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protocols::rna::denovo::coarse::MultipleDomainMover Class Reference

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

#include <MultipleDomainMover.hh>

Inheritance diagram for protocols::rna::denovo::coarse::MultipleDomainMover:
Inheritance graph

Public Member Functions

 MultipleDomainMover (core::pose::Pose const &pose, protocols::rna::denovo::coarse::CoarseRNA_LoopCloserOP rna_loop_closer)
 Construct the protocol object. More...
protocols::moves::MoverOP clone () const override
 Clone this object. More...
void apply (core::pose::Pose &pose) override
 Apply the loop-rebuild protocol to the input pose. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
core::Size apply_and_return_jump (core::pose::Pose &pose)
core::Size apply_at_domain (core::pose::Pose &pose, core::Size const &n)
void randomize_pose_rigid_bodies (core::pose::Pose &pose)
void slide_back_to_origin (core::pose::Pose &pose)
core::Size num_domains ()
void update_rot_trans_mag (core::Real const &rot_mag, core::Real const &trans_mag)
- 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions

void initialize (core::pose::Pose const &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map)
void setup_jump_numbers_and_partner (core::pose::Pose const &pose)
void setup_ok_for_centroid_calculation (core::pose::toolbox::AtomLevelDomainMapOP &atom_level_domain_map)
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_
core::Real rot_mag_
core::Real trans_mag_
core::Size num_domains_
protocols::rna::denovo::coarse::CoarseRNA_LoopCloserOP rna_loop_closer_
utility::vector1< int > jump_numbers_
< protocols::rigid::Partner
utility::vector1< boolok_for_centroid_calculation_
< protocols::rigid::RigidBodyPerturbMoverOP

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...

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::rna::denovo::coarse::MultipleDomainMover::MultipleDomainMover ( core::pose::Pose const &  pose,
protocols::rna::denovo::coarse::CoarseRNA_LoopCloserOP  rna_loop_closer 

Construct the protocol object.

References initialize(), and rna_loop_closer_.

Member Function Documentation

void protocols::rna::denovo::coarse::MultipleDomainMover::apply ( core::pose::Pose pose)

Apply the loop-rebuild protocol to the input pose.

Implements protocols::moves::Mover.

References apply_and_return_jump().

Size protocols::rna::denovo::coarse::MultipleDomainMover::apply_and_return_jump ( core::pose::Pose pose)

References apply_at_domain(), num_domains_, and core::scoring::rg.

Referenced by apply().

Size protocols::rna::denovo::coarse::MultipleDomainMover::apply_at_domain ( core::pose::Pose pose,
core::Size const &  n 
protocols::moves::MoverOP protocols::rna::denovo::coarse::MultipleDomainMover::clone ( ) const

Clone this object.

Reimplemented from protocols::moves::Mover.

void protocols::rna::denovo::coarse::MultipleDomainMover::close_all_loops ( core::pose::Pose pose)
Vector protocols::rna::denovo::coarse::MultipleDomainMover::get_centroid ( core::pose::Pose const &  pose)
std::string protocols::rna::denovo::coarse::MultipleDomainMover::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::rna::denovo::coarse::MultipleDomainMover::initialize ( core::pose::Pose const &  pose,
core::pose::toolbox::AtomLevelDomainMapOP  atom_level_domain_map 
void protocols::rna::denovo::coarse::MultipleDomainMover::initialize_rigid_body_movers ( )
core::Size protocols::rna::denovo::coarse::MultipleDomainMover::num_domains ( )

References num_domains_.

void protocols::rna::denovo::coarse::MultipleDomainMover::randomize_orientations ( core::pose::Pose pose)
void protocols::rna::denovo::coarse::MultipleDomainMover::randomize_pose_rigid_bodies ( core::pose::Pose pose)
void protocols::rna::denovo::coarse::MultipleDomainMover::setup_jump_numbers_and_partner ( core::pose::Pose const &  pose)
void protocols::rna::denovo::coarse::MultipleDomainMover::setup_ok_for_centroid_calculation ( core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map)

References ok_for_centroid_calculation_, and verbose_.

Referenced by initialize().

void protocols::rna::denovo::coarse::MultipleDomainMover::slide_back_to_origin ( core::pose::Pose pose)
void protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact ( core::pose::Pose pose)
void protocols::rna::denovo::coarse::MultipleDomainMover::update_rot_trans_mag ( core::Real const &  rot_mag,
core::Real const &  trans_mag 

Member Data Documentation

utility::vector1< int > protocols::rna::denovo::coarse::MultipleDomainMover::jump_numbers_
core::Size protocols::rna::denovo::coarse::MultipleDomainMover::num_domains_
utility::vector1< bool > protocols::rna::denovo::coarse::MultipleDomainMover::ok_for_centroid_calculation_
utility::vector1< protocols::rigid::Partner > protocols::rna::denovo::coarse::MultipleDomainMover::partner_
utility::vector1< protocols::rigid::RigidBodyPerturbMoverOP > protocols::rna::denovo::coarse::MultipleDomainMover::rb_movers_
protocols::rna::denovo::coarse::CoarseRNA_LoopCloserOP protocols::rna::denovo::coarse::MultipleDomainMover::rna_loop_closer_
core::Real protocols::rna::denovo::coarse::MultipleDomainMover::rot_mag_
core::Real protocols::rna::denovo::coarse::MultipleDomainMover::trans_mag_
bool protocols::rna::denovo::coarse::MultipleDomainMover::verbose_

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