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

#include <PhosphateMover.hh>

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

 PhosphateMover (core::Size const sample_res, PhosphateTerminus which_terminus_, core::scoring::ScoreFunctionCOP scorefxn)
 
 PhosphateMover (PhosphateMove const &phosphate_move, core::scoring::ScoreFunctionCOP scorefxn)
 
 ~PhosphateMover () override
 
void apply (core::pose::Pose &pose_to_visualize) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void screen_phosphate (core::pose::Pose &pose)
 
bool instantiated_phosphate () const
 
void set_force_phosphate_instantiation (bool const &setting)
 
bool force_phosphate_instantiation () const
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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_variables ()
 
void setup_variants_and_free_pose_for_terminal_phosphate (core::pose::Pose &pose)
 
void setup_variants_and_free_pose_for_five_prime_phosphate (core::pose::Pose &pose)
 
void setup_variants_and_free_pose_for_three_prime_phosphate (core::pose::Pose &pose)
 
void screen_five_prime_phosphate (core::pose::Pose &pose)
 
void screen_three_prime_phosphate (core::pose::Pose &pose)
 
void setup_atom_and_neighbor_list (core::pose::Pose &pose)
 
bool check_phosphate_contacts_donor (core::pose::Pose &pose) const
 
bool pass_clash_check (std::string const &atom_name, core::Size const n, core::pose::Pose &pose)
 
void apply_Aform_torsions_to_five_prime_phosphate (core::pose::Pose &pose, core::Size const sample_res) const
 
void apply_Aform_torsions_to_three_prime_phosphate (core::pose::Pose &pose, core::Size const sample_res) const
 

Private Attributes

PhosphateMove const phosphate_move_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
bool do_screening_
 
bool screen_for_donor_contact_
 
bool instantiated_phosphate_
 
bool force_phosphate_instantiation_
 
core::pose::PoseOP pose_free_
 
utility::vector1< core::Vectordonor_atom_xyz_list_
 
utility::vector1< core::Vectordonor_base_atom_xyz_list_
 
utility::vector1< core::Sizeneighbor_copy_dofs_
 
core::Size op1_atom_idx_
 
core::Size op2_atom_idx_
 
core::Size number_score_calls_
 
core::chemical::rna::RNA_FittedTorsionInfo
const 
torsion_info_
 

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::PhosphateMover::PhosphateMover ( core::Size const  sample_res,
PhosphateTerminus  which_terminus_,
core::scoring::ScoreFunctionCOP  scorefxn 
)
protocols::stepwise::modeler::rna::phosphate::PhosphateMover::PhosphateMover ( PhosphateMove const &  phosphate_move,
core::scoring::ScoreFunctionCOP  scorefxn 
)
protocols::stepwise::modeler::rna::phosphate::PhosphateMover::~PhosphateMover ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply ( core::pose::Pose )
overridevirtual
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply_Aform_torsions_to_five_prime_phosphate ( core::pose::Pose pose,
core::Size const  sample_res 
) const
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply_Aform_torsions_to_three_prime_phosphate ( core::pose::Pose pose,
core::Size const  sample_res 
) const
private
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::check_phosphate_contacts_donor ( core::pose::Pose pose) const
private
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::force_phosphate_instantiation ( ) const
inline
std::string protocols::stepwise::modeler::rna::phosphate::PhosphateMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::initialize_variables ( )
private
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::instantiated_phosphate ( ) const
inline
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check ( std::string const &  atom_name,
core::Size const  n,
core::pose::Pose pose 
)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_five_prime_phosphate ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_phosphate ( core::pose::Pose pose)
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::set_force_phosphate_instantiation ( bool const &  setting)
inline
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_atom_and_neighbor_list ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_terminal_phosphate ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_three_prime_phosphate ( core::pose::Pose pose)
private

Member Data Documentation

bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::do_screening_
private

Referenced by apply(), and initialize_variables().

utility::vector1< core::Vector > protocols::stepwise::modeler::rna::phosphate::PhosphateMover::donor_atom_xyz_list_
private
utility::vector1< core::Vector > protocols::stepwise::modeler::rna::phosphate::PhosphateMover::donor_base_atom_xyz_list_
private
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::force_phosphate_instantiation_
private
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::instantiated_phosphate_
private
utility::vector1< core::Size > protocols::stepwise::modeler::rna::phosphate::PhosphateMover::neighbor_copy_dofs_
private
core::Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::number_score_calls_
private
core::Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::op1_atom_idx_
private
core::Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::op2_atom_idx_
private
PhosphateMove const protocols::stepwise::modeler::rna::phosphate::PhosphateMover::phosphate_move_
private
core::pose::PoseOP protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pose_free_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::PhosphateMover::scorefxn_
private
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_for_donor_contact_
private
core::chemical::rna::RNA_FittedTorsionInfo const protocols::stepwise::modeler::rna::phosphate::PhosphateMover::torsion_info_
private

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