Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::farna::MultipleDomainMover Class Reference

The RNA de novo structure modeling protocol. More...

#include <MultipleDomainMover.hh>

Public Member Functions

 MultipleDomainMover (core::pose::Pose const &pose, protocols::coarse_rna::CoarseRNA_LoopCloserOP rna_loop_closer)
 Construct the protocol object. More...
 
virtual protocols::moves::MoverOP clone () const
 Clone this object. More...
 
void apply (core::pose::Pose &pose)
 Apply the loop-rebuild protocol to the input pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
Size apply_and_return_jump (core::pose::Pose &pose)
 
Size apply_at_domain (core::pose::Pose &pose, Size const &n)
 
void randomize_pose_rigid_bodies (core::pose::Pose &pose)
 
void slide_back_to_origin (core::pose::Pose &pose)
 
Size num_domains ()
 
void update_rot_trans_mag (Real const &rot_mag, Real const &trans_mag)
 
- 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 (core::pose::Pose const &pose, protocols::toolbox::AllowInsertOP allow_insert)
 
void setup_jump_numbers_and_partner (core::pose::Pose const &pose)
 
void setup_ok_for_centroid_calculation (protocols::toolbox::AllowInsertOP &allow_insert)
 
void randomize_orientations (core::pose::Pose &pose)
 
void try_to_slide_into_contact (core::pose::Pose &pose)
 
void close_all_loops (core::pose::Pose &pose)
 
void initialize_rigid_body_movers ()
 
numeric::xyzVector< core::Realget_centroid (core::pose::Pose const &pose)
 

Private Attributes

bool verbose_
 
Real rot_mag_
 
Real trans_mag_
 
Size num_domains_
 
protocols::coarse_rna::CoarseRNA_LoopCloserOP rna_loop_closer_
 
utility::vector1< intjump_numbers_
 
utility::vector1
< protocols::rigid::Partner
partner_
 
utility::vector1< boolok_for_centroid_calculation_
 
utility::vector1
< protocols::rigid::RigidBodyPerturbMoverOP
rb_movers_
 

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...
 

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::farna::MultipleDomainMover::MultipleDomainMover ( core::pose::Pose const &  pose,
protocols::coarse_rna::CoarseRNA_LoopCloserOP  rna_loop_closer 
)

Construct the protocol object.

References initialize(), and rna_loop_closer_.

Referenced by clone().

Member Function Documentation

void protocols::farna::MultipleDomainMover::apply ( core::pose::Pose pose)
virtual

Apply the loop-rebuild protocol to the input pose.

Implements protocols::moves::Mover.

References apply_and_return_jump().

Size protocols::farna::MultipleDomainMover::apply_and_return_jump ( core::pose::Pose pose)
Size protocols::farna::MultipleDomainMover::apply_at_domain ( core::pose::Pose pose,
Size const &  n 
)
virtual protocols::moves::MoverOP protocols::farna::MultipleDomainMover::clone ( ) const
inlinevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References MultipleDomainMover().

void protocols::farna::MultipleDomainMover::close_all_loops ( core::pose::Pose pose)
private
Vector protocols::farna::MultipleDomainMover::get_centroid ( core::pose::Pose const &  pose)
private
std::string protocols::farna::MultipleDomainMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::farna::MultipleDomainMover::initialize ( core::pose::Pose const &  pose,
protocols::toolbox::AllowInsertOP  allow_insert 
)
private
void protocols::farna::MultipleDomainMover::initialize_rigid_body_movers ( )
private
Size protocols::farna::MultipleDomainMover::num_domains ( )
inline

References num_domains_.

void protocols::farna::MultipleDomainMover::randomize_orientations ( core::pose::Pose pose)
private
void protocols::farna::MultipleDomainMover::randomize_pose_rigid_bodies ( core::pose::Pose pose)
void protocols::farna::MultipleDomainMover::setup_jump_numbers_and_partner ( core::pose::Pose const &  pose)
private
void protocols::farna::MultipleDomainMover::setup_ok_for_centroid_calculation ( protocols::toolbox::AllowInsertOP allow_insert)
private
void protocols::farna::MultipleDomainMover::slide_back_to_origin ( core::pose::Pose pose)
void protocols::farna::MultipleDomainMover::try_to_slide_into_contact ( core::pose::Pose pose)
private
void protocols::farna::MultipleDomainMover::update_rot_trans_mag ( Real const &  rot_mag,
Real const &  trans_mag 
)

Member Data Documentation

utility::vector1< int > protocols::farna::MultipleDomainMover::jump_numbers_
private
Size protocols::farna::MultipleDomainMover::num_domains_
private
utility::vector1< bool > protocols::farna::MultipleDomainMover::ok_for_centroid_calculation_
private
utility::vector1< protocols::rigid::Partner > protocols::farna::MultipleDomainMover::partner_
private
utility::vector1< protocols::rigid::RigidBodyPerturbMoverOP > protocols::farna::MultipleDomainMover::rb_movers_
private
protocols::coarse_rna::CoarseRNA_LoopCloserOP protocols::farna::MultipleDomainMover::rna_loop_closer_
private
Real protocols::farna::MultipleDomainMover::rot_mag_
private
Real protocols::farna::MultipleDomainMover::trans_mag_
private
bool protocols::farna::MultipleDomainMover::verbose_
private

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