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protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler Class Reference

#include <MultiPhosphateSampler.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler:
Inheritance graph
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Public Member Functions

 MultiPhosphateSampler (core::pose::Pose const &reference_pose)
 
 MultiPhosphateSampler (core::pose::Pose &pose_to_prepack, core::Size const moving_res)
 
 ~MultiPhosphateSampler () override
 
MultiPhosphateSamplerOP clone_sampler () const
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void sample_phosphates ()
 
void sample_phosphates (core::pose::PoseOP &viewer_pose_op)
 
void copy_phosphates (core::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< core::Size > const &setting)
 
void set_five_prime_phosphate_res (utility::vector1< core::Size > const &setting)
 
void set_three_prime_phosphate_res (utility::vector1< core::Size > const &setting)
 
void set_force_phosphate_instantiation (bool const &setting)
 
bool force_phosphate_instantiation () const
 
core::pose::Posepose ()
 
void set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
 
core::scoring::ScoreFunctionCOP get_scorefxn ()
 
utility::vector1< PhosphateMovephosphate_move_list () const
 
void set_phosphate_move_list (utility::vector1< PhosphateMove > const &setting)
 
utility::vector1< core::Size >
const & 
moving_partition_res ()
 
void reset (core::pose::Pose const &pose)
 
void initialize_by_prepack (core::pose::Pose &pose, core::Size const moving_res)
 
void initialize_by_prepack (core::pose::Pose &pose, utility::vector1< core::Size > const &moving_res_list)
 
void do_prepack (core::pose::Pose &pose, utility::vector1< core::Size > const &moving_res_list)
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Member Functions

void initialize_parameters ()
 
utility::vector1< PhosphateMoveinitialize_phosphate_move_list (core::pose::Pose &pose)
 
utility::vector1< PhosphateMovecheck_moved (utility::vector1< PhosphateMove > phosphate_move_list, core::pose::Pose const &pose) const
 
void find_uninstantiated_phosphates (core::pose::Pose const &pose, utility::vector1< PhosphateMove > const &phosphate_move_list, utility::vector1< PhosphateMove > &actual_phosphate_move_list) const
 
void find_phosphate_contacts_other_partition (utility::vector1< core::Size > const &partition_res1, utility::vector1< core::Size > const &partition_res2, core::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 (core::pose::Pose const &pose, utility::vector1< core::Size > const &other_partition_res, core::Vector const &takeoff_xyz) const
 

Private Attributes

core::pose::PoseCOP pose_with_original_phosphates_
 
core::pose::PoseOP phosphate_sample_pose_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
core::Real phosphate_takeoff_donor_distance_cutoff2_
 
bool screen_all_
 
bool force_phosphate_instantiation_
 
utility::vector1< core::Sizemoving_partition_res_
 
utility::vector1< core::Sizefive_prime_phosphate_res_input_
 
utility::vector1< core::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 std::list< std::string > Strings
 
- 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 ( core::pose::Pose const &  reference_pose)

References initialize_parameters(), and reset().

Referenced by clone_sampler().

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

Member Function Documentation

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::apply ( core::pose::Pose )
inlineoverridevirtual

Main Method.

Implements protocols::moves::Mover.

References copy_phosphates().

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

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 clone_sampler().

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

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

Implements protocols::moves::Mover.

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::get_scorefxn ( )
inline

References scorefxn_.

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

Referenced by MultiPhosphateSampler().

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack ( core::pose::Pose pose,
utility::vector1< core::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 ( core::pose::Pose pose)
private
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::instantiated_some_phosphate ( ) const
inline
utility::vector1< core::Size > const& protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::moving_partition_res ( )
inline

References moving_partition_res_.

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 ( core::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 ( core::pose::PoseOP viewer_pose_op)
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::screen_all ( ) const
inline

References screen_all_.

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_five_prime_phosphate_res ( utility::vector1< core::Size > const &  setting)
inline
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_force_phosphate_instantiation ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_moving_partition_res ( utility::vector1< core::Size > const &  setting)
inline

References moving_partition_res_.

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_phosphate_move_list ( utility::vector1< PhosphateMove > const &  setting)
inline

References phosphate_move_list_.

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)
void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_screen_all ( bool const &  setting)
inline

References screen_all_.

void protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::set_three_prime_phosphate_res ( utility::vector1< core::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< core::Size > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::five_prime_phosphate_res_input_
private
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::force_phosphate_instantiation_
private
bool protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::instantiated_some_phosphate_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::moving_partition_res_
private
utility::vector1< PhosphateMove> protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_move_list_
private
core::pose::PoseOP protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_sample_pose_
private
core::Real protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::phosphate_takeoff_donor_distance_cutoff2_
private
core::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().

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

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