Rosetta Protocols  2014.35
Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | List of all members
protocols::medal::MedalMover Class Reference

#include <MedalMover.hh>

Public Member Functions

 MedalMover ()
 
void apply (core::pose::Pose &pose)
 
std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 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...
 
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 Types

typedef utility::vector1< doubleProbabilities
 

Protected Member Functions

void do_loop_closure (core::pose::Pose *pose) const
 Closes chainbreaks in <pose> More...
 
void compute_per_residue_probabilities (const unsigned num_residues, const core::sequence::SequenceAlignment &alignment, const protocols::loops::Loops &chunks, const core::kinematics::FoldTree &tree, const core::fragment::FragSet &fragments, Probabilities *probs) const
 Computes per-residue sampling probabilities. More...
 
void decompose_structure (const core::pose::Pose &pose, protocols::loops::LoopsOP &chunks) const
 Partitions the structure into non-overlapping chunks. More...
 
protocols::moves::MoverOP create_fragment_mover (core::pose::PoseOP native, core::scoring::ScoreFunctionOP score, core::fragment::FragSetOP fragments, const Probabilities &probs, const std::string &policy, unsigned library_size) const
 Configures a mover for biased fragment insertion. More...
 
protocols::moves::MoverOP create_fragment_and_rigid_mover (const core::pose::Pose &pose, core::pose::PoseOP native, core::scoring::ScoreFunctionOP score, core::fragment::FragSetOP fragments, const Probabilities &probs, const std::string &policy, unsigned library_size) const
 Configures a mover for alternating biased fragment insertion and rigid body moves. More...
 
protocols::moves::MoverOP create_small_mover (core::pose::PoseOP native, core::scoring::ScoreFunctionOP score) const
 Configures a mover for performing alternating small and shear moves. More...
 
core::scoring::ScoreFunctionOP score_function () const
 Configures a basic score functions which callers can then specialize. 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...
 

Protected Attributes

core::fragment::FragSetOP fragments_sm_
 
core::fragment::FragSetOP fragments_lg_
 

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::medal::MedalMover::MedalMover ( )

Member Function Documentation

void protocols::medal::MedalMover::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::medal::MedalMover::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 MedalMover().

void protocols::medal::MedalMover::compute_per_residue_probabilities ( const unsigned  num_residues,
const core::sequence::SequenceAlignment alignment,
const protocols::loops::Loops chunks,
const core::kinematics::FoldTree tree,
const core::fragment::FragSet fragments,
Probabilities probs 
) const
protected
protocols::moves::MoverOP protocols::medal::MedalMover::create_fragment_and_rigid_mover ( const core::pose::Pose pose,
core::pose::PoseOP  native,
core::scoring::ScoreFunctionOP  score,
core::fragment::FragSetOP  fragments,
const Probabilities probs,
const std::string policy,
unsigned  library_size 
) const
protected

Configures a mover for alternating biased fragment insertion and rigid body moves.

References core::pose::Pose::fold_tree(), protocols::medal::on_pose_accept(), and option.

Referenced by apply().

protocols::moves::MoverOP protocols::medal::MedalMover::create_fragment_mover ( core::pose::PoseOP  native,
core::scoring::ScoreFunctionOP  score,
core::fragment::FragSetOP  fragments,
const Probabilities probs,
const std::string policy,
unsigned  library_size 
) const
protected

Configures a mover for biased fragment insertion.

References protocols::medal::on_pose_accept(), and option.

protocols::moves::MoverOP protocols::medal::MedalMover::create_small_mover ( core::pose::PoseOP  native,
core::scoring::ScoreFunctionOP  score 
) const
protected

Configures a mover for performing alternating small and shear moves.

References protocols::medal::on_pose_accept(), and option.

Referenced by apply().

void protocols::medal::MedalMover::decompose_structure ( const core::pose::Pose pose,
protocols::loops::LoopsOP chunks 
) const
protected

Partitions the structure into non-overlapping chunks.

References protocols::nonlocal::chunks_by_CA_CA_distance(), and option.

Referenced by apply().

void protocols::medal::MedalMover::do_loop_closure ( core::pose::Pose pose) const
protected
protocols::moves::MoverOP protocols::medal::MedalMover::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 MedalMover().

std::string protocols::medal::MedalMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

core::scoring::ScoreFunctionOP protocols::medal::MedalMover::score_function ( ) const
protected

Configures a basic score functions which callers can then specialize.

Configures the score function used during the simulation. Precedence:

  1. User-specified patch file (i.e. -rigid:patch)
  2. User-specified options (e.g. -jumps:increase_chainbreak)
  3. Default values

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::linear_chainbreak, option, options, score, and user.

Referenced by apply().

Member Data Documentation

core::fragment::FragSetOP protocols::medal::MedalMover::fragments_lg_
protected

Referenced by MedalMover().

core::fragment::FragSetOP protocols::medal::MedalMover::fragments_sm_
protected

Referenced by apply(), do_loop_closure(), and MedalMover().


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