Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler Class Reference

#include <MultiPhosphateSampler.hh>

Public Member Functions

 MultiPhosphateSampler (pose::Pose const &reference_pose)
 
 MultiPhosphateSampler (pose::Pose &pose_to_prepack, Size const moving_res)
 
 ~MultiPhosphateSampler ()
 
MultiPhosphateSamplerOP clone_sampler () const
 
virtual moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose)
 
std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void sample_phosphates ()
 
void sample_phosphates (pose::PoseOP &viewer_pose_op)
 
void copy_phosphates (pose::Pose &mod_pose) const
 
void reset_to_original_pose ()
 
void set_screen_all (bool const &setting)
 
bool screen_all () const
 
bool instantiated_some_phosphate () const
 
void set_moving_partition_res (utility::vector1< Size > const &setting)
 
void set_five_prime_phosphate_res (utility::vector1< Size > const &setting)
 
void set_three_prime_phosphate_res (utility::vector1< Size > const &setting)
 
pose::Posepose ()
 
void set_scorefxn (scoring::ScoreFunctionCOP scorefxn)
 
utility::vector1< PhosphateMovephosphate_move_list () const
 
void set_phosphate_move_list (utility::vector1< PhosphateMove > const &setting)
 
utility::vector1< Size > const & moving_partition_res ()
 
void reset (pose::Pose const &pose)
 
void initialize_by_prepack (pose::Pose &pose, Size const moving_res)
 
void initialize_by_prepack (pose::Pose &pose, utility::vector1< Size > const &moving_res_list)
 
void do_prepack (pose::Pose &pose, utility::vector1< Size > const &moving_res_list)
 
- 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...
 
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 initialize_parameters ()
 
utility::vector1< PhosphateMoveinitialize_phosphate_move_list (pose::Pose &pose)
 
utility::vector1< PhosphateMovecheck_moved (utility::vector1< PhosphateMove > phosphate_move_list, pose::Pose const &pose) const
 
void find_phosphate_contacts_other_partition (utility::vector1< Size > const &partition_res1, utility::vector1< Size > const &partition_res2, pose::Pose const &pose, utility::vector1< PhosphateMove > const &phosphate_move_list, utility::vector1< PhosphateMove > &actual_phosphate_move_list) const
 
bool check_other_partition_for_contact (pose::Pose const &pose, utility::vector1< Size > const &other_partition_res, Vector const &takeoff_xyz) const
 

Private Attributes

pose::PoseCOP pose_with_original_phosphates_
 
pose::PoseOP phosphate_sample_pose_
 
scoring::ScoreFunctionCOP scorefxn_
 
Real phosphate_takeoff_donor_distance_cutoff2_
 
bool screen_all_
 
utility::vector1< Sizemoving_partition_res_
 
utility::vector1< Sizefive_prime_phosphate_res_input_
 
utility::vector1< Sizethree_prime_phosphate_res_input_
 
utility::vector1< PhosphateMovephosphate_move_list_
 
utility::vector1< PhosphateMoveactual_phosphate_move_list_
 
bool instantiated_some_phosphate_
 
bool prepacked_
 

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::modeler::rna::phosphate::MultiPhosphateSampler::MultiPhosphateSampler ( pose::Pose const &  reference_pose)

References initialize_parameters(), and reset().

Referenced by clone_sampler().

protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::MultiPhosphateSampler ( pose::Pose pose_to_prepack,
Size const  moving_res 
)
protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::~MultiPhosphateSampler ( )

Member Function Documentation

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::apply ( core::pose::Pose pose)
inlinevirtual
utility::vector1< PhosphateMove > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_moved ( utility::vector1< PhosphateMove phosphate_move_list,
pose::Pose const &  pose 
) const
private
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::check_other_partition_for_contact ( pose::Pose const &  pose,
utility::vector1< Size > const &  other_partition_res,
Vector const &  takeoff_xyz 
) const
private
virtual moves::MoverOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::clone ( ) const
inlinevirtual

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.

MultiPhosphateSamplerOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::clone_sampler ( ) const
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::copy_phosphates ( pose::Pose mod_pose) const
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::do_prepack ( pose::Pose pose,
utility::vector1< Size > const &  moving_res_list 
)
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::find_phosphate_contacts_other_partition ( utility::vector1< Size > const &  partition_res1,
utility::vector1< Size > const &  partition_res2,
pose::Pose const &  pose,
utility::vector1< PhosphateMove > const &  phosphate_move_list,
utility::vector1< PhosphateMove > &  actual_phosphate_move_list 
) const
private
std::string protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::get_name ( ) const
inlinevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack ( pose::Pose pose,
Size const  moving_res 
)

References make_vector1().

Referenced by MultiPhosphateSampler().

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack ( pose::Pose pose,
utility::vector1< Size > const &  moving_res_list 
)
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_parameters ( )
private
utility::vector1< PhosphateMove > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list ( pose::Pose pose)
private
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::instantiated_some_phosphate ( ) const
inline
utility::vector1< Size > const& protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::moving_partition_res ( )
inline
utility::vector1< PhosphateMove> protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_move_list ( ) const
inline
pose::Pose & protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::pose ( )
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::reset ( pose::Pose const &  pose)
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::reset_to_original_pose ( )
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates ( )
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates ( pose::PoseOP viewer_pose_op)
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::screen_all ( ) const
inline
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_five_prime_phosphate_res ( utility::vector1< Size > const &  setting)
inline
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_moving_partition_res ( utility::vector1< Size > const &  setting)
inline
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_phosphate_move_list ( utility::vector1< PhosphateMove > const &  setting)
inline
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_scorefxn ( scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_screen_all ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_three_prime_phosphate_res ( utility::vector1< Size > const &  setting)
inline

Member Data Documentation

utility::vector1< PhosphateMove> protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::actual_phosphate_move_list_
private

Referenced by sample_phosphates().

utility::vector1< Size > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::five_prime_phosphate_res_input_
private
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::instantiated_some_phosphate_
private

Referenced by sample_phosphates().

utility::vector1< Size > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::moving_partition_res_
private
utility::vector1< PhosphateMove> protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_move_list_
private
pose::PoseOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_sample_pose_
private
Real protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_takeoff_donor_distance_cutoff2_
private
pose::PoseCOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::pose_with_original_phosphates_
private
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::prepacked_
private

Referenced by check_moved(), and do_prepack().

scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::scorefxn_
private
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::screen_all_
private
utility::vector1< Size > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::three_prime_phosphate_res_input_
private

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