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protocols::rna::denovo::movers::RNA_DeNovoMasterMover Class Reference

#include <RNA_DeNovoMasterMover.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNA_DeNovoMasterMover:
Inheritance graph
[legend]

Public Member Functions

 RNA_DeNovoMasterMover (core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map, core::import_pose::RNA_BasePairHandlerCOP rna_base_pair_handler, protocols::rna::movers::RNA_LoopCloserOP rna_loop_closer, core::import_pose::libraries::RNA_ChunkLibraryOP rna_chunk_library, core::scoring::ScoreFunctionOP sfxn)
 
 ~RNA_DeNovoMasterMover () override
 
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 apply (core::pose::Pose &pose, core::Size const &cycle_number)
 
void setup_rnp_fold_tree (core::pose::Pose &pose, bool const &refine_pose, bool const &randomize)
 
void setup_rigid_body_mover (core::pose::Pose const &pose, core::Real const &rot_mag, core::Real const &trans_mag)
 
void setup_dock_into_density_mover (core::pose::Pose const &pose, core::Real const &rot_mag, core::Real const &trans_mag)
 Only used for legacy RNP setup, will remove once all testing is complete. More...
 
void setup_rna_protein_docking_mover (core::pose::Pose const &pose, core::Real const &rot_mag, core::Real const &trans_mag)
 
movers::RNA_FragmentMoverOP rna_fragment_mover ()
 
core::import_pose::RNA_JumpMoverOP rna_jump_mover ()
 
void do_random_moves (core::pose::Pose &pose, core::Size const &monte_carlo_cycles, bool const &check_num_rna_res=false)
 
void set_close_loops (bool const &setting)
 
bool close_loops () const
 
void set_frag_size (core::Size const &setting)
 
core::Size frag_size () const
 
std::string move_type () const
 
bool success () const
 
void search_rigid_body_orientation (core::pose::Pose &pose)
 
void set_rna_helix_mover (movers::RNA_HelixMoverOP const rna_helix_mover)
 
movers::RNA_HelixMoverOP rna_helix_mover ()
 
void set_helix_mover_magnitude (core::Real const &rot_mag, core::Real const &trans_mag)
 
void set_sfxn (core::scoring::ScoreFunctionOP const &sfxn)
 
- 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 do_move_trial (core::Size const &i, core::pose::Pose &pose)
 
void RNA_move_trial (core::pose::Pose &pose)
 
void dock_into_density_trial (core::pose::Pose &pose)
 
void random_jump_trial (core::pose::Pose &pose)
 
void rnp_docking_trial (core::pose::Pose &pose)
 
void random_fragment_trial (core::pose::Pose &pose)
 
bool random_chunk_trial (core::pose::Pose &pose)
 
void randomize_rigid_body_orientations (core::pose::Pose &pose)
 
void randomize_rnp_rigid_body_orientations (core::pose::Pose &pose)
 

Private Attributes

core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options_
 
core::Size frag_size_
 
core::Real jump_change_frequency_
 
core::Real dock_into_density_freq_
 
bool close_loops_
 
bool do_rnp_docking_
 
std::string move_type_
 
movers::RNA_FragmentMoverOP rna_fragment_mover_
 
core::import_pose::RNA_JumpMoverOP rna_jump_mover_
 
core::import_pose::libraries::RNA_ChunkLibraryOP rna_chunk_library_
 
protocols::rna::movers::RNA_LoopCloserOP rna_loop_closer_
 
protocols::rigid::RigidBodyPerturbMoverOP rigid_body_mover_
 
protocols::rigid::RigidBodyPerturbMoverOP rnp_docking_mover_
 
protocols::rigid::RigidBodyPerturbMoverOP dock_into_density_mover_
 
core::kinematics::FoldTree rnp_docking_ft_
 
movers::RNA_HelixMoverOP rna_helix_mover_
 
core::scoring::ScoreFunctionOP sfxn_
 

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::rna::denovo::movers::RNA_DeNovoMasterMover::RNA_DeNovoMasterMover ( core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP  options,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map,
core::import_pose::RNA_BasePairHandlerCOP  rna_base_pair_handler,
protocols::rna::movers::RNA_LoopCloserOP  rna_loop_closer,
core::import_pose::libraries::RNA_ChunkLibraryOP  rna_chunk_library,
core::scoring::ScoreFunctionOP  sfxn 
)
protocols::rna::denovo::movers::RNA_DeNovoMasterMover::~RNA_DeNovoMasterMover ( )
overridedefault

Member Function Documentation

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::apply ( core::pose::Pose pose,
core::Size const &  cycle_number 
)

References do_move_trial().

bool protocols::rna::denovo::movers::RNA_DeNovoMasterMover::close_loops ( ) const
inline

References close_loops_.

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_move_trial ( core::Size const &  i,
core::pose::Pose pose 
)
private

Do a move. RNA moves are fragment/jump/chunks. Every 10th iteration, try a RNA/protein docking move (K. Kappel)

References do_rnp_docking_, move_type_, options_, RNA_move_trial(), and rnp_docking_trial().

Referenced by apply().

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_random_moves ( core::pose::Pose pose,
core::Size const &  monte_carlo_cycles,
bool const &  check_num_rna_res = false 
)
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::dock_into_density_trial ( core::pose::Pose pose)
private
core::Size protocols::rna::denovo::movers::RNA_DeNovoMasterMover::frag_size ( ) const
inline

References frag_size_.

std::string protocols::rna::denovo::movers::RNA_DeNovoMasterMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

std::string protocols::rna::denovo::movers::RNA_DeNovoMasterMover::move_type ( ) const
inline
bool protocols::rna::denovo::movers::RNA_DeNovoMasterMover::random_chunk_trial ( core::pose::Pose pose)
private
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::random_fragment_trial ( core::pose::Pose pose)
private
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::random_jump_trial ( core::pose::Pose pose)
private
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rigid_body_orientations ( core::pose::Pose pose)
private
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::randomize_rnp_rigid_body_orientations ( core::pose::Pose pose)
private

Kalli – this copies code from randomize_rigid_body_orientations – can we unify? – rhiju, 2017 yes, unified! but still need to keep this here for legacy RNP setup. will remove later once all testing is complete - Kalli, late 2017

References protocols::rigid::RigidBodyRandomizeMover::apply(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::kinematics::FoldTree::num_jump(), protocols::rigid::partner_upstream, core::pose::Pose::residue(), rnp_docking_ft_, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by setup_rnp_fold_tree().

movers::RNA_FragmentMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rna_fragment_mover ( )
inline

References rna_fragment_mover_.

movers::RNA_HelixMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rna_helix_mover ( )
inline

References rna_helix_mover_.

Referenced by set_rna_helix_mover().

core::import_pose::RNA_JumpMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rna_jump_mover ( )
inline

References rna_jump_mover_.

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::RNA_move_trial ( core::pose::Pose pose)
private

There are three kinds of insertions – (1) fragment insertions for, e.g., contiguous 3-mers (2) jump changes (tweaking base pairs) and (3) "chunk insertions", which change out whole loops, motifs, or junctions based on previous models stored in silent files

References dock_into_density_freq_, dock_into_density_trial(), jump_change_frequency_, options_, random_chunk_trial(), random_fragment_trial(), random_jump_trial(), core::scoring::rg, and rna_chunk_library_.

Referenced by do_move_trial().

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rnp_docking_trial ( core::pose::Pose pose)
private
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::search_rigid_body_orientation ( core::pose::Pose pose)
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::set_close_loops ( bool const &  setting)
inline

References close_loops_.

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::set_frag_size ( core::Size const &  setting)
inline

References frag_size_.

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::set_helix_mover_magnitude ( core::Real const &  rot_mag,
core::Real const &  trans_mag 
)

References rna_helix_mover_.

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::set_rna_helix_mover ( movers::RNA_HelixMoverOP const  rna_helix_mover)
inline
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::set_sfxn ( core::scoring::ScoreFunctionOP const &  sfxn)
inline

References sfxn_.

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_dock_into_density_mover ( core::pose::Pose const &  pose,
core::Real const &  rot_mag,
core::Real const &  trans_mag 
)
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rigid_body_mover ( core::pose::Pose const &  pose,
core::Real const &  rot_mag,
core::Real const &  trans_mag 
)
void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover ( core::pose::Pose const &  pose,
core::Real const &  rot_mag,
core::Real const &  trans_mag 
)

Kalli – this copies code from setup_rigid_body_mover – can we unify? – rhiju, 2017 yes, unified! but still need to keep this here for legacy RNP setup. will remove later once all testing is complete - Kalli, late 2017

References do_rnp_docking_, core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::kinematics::FoldTree::num_jump(), protocols::rigid::partner_upstream, core::pose::Pose::residue(), rnp_docking_ft_, rnp_docking_mover_, core::kinematics::MoveMap::set_jump(), protocols::rna::denovo::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

void protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rnp_fold_tree ( core::pose::Pose pose,
bool const &  refine_pose,
bool const &  randomize 
)
bool protocols::rna::denovo::movers::RNA_DeNovoMasterMover::success ( ) const
inline

References move_type_.

Referenced by random_jump_trial().

Member Data Documentation

bool protocols::rna::denovo::movers::RNA_DeNovoMasterMover::close_loops_
private
bool protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_rnp_docking_
private
core::Real protocols::rna::denovo::movers::RNA_DeNovoMasterMover::dock_into_density_freq_
private

Referenced by RNA_move_trial().

protocols::rigid::RigidBodyPerturbMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::dock_into_density_mover_
private
core::Size protocols::rna::denovo::movers::RNA_DeNovoMasterMover::frag_size_
private
core::Real protocols::rna::denovo::movers::RNA_DeNovoMasterMover::jump_change_frequency_
private
std::string protocols::rna::denovo::movers::RNA_DeNovoMasterMover::move_type_
private
core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::options_
private
protocols::rigid::RigidBodyPerturbMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rigid_body_mover_
private
core::import_pose::libraries::RNA_ChunkLibraryOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rna_chunk_library_
private
movers::RNA_FragmentMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rna_fragment_mover_
private
movers::RNA_HelixMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rna_helix_mover_
private
core::import_pose::RNA_JumpMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rna_jump_mover_
private
protocols::rna::movers::RNA_LoopCloserOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rna_loop_closer_
private
core::kinematics::FoldTree protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rnp_docking_ft_
private
protocols::rigid::RigidBodyPerturbMoverOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::rnp_docking_mover_
private
core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_DeNovoMasterMover::sfxn_
private

Referenced by RNA_DeNovoMasterMover(), and set_sfxn().


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