Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::monte_carlo::mover::AddMover Class Reference

#include <AddMover.hh>

Public Member Functions

 AddMover (core::scoring::ScoreFunctionOP scorefxn)
 
 ~AddMover ()
 
void apply (core::pose::Pose &pose, Size const res_to_add_in_full_model_numbering, Size const res_to_build_off_in_full_model_numbering)
 
void apply (core::pose::Pose &pose, SWA_Move const &swa_move)
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_kT (core::Real const &setting)
 
void set_sample_range_small (core::Real const setting)
 
void set_sample_range_large (core::Real const setting)
 
void set_internal_cycles (Size const setting)
 
void set_presample_added_residue (Size const setting)
 
void set_presample_by_swa (Size const setting)
 
void set_start_added_residue_in_aform (Size const setting)
 
void set_minimize_single_res (Size const setting)
 
void set_stepwise_modeler (protocols::stepwise::modeler::StepWiseModelerOP stepwise_modeler)
 
- 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...
 

Private Member Functions

void sample_by_swa (core::pose::Pose &pose, Size const res_to_add) const
 
void sample_by_monte_carlo_internal (core::pose::Pose &pose) const
 
void do_append (core::pose::Pose &pose)
 
void do_prepend (core::pose::Pose &pose)
 
void append_other_pose (pose::Pose &pose, Size const offset, Size const other_pose_idx)
 
void prepend_other_pose (pose::Pose &pose, Size const offset, Size const other_pose_idx)
 
void append_residue (pose::Pose &pose, Size const offset)
 
void prepend_residue (pose::Pose &pose, Size const offset)
 
bool check_same_chain (pose::Pose const &pose, Size const res_to_add_in_full_model_numbering, Size const res_to_build_off_in_full_model_numbering)
 
bool check_same_chain (pose::Pose const &pose)
 
void setup_initial_torsions (pose::Pose &pose)
 

Private Attributes

core::chemical::ResidueTypeSetCAP rsd_set_
 
core::scoring::ScoreFunctionOP scorefxn_
 
bool presample_added_residue_
 
bool presample_by_swa_
 
bool minimize_single_res_
 
bool start_added_residue_in_aform_
 
Size internal_cycles_
 
rna::RNA_TorsionMoverOP rna_torsion_mover_
 
core::Real sample_range_small_
 
core::Real sample_range_large_
 
core::Real kT_
 
protocols::stepwise::modeler::StepWiseModelerOP stepwise_modeler_
 
Size suite_num_
 
Size nucleoside_num_
 
Size res_to_add_in_full_model_numbering_
 
Size res_to_build_off_in_full_model_numbering_
 
SWA_Move swa_move_
 

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...
 
- 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...
 

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::mover::AddMover::AddMover ( core::scoring::ScoreFunctionOP  scorefxn)

References rna.

protocols::stepwise::monte_carlo::mover::AddMover::~AddMover ( )

Member Function Documentation

void protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose ( pose::Pose pose,
Size const  offset,
Size const  other_pose_idx 
)
private
void protocols::stepwise::monte_carlo::mover::AddMover::append_residue ( pose::Pose pose,
Size const  offset 
)
private
void protocols::stepwise::monte_carlo::mover::AddMover::apply ( core::pose::Pose pose,
Size const  res_to_add_in_full_model_numbering,
Size const  res_to_build_off_in_full_model_numbering 
)
void protocols::stepwise::monte_carlo::mover::AddMover::apply ( core::pose::Pose pose,
SWA_Move const &  swa_move 
)
void protocols::stepwise::monte_carlo::mover::AddMover::apply ( core::pose::Pose pose_to_visualize)
virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

bool protocols::stepwise::monte_carlo::mover::AddMover::check_same_chain ( pose::Pose const &  pose,
Size const  res_to_add_in_full_model_numbering,
Size const  res_to_build_off_in_full_model_numbering 
)
private
bool protocols::stepwise::monte_carlo::mover::AddMover::check_same_chain ( pose::Pose const &  pose)
private
void protocols::stepwise::monte_carlo::mover::AddMover::do_append ( core::pose::Pose pose)
private
void protocols::stepwise::monte_carlo::mover::AddMover::do_prepend ( core::pose::Pose pose)
private
std::string protocols::stepwise::monte_carlo::mover::AddMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose ( pose::Pose pose,
Size const  offset,
Size const  other_pose_idx 
)
private
void protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue ( pose::Pose pose,
Size const  offset 
)
private
void protocols::stepwise::monte_carlo::mover::AddMover::sample_by_monte_carlo_internal ( core::pose::Pose pose) const
private
void protocols::stepwise::monte_carlo::mover::AddMover::sample_by_swa ( core::pose::Pose pose,
Size const  res_to_add 
) const
private
void protocols::stepwise::monte_carlo::mover::AddMover::set_internal_cycles ( Size const  setting)
inline

References internal_cycles_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_kT ( core::Real const &  setting)
inline

References kT_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_minimize_single_res ( Size const  setting)
inline

References minimize_single_res_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_presample_added_residue ( Size const  setting)
inline
void protocols::stepwise::monte_carlo::mover::AddMover::set_presample_by_swa ( Size const  setting)
inline
void protocols::stepwise::monte_carlo::mover::AddMover::set_sample_range_large ( core::Real const  setting)
inline

References sample_range_large_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_sample_range_small ( core::Real const  setting)
inline

References sample_range_small_.

void protocols::stepwise::monte_carlo::mover::AddMover::set_start_added_residue_in_aform ( Size const  setting)
inline
void protocols::stepwise::monte_carlo::mover::AddMover::set_stepwise_modeler ( protocols::stepwise::modeler::StepWiseModelerOP  stepwise_modeler)
void protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_torsions ( pose::Pose pose)
private

Member Data Documentation

Size protocols::stepwise::monte_carlo::mover::AddMover::internal_cycles_
private
core::Real protocols::stepwise::monte_carlo::mover::AddMover::kT_
private
bool protocols::stepwise::monte_carlo::mover::AddMover::minimize_single_res_
private
Size protocols::stepwise::monte_carlo::mover::AddMover::nucleoside_num_
private
bool protocols::stepwise::monte_carlo::mover::AddMover::presample_added_residue_
private
bool protocols::stepwise::monte_carlo::mover::AddMover::presample_by_swa_
private

Referenced by apply(), and set_presample_by_swa().

Size protocols::stepwise::monte_carlo::mover::AddMover::res_to_add_in_full_model_numbering_
private
Size protocols::stepwise::monte_carlo::mover::AddMover::res_to_build_off_in_full_model_numbering_
private
rna::RNA_TorsionMoverOP protocols::stepwise::monte_carlo::mover::AddMover::rna_torsion_mover_
private
core::chemical::ResidueTypeSetCAP protocols::stepwise::monte_carlo::mover::AddMover::rsd_set_
private
core::Real protocols::stepwise::monte_carlo::mover::AddMover::sample_range_large_
private
core::Real protocols::stepwise::monte_carlo::mover::AddMover::sample_range_small_
private
core::scoring::ScoreFunctionOP protocols::stepwise::monte_carlo::mover::AddMover::scorefxn_
private
bool protocols::stepwise::monte_carlo::mover::AddMover::start_added_residue_in_aform_
private
protocols::stepwise::modeler::StepWiseModelerOP protocols::stepwise::monte_carlo::mover::AddMover::stepwise_modeler_
private
Size protocols::stepwise::monte_carlo::mover::AddMover::suite_num_
private
SWA_Move protocols::stepwise::monte_carlo::mover::AddMover::swa_move_
private

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