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

#include <PhosphateMover.hh>

Public Member Functions

 PhosphateMover (Size const sample_res, PhosphateTerminus which_terminus_, scoring::ScoreFunctionCOP scorefxn)
 
 PhosphateMover (PhosphateMove const phosphate_move, scoring::ScoreFunctionCOP scorefxn)
 
 ~PhosphateMover ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void screen_phosphate (pose::Pose &pose)
 
bool instantiated_phosphate () const
 
- 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 initialize_variables ()
 
void setup_variants_and_free_pose_for_terminal_phosphate (pose::Pose &pose)
 
void setup_variants_and_free_pose_for_five_prime_phosphate (pose::Pose &pose)
 
void setup_variants_and_free_pose_for_three_prime_phosphate (pose::Pose &pose)
 
void screen_five_prime_phosphate (pose::Pose &pose)
 
void screen_three_prime_phosphate (pose::Pose &pose)
 
void setup_atom_and_neighbor_list (pose::Pose &pose)
 
bool check_phosphate_contacts_donor (pose::Pose &pose) const
 
bool pass_clash_check (std::string const atom_name, Size const n, pose::Pose &pose)
 

Private Attributes

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

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

Member Function Documentation

void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply ( core::pose::Pose pose_to_visualize)
virtual
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::check_phosphate_contacts_donor ( pose::Pose pose) const
private
std::string protocols::stepwise::modeler::rna::phosphate::PhosphateMover::get_name ( ) const
virtual

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,
Size const  n,
pose::Pose pose 
)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_five_prime_phosphate ( pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_phosphate ( pose::Pose pose)
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_three_prime_phosphate ( pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_atom_and_neighbor_list ( pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate ( pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_terminal_phosphate ( pose::Pose pose)
private
void protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_three_prime_phosphate ( 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< Vector > protocols::stepwise::modeler::rna::phosphate::PhosphateMover::donor_atom_xyz_list_
private
utility::vector1< 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< Size > protocols::stepwise::modeler::rna::phosphate::PhosphateMover::neighbor_copy_dofs_
private
Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::number_score_calls_
private
Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::op1_atom_idx_
private
Size protocols::stepwise::modeler::rna::phosphate::PhosphateMover::op2_atom_idx_
private
PhosphateMove const protocols::stepwise::modeler::rna::phosphate::PhosphateMover::phosphate_move_
private
pose::PoseOP protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pose_free_
private
scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::PhosphateMover::scorefxn_
private
bool protocols::stepwise::modeler::rna::phosphate::PhosphateMover::screen_for_donor_contact_
private

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