector, std::string const &moverkey)
 
virtual ~FragmentJumpCM ()
 
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...
 
void set_topology (std::string const &topology_file)
 Set the topology using a topology file. More...
 
void set_topology (std::string const &ss_info_file, std::string const &pairing_file, core::Size const &n_sheets, bool bRandomSheets)
 Set the topology using a psipred_ss2 file, a pairing list file, and a number of random sheets to pick. More...
 
void set_moverkey (std::string const &key)
 
std::string const & moverkey ()
 
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 fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
- Public Member Functions inherited from protocols::abinitio::abscript::FragmentCM
 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 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)
 
core::pack::task::residue_selector::ResidueSelectorCOP
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)
 
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...
 
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

jumping::JumpSample calculate_jump_sample () const
 
void setup_fragments (jumping::JumpSample const &)
 
EnvClaims build_claims (utility::vector1< bool > const &selection, jumping::JumpSample const &)
 
- Protected Member Functions inherited from protocols::abinitio::abscript::FragmentCM
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

typedef FragmentCM Parent
 
typedef
environment::claims::EnvClaims 
EnvClaims
 

Private Attributes

jumping::BaseJumpSetupOP jump_def_
 
std::string moverkey_
 

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::FragmentJumpCM::FragmentJumpCM ( )

Referenced by clone(), and fresh_instance().

protocols::abinitio::abscript::FragmentJumpCM::FragmentJumpCM ( std::string const &  topol_filename,
core::pack::task::residue_selector::ResidueSelectorCOP  selector,
std::string const &  moverkey 
)
virtual protocols::abinitio::abscript::FragmentJumpCM::~FragmentJumpCM ( )
inlinevirtual

Member Function Documentation

claims::EnvClaims protocols::abinitio::abscript::FragmentJumpCM::build_claims ( utility::vector1< bool > const &  selection,
jumping::JumpSample const &  jump_sample 
)
protected
jumping::JumpSample protocols::abinitio::abscript::FragmentJumpCM::calculate_jump_sample ( ) const
protected
moves::MoverOP protocols::abinitio::abscript::FragmentJumpCM::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 FragmentJumpCM().

moves::MoverOP protocols::abinitio::abscript::FragmentJumpCM::fresh_instance ( ) const
virtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References FragmentJumpCM().

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

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

Reimplemented from protocols::abinitio::abscript::FragmentCM.

Referenced by build_claims(), calculate_jump_sample(), parse_my_tag(), and yield_claims().

std::string const& protocols::abinitio::abscript::FragmentJumpCM::moverkey ( )
inline

References moverkey_.

Referenced by parse_my_tag(), and yield_claims().

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

References basic::datacache::DataMap::get(), get_name(), protocols::abinitio::abscript::FragmentCM::initialize(), moverkey(), pairing_file, protocols::abinitio::abscript::FragmentCM::selector(), set_moverkey(), protocols::abinitio::abscript::FragmentCM::set_selector(), set_topology(), and tr.

void protocols::abinitio::abscript::FragmentJumpCM::set_moverkey ( std::string const &  key)
inline

References moverkey_.

Referenced by parse_my_tag().

void protocols::abinitio::abscript::FragmentJumpCM::set_topology ( std::string const &  topology_file)
void protocols::abinitio::abscript::FragmentJumpCM::set_topology ( std::string const &  ss_info_file,
std::string const &  pairing_file,
core::Size const &  n_sheets,
bool  bRandomSheets 
)

Set the topology using a psipred_ss2 file, a pairing list file, and a number of random sheets to pick.

References calculate_jump_sample(), jump_def_, protocols::abinitio::abscript::FragmentCM::mover(), core::scoring::dssp::read_pairing_list(), sheets, ss, and tr.

void protocols::abinitio::abscript::FragmentJumpCM::setup_fragments ( jumping::JumpSample const &  jump_sample)
protected
claims::EnvClaims protocols::abinitio::abscript::FragmentJumpCM::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!

Reimplemented from protocols::abinitio::abscript::FragmentCM.

References build_claims(), calculate_jump_sample(), utility::pointer::owning_ptr< T >::get(), get_name(), jump_def_, moverkey(), protocols::abinitio::abscript::FragmentCM::selector(), core::pose::Pose::total_residue(), and tr.

Member Data Documentation

jumping::BaseJumpSetupOP protocols::abinitio::abscript::FragmentJumpCM::jump_def_
private
std::string protocols::abinitio::abscript::FragmentJumpCM::moverkey_
private

Referenced by moverkey(), and set_moverkey().


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