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

#include <Protocol.hh>

Public Types

typedef Mover BaseClass
 
- 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
 

Public Member Functions

 Protocol ()
 
 ~Protocol ()
 
virtual void init (core::pose::Pose const &)
 
void set_evaluation (evaluation::MetaPoseEvaluatorOP ev)
 
void add_evaluation (evaluation::PoseEvaluatorOP ev)
 
void evaluate_pose (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const
 
evaluation::MetaPoseEvaluatorOP evaluator ()
 
virtual void output_debug_structure (core::pose::Pose &pose, std::string prefix)
 
void set_kinematics (abinitio::KinematicControlOP kc)
 
abinitio::KinematicControl const & kinematics ()
 
virtual bool start_from_centroid () const
 
virtual bool return_centroid () const
 
virtual void return_centroid (bool setting)
 
virtual void apply (core::pose::Pose &)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_fullatom_scorefxn (core::scoring::ScoreFunctionOP sfxn)
 
void set_centroid_scorefxn (core::scoring::ScoreFunctionOP sfxn)
 
void set_silentout_file_name (std::string str)
 
core::scoring::ScoreFunctionOP fullatom_scorefxn ()
 
core::scoring::ScoreFunctionOP centroid_scorefxn ()
 
virtual checkpoint::CheckPointerget_checkpoints ()
 
- 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...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...
 

Static Public Member Functions

static void register_options ()
 
- 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...
 

Private Attributes

checkpoint::CheckPointer checkpoints_
 
evaluation::MetaPoseEvaluatorOP evaluator_
 
abinitio::KinematicControlOP kinematic_control_
 
core::scoring::ScoreFunctionOP scorefxn_fa_
 
core::scoring::ScoreFunctionOP scorefxn_centroid_
 
bool return_centroid_
 
std::string silentout_file_name_
 

Additional Inherited Members

- 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::Protocol::Protocol ( )
protocols::abinitio::Protocol::~Protocol ( )
inline

Member Function Documentation

void protocols::abinitio::Protocol::add_evaluation ( evaluation::PoseEvaluatorOP  ev)

References evaluator_.

void protocols::abinitio::Protocol::apply ( core::pose::Pose )
virtual
core::scoring::ScoreFunctionOP protocols::abinitio::Protocol::centroid_scorefxn ( )
inline

References scorefxn_centroid_.

void protocols::abinitio::Protocol::evaluate_pose ( core::pose::Pose pose,
std::string  tag,
core::io::silent::SilentStruct pss 
) const
evaluation::MetaPoseEvaluatorOP protocols::abinitio::Protocol::evaluator ( )
inline
core::scoring::ScoreFunctionOP protocols::abinitio::Protocol::fullatom_scorefxn ( )
inline

References scorefxn_fa_.

virtual checkpoint::CheckPointer& protocols::abinitio::Protocol::get_checkpoints ( )
inlinevirtual
std::string protocols::abinitio::Protocol::get_name ( ) const
virtual
virtual void protocols::abinitio::Protocol::init ( core::pose::Pose const &  )
inlinevirtual
abinitio::KinematicControl const& protocols::abinitio::Protocol::kinematics ( )
inline
void protocols::abinitio::Protocol::output_debug_structure ( core::pose::Pose pose,
std::string  prefix 
)
virtual
void protocols::abinitio::Protocol::register_options ( )
static
virtual bool protocols::abinitio::Protocol::return_centroid ( ) const
inlinevirtual
virtual void protocols::abinitio::Protocol::return_centroid ( bool  setting)
inlinevirtual

References return_centroid_.

void protocols::abinitio::Protocol::set_centroid_scorefxn ( core::scoring::ScoreFunctionOP  sfxn)
inline
void protocols::abinitio::Protocol::set_evaluation ( evaluation::MetaPoseEvaluatorOP  ev)
void protocols::abinitio::Protocol::set_fullatom_scorefxn ( core::scoring::ScoreFunctionOP  sfxn)
inline
void protocols::abinitio::Protocol::set_kinematics ( abinitio::KinematicControlOP  kc)
inline
void protocols::abinitio::Protocol::set_silentout_file_name ( std::string  str)
inline
virtual bool protocols::abinitio::Protocol::start_from_centroid ( ) const
inlinevirtual

Member Data Documentation

checkpoint::CheckPointer protocols::abinitio::Protocol::checkpoints_
private

Referenced by get_checkpoints().

evaluation::MetaPoseEvaluatorOP protocols::abinitio::Protocol::evaluator_
private
abinitio::KinematicControlOP protocols::abinitio::Protocol::kinematic_control_
private

Referenced by kinematics(), and set_kinematics().

bool protocols::abinitio::Protocol::return_centroid_
private

Referenced by return_centroid().

core::scoring::ScoreFunctionOP protocols::abinitio::Protocol::scorefxn_centroid_
private
core::scoring::ScoreFunctionOP protocols::abinitio::Protocol::scorefxn_fa_
private
std::string protocols::abinitio::Protocol::silentout_file_name_
private

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