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protocols::rna::denovo::RNA_FragmentMonteCarlo Class Reference

#include <RNA_FragmentMonteCarlo.hh>

Inheritance diagram for protocols::rna::denovo::RNA_FragmentMonteCarlo:
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Public Member Functions

 RNA_FragmentMonteCarlo (core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP=nullptr)
 
 ~RNA_FragmentMonteCarlo () override
 
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...
 
void set_refine_pose (bool const setting)
 
void set_all_lores_score_final (std::list< core::Real > const &setting)
 
void set_denovo_scorefxn (core::scoring::ScoreFunctionCOP setting)
 
void set_hires_scorefxn (core::scoring::ScoreFunctionCOP setting)
 
void set_vdw_grid (protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP setting)
 
void set_is_rna_and_protein (bool const &setting)
 
void set_out_file_tag (std::string const &setting)
 
std::list< core::Real > const & all_lores_score_final () const
 
core::pose::PoseOP lores_pose ()
 
core::pose::PoseOP get_additional_output () override
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
core::Real lores_score_early () const
 
core::Real lores_score_final () const
 
void set_rna_base_pair_handler (core::import_pose::RNA_BasePairHandlerCOP setting)
 
core::import_pose::RNA_BasePairHandlerCOP rna_base_pair_handler () const
 
void set_rna_de_novo_pose_initializer (protocols::rna::denovo::RNA_DeNovoPoseInitializerCOP setting)
 
void set_user_input_chunk_library (core::import_pose::libraries::RNA_ChunkLibraryCOP setting)
 
void set_user_input_chunk_initialization_library (core::import_pose::libraries::RNA_ChunkLibraryCOP setting)
 
core::import_pose::libraries::RNA_ChunkLibraryCOP rna_chunk_library () const
 
void show (std::ostream &output) const override
 Outputs details about the Mover, including current settings. More...
 
void align_pose (core::pose::Pose &pose, bool const verbose=false) const
 
core::Real get_rmsd_no_superimpose (core::pose::Pose const &pose) const
 
core::Real get_rmsd_stems_no_superimpose (core::pose::Pose const &pose) const
 
core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map () const
 
protocols::rna::movers::RNA_LoopCloserCOP rna_loop_closer () const
 
bool loop_modeling () const
 
void set_outputter (output::RNA_FragmentMonteCarloOutputterOP const &setting)
 
output::RNA_FragmentMonteCarloOutputterOP outputter () 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...
 
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 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 &pose)
 
void initialize_libraries (core::pose::Pose &pose)
 
void initialize_movers (core::pose::Pose const &pose)
 
void initialize_score_functions ()
 
void initialize_parameters ()
 
void update_denovo_scorefxn_weights (core::Size const r)
 
core::Size figure_out_constraint_separation_cutoff (core::Size const r, core::Size const max_dist)
 
void update_pose_constraints (core::Size const r, core::pose::Pose &pose)
 
void update_rna_denovo_master_mover (core::Size const &r, core::pose::Pose const &pose)
 moves should get finer as simulation progresses through rounds More...
 
core::Size update_frag_size (core::Size const &r) const
 
void get_rigid_body_move_mags (core::Size const &r, core::Real &rot_mag, core::Real &trans_mag, core::Real const &rot_mag_init, core::Real const &trans_mag_init, core::Real const &rot_mag_final, core::Real const &trans_mag_final) const
 
bool check_score_filter (core::Real const lores_score_, std::list< core::Real > &all_lores_score_)
 
void apply_chem_shift_data (core::pose::Pose &pose)
 
void setup_monte_carlo_cycles (core::pose::Pose const &pose)
 
void final_score (core::pose::Pose &pose)
 
utility::vector1< core::Sizereroot_pose_before_align_and_return_moving_res (core::pose::Pose &pose) const
 
core::Real get_rmsd (core::pose::Pose const &const_pose) const
 
void check_for_loop_modeling_case (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map) const
 
void setup_full_initial_structure (core::pose::Pose &pose) const
 
core::Real randomize_and_close_all_chains (core::pose::Pose &pose, bool const &close_chains) const
 
void check_fold_tree_cutpoints_ok (core::pose::Pose const &pose) const
 
void copy_structure_keep_fold_tree (core::pose::Pose &pose, core::pose::Pose const &pose_to_copy) const
 

Private Attributes

core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP options_
 
std::string out_file_tag_
 
core::import_pose::RNA_BasePairHandlerCOP rna_base_pair_handler_
 
core::import_pose::libraries::RNA_ChunkLibraryCOP user_input_rna_chunk_library_
 
core::import_pose::libraries::RNA_ChunkLibraryCOP user_input_rna_chunk_initialization_library_
 
core::import_pose::libraries::RNA_ChunkLibraryOP rna_chunk_library_
 
core::import_pose::libraries::RNA_ChunkLibraryOP rna_chunk_initialization_library_
 
protocols::rna::denovo::RNA_DeNovoPoseInitializerCOP rna_de_novo_pose_initializer_
 
protocols::rna::movers::RNA_LoopCloserOP rna_loop_closer_
 
protocols::rna::movers::RNA_LoopCloserOP rna_loop_closer_init_
 
movers::RNA_DeNovoMasterMoverOP rna_denovo_master_mover_
 
movers::RNA_DeNovoMasterMoverOP rna_denovo_master_mover_init_
 
movers::RNA_HelixMoverOP rna_helix_mover_
 
movers::RNA_MinimizerOP rna_minimizer_
 
movers::RNA_RelaxerOP rna_relaxer_
 
movers::RNP_HighResMoverOP rnp_high_res_mover_
 
core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map_
 
core::scoring::ScoreFunctionCOP denovo_scorefxn_
 
core::scoring::ScoreFunctionCOP hires_scorefxn_
 
core::scoring::ScoreFunctionCOP chem_shift_scorefxn_
 
core::scoring::ScoreFunctionOP chainbreak_sfxn_
 
core::scoring::ScoreFunctionCOP final_scorefxn_
 
core::scoring::ScoreFunctionOP working_denovo_scorefxn_
 
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP vdw_grid_
 
core::Size const monte_carlo_cycles_max_default_
 
core::Size monte_carlo_cycles_
 
core::Size rounds_
 
bool refine_pose_
 
core::Real lores_score_early_
 
core::Real lores_score_final_
 
std::list< core::Realall_lores_score_final_
 
core::scoring::constraints::ConstraintSetOP constraint_set_
 
core::pose::PoseCOP align_pose_
 
core::pose::PoseOP lores_pose_
 
bool is_rna_and_protein_
 
output::RNA_FragmentMonteCarloOutputterOP outputter_
 

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::RNA_FragmentMonteCarlo::RNA_FragmentMonteCarlo ( core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP  options = nullptr)

Holds the main loop for Fragment assembly of RNA (FARNA).

Two major modes: in classic mode, assumes pose is unfolded, and tries to fold from scratch; several stages gradually turn on chain closure, apply filters, etc.

in refine_pose mode, carries out the last stage of classic modeling, with all score terms on, all constraints on, and loop closing active.

Can be called by two wrapper classes – RNA_DeNovoProtocol (setup through .params file or command lines in 'classic' rna_denovo application) RNA_DeNovoOptimizer (better encapsulation, used inside stepwise)

TODO

  • simulated tempering as an alternative to gradual turn on of score terms
  • factor out alignment stuff, unify with stepwise. [Move StepWisePoseAligner to toolbox?]
  • encapsulate filters into function outside of main loop.
protocols::rna::denovo::RNA_FragmentMonteCarlo::~RNA_FragmentMonteCarlo ( )
overridedefault

Member Function Documentation

void protocols::rna::denovo::RNA_FragmentMonteCarlo::align_pose ( core::pose::Pose pose,
bool const  verbose = false 
) const
std::list< core::Real > const& protocols::rna::denovo::RNA_FragmentMonteCarlo::all_lores_score_final ( ) const
inline
void protocols::rna::denovo::RNA_FragmentMonteCarlo::apply ( core::pose::Pose pose)
overridevirtual

Apply the loop-rebuild protocol to the input pose.

Implements protocols::moves::Mover.

References align_pose(), align_pose_, protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), all_lores_score_final_, apply_chem_shift_data(), atom_level_domain_map_, core::chemical::CENTROID, check_fold_tree_cutpoints_ok(), check_score_filter(), core::pose::Pose::clone(), core::pose::Pose::constraint_set(), constraint_set_, core::pose::copydofs::copy_dofs_match_atom_names(), copy_structure_keep_fold_tree(), denovo_scorefxn_, core::chemical::FA_STANDARD, final_score(), final_scorefxn_, core::pose::get_center_of_mass(), protocols::moves::Mover::get_native_pose(), get_rmsd(), get_rmsd_no_superimpose(), get_rmsd_stems_no_superimpose(), hires_scorefxn_, initialize(), is_rna_and_protein_, lores_pose_, lores_score_early(), lores_score_early_, lores_score_final(), lores_score_final_, monte_carlo_cycles_, options_, out_file_tag_, outputter_, refine_pose_, reroot_pose_before_align_and_return_moving_res(), rna_base_pair_handler_, rna_chunk_library_, rna_de_novo_pose_initializer_, rna_denovo_master_mover_, rna_loop_closer_, rna_minimizer_, rna_relaxer_, rnp_high_res_mover_, rounds_, core::pose::setPoseExtraScore(), setup_full_initial_structure(), setup_monte_carlo_cycles(), core::util::switch_to_residue_type_set(), protocols::rna::denovo::TR(), update_denovo_scorefxn_weights(), update_pose_constraints(), update_rna_denovo_master_mover(), vdw_grid_, protocols::rna::denovo::virtualize_bulges(), and working_denovo_scorefxn_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::apply_chem_shift_data ( core::pose::Pose pose)
private
core::pose::toolbox::AtomLevelDomainMapCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::atom_level_domain_map ( ) const
inline
void protocols::rna::denovo::RNA_FragmentMonteCarlo::check_fold_tree_cutpoints_ok ( core::pose::Pose const &  pose) const
private
void protocols::rna::denovo::RNA_FragmentMonteCarlo::check_for_loop_modeling_case ( std::map< core::id::AtomID, core::id::AtomID > &  atom_id_map) const
private
bool protocols::rna::denovo::RNA_FragmentMonteCarlo::check_score_filter ( core::Real const  lores_score_,
std::list< core::Real > &  all_lores_score_ 
)
private
void protocols::rna::denovo::RNA_FragmentMonteCarlo::copy_structure_keep_fold_tree ( core::pose::Pose pose,
core::pose::Pose const &  pose_to_copy 
) const
private
Size protocols::rna::denovo::RNA_FragmentMonteCarlo::figure_out_constraint_separation_cutoff ( core::Size const  r,
core::Size const  max_dist 
)
private

Used in staged_constraints only.

References rounds_.

Referenced by update_pose_constraints().

void protocols::rna::denovo::RNA_FragmentMonteCarlo::final_score ( core::pose::Pose pose)
private

Having this final_score function allows slow terms to not be applied during Monte Carlo but only as an extra score at end.

References final_scorefxn_, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), options_, and core::scoring::rna_chem_map.

Referenced by apply().

PoseOP protocols::rna::denovo::RNA_FragmentMonteCarlo::get_additional_output ( )
overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References lores_pose_, and options_.

std::string protocols::rna::denovo::RNA_FragmentMonteCarlo::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rigid_body_move_mags ( core::Size const &  r,
core::Real rot_mag,
core::Real trans_mag,
core::Real const &  rot_mag_init,
core::Real const &  trans_mag_init,
core::Real const &  rot_mag_final,
core::Real const &  trans_mag_final 
) const
private

References options_, and rounds_.

Referenced by update_rna_denovo_master_mover().

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd ( core::pose::Pose const &  const_pose) const
private

References align_pose(), and get_rmsd_no_superimpose().

Referenced by apply().

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_no_superimpose ( core::pose::Pose const &  pose) const
core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::get_rmsd_stems_no_superimpose ( core::pose::Pose const &  pose) const
void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize ( core::pose::Pose pose)
private
void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_libraries ( core::pose::Pose pose)
private
void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_movers ( core::pose::Pose const &  pose)
private
void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_parameters ( )
private
void protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_score_functions ( )
private
bool protocols::rna::denovo::RNA_FragmentMonteCarlo::loop_modeling ( ) const
core::pose::PoseOP protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_pose ( )
inline

References lores_pose_.

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_score_early ( ) const
inline

References lores_score_early_.

Referenced by apply().

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_score_final ( ) const
inline

References lores_score_final_.

Referenced by apply().

output::RNA_FragmentMonteCarloOutputterOP protocols::rna::denovo::RNA_FragmentMonteCarlo::outputter ( ) const
inline

References outputter_.

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::randomize_and_close_all_chains ( core::pose::Pose pose,
bool const &  close_chains 
) const
private
vector1< core::Size > protocols::rna::denovo::RNA_FragmentMonteCarlo::reroot_pose_before_align_and_return_moving_res ( core::pose::Pose pose) const
private
core::import_pose::RNA_BasePairHandlerCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_base_pair_handler ( ) const
inline
core::import_pose::libraries::RNA_ChunkLibraryCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_chunk_library ( ) const
inline

References rna_chunk_library_.

protocols::rna::movers::RNA_LoopCloserCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_loop_closer ( ) const
inline

References rna_loop_closer_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_all_lores_score_final ( std::list< core::Real > const &  setting)
inline
void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_denovo_scorefxn ( core::scoring::ScoreFunctionCOP  setting)
inline

References denovo_scorefxn_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_hires_scorefxn ( core::scoring::ScoreFunctionCOP  setting)
inline

References hires_scorefxn_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_is_rna_and_protein ( bool const &  setting)
inline

References is_rna_and_protein_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_out_file_tag ( std::string const &  setting)
inline

References out_file_tag_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_outputter ( output::RNA_FragmentMonteCarloOutputterOP const &  setting)
inline

References outputter_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_refine_pose ( bool const  setting)
inline

References refine_pose_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_rna_base_pair_handler ( core::import_pose::RNA_BasePairHandlerCOP  setting)
inline
void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_rna_de_novo_pose_initializer ( protocols::rna::denovo::RNA_DeNovoPoseInitializerCOP  setting)
inline
void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_user_input_chunk_initialization_library ( core::import_pose::libraries::RNA_ChunkLibraryCOP  setting)
inline
void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_user_input_chunk_library ( core::import_pose::libraries::RNA_ChunkLibraryCOP  setting)
inline
void protocols::rna::denovo::RNA_FragmentMonteCarlo::set_vdw_grid ( protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP  setting)
inline

References vdw_grid_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_full_initial_structure ( core::pose::Pose pose) const
private
void protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_monte_carlo_cycles ( core::pose::Pose const &  pose)
private
void protocols::rna::denovo::RNA_FragmentMonteCarlo::show ( std::ostream &  output) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References lores_score_early_, lores_score_final_, monte_carlo_cycles_, monte_carlo_cycles_max_default_, and rounds_.

void protocols::rna::denovo::RNA_FragmentMonteCarlo::update_denovo_scorefxn_weights ( core::Size const  r)
private

Progressive upweighting of 'fine-scale' RNA modeling terms. Stack geometry, chainbreak, and constraint terms are zero for first of 10 rna_denovo rounds, then titrated up to final weight. Analogous to abinitio protocol for proteins, where strand geometry terms are turned on late.

References core::scoring::atom_pair_constraint, core::scoring::base_pair_constraint, core::scoring::chainbreak, core::scoring::coordinate_constraint, denovo_scorefxn_, core::scoring::linear_chainbreak, options_, core::scoring::rna_base_axis, core::scoring::rna_base_stack_axis, core::scoring::rna_base_stagger, core::scoring::rna_chem_map_lores, core::scoring::rnp_vdw, rounds_, and working_denovo_scorefxn_.

Referenced by apply().

Size protocols::rna::denovo::RNA_FragmentMonteCarlo::update_frag_size ( core::Size const &  r) const
private

Classic 3->2->1 RNA fragment size reduction, set by round r.

References options_, and rounds_.

Referenced by update_rna_denovo_master_mover().

void protocols::rna::denovo::RNA_FragmentMonteCarlo::update_pose_constraints ( core::Size const  r,
core::pose::Pose pose 
)
private

Only does something if -staged_constraints flag is on. Progressively introduces constraints, with shortest range first (as determined by distance in fold-tree). Inspired by classic fold_constraints protocol for proteins.

References core::pose::Pose::constraint_set(), constraint_set_, figure_out_constraint_separation_cutoff(), core::pose::Pose::fold_tree(), options_, rounds_, and protocols::rna::denovo::TR().

Referenced by apply().

void protocols::rna::denovo::RNA_FragmentMonteCarlo::update_rna_denovo_master_mover ( core::Size const &  r,
core::pose::Pose const &  pose 
)
private

moves should get finer as simulation progresses through rounds

References get_rigid_body_move_mags(), is_rna_and_protein_, options_, rna_denovo_master_mover_, protocols::rna::denovo::TR(), update_frag_size(), and working_denovo_scorefxn_.

Referenced by apply().

Member Data Documentation

core::pose::PoseCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::align_pose_
private
std::list< core::Real > protocols::rna::denovo::RNA_FragmentMonteCarlo::all_lores_score_final_
private
core::pose::toolbox::AtomLevelDomainMapOP protocols::rna::denovo::RNA_FragmentMonteCarlo::atom_level_domain_map_
private
core::scoring::ScoreFunctionOP protocols::rna::denovo::RNA_FragmentMonteCarlo::chainbreak_sfxn_
private
core::scoring::ScoreFunctionCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::chem_shift_scorefxn_
private
core::scoring::constraints::ConstraintSetOP protocols::rna::denovo::RNA_FragmentMonteCarlo::constraint_set_
private

Referenced by apply(), and update_pose_constraints().

core::scoring::ScoreFunctionCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::denovo_scorefxn_
private
core::scoring::ScoreFunctionCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::final_scorefxn_
private
core::scoring::ScoreFunctionCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::hires_scorefxn_
private
bool protocols::rna::denovo::RNA_FragmentMonteCarlo::is_rna_and_protein_
private
core::pose::PoseOP protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_pose_
private
core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_score_early_
private

Referenced by apply(), lores_score_early(), and show().

core::Real protocols::rna::denovo::RNA_FragmentMonteCarlo::lores_score_final_
private

Referenced by apply(), lores_score_final(), and show().

core::Size protocols::rna::denovo::RNA_FragmentMonteCarlo::monte_carlo_cycles_
private
core::Size const protocols::rna::denovo::RNA_FragmentMonteCarlo::monte_carlo_cycles_max_default_
private

Referenced by setup_monte_carlo_cycles(), and show().

core::import_pose::options::RNA_FragmentMonteCarloOptionsCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::options_
private
std::string protocols::rna::denovo::RNA_FragmentMonteCarlo::out_file_tag_
private

Referenced by apply(), and set_out_file_tag().

output::RNA_FragmentMonteCarloOutputterOP protocols::rna::denovo::RNA_FragmentMonteCarlo::outputter_
private
bool protocols::rna::denovo::RNA_FragmentMonteCarlo::refine_pose_
private
core::import_pose::RNA_BasePairHandlerCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_base_pair_handler_
private
core::import_pose::libraries::RNA_ChunkLibraryOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_chunk_initialization_library_
private
core::import_pose::libraries::RNA_ChunkLibraryOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_chunk_library_
private
protocols::rna::denovo::RNA_DeNovoPoseInitializerCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_de_novo_pose_initializer_
private
movers::RNA_DeNovoMasterMoverOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_denovo_master_mover_
private
movers::RNA_DeNovoMasterMoverOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_denovo_master_mover_init_
private
movers::RNA_HelixMoverOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_helix_mover_
private

Referenced by initialize_movers().

protocols::rna::movers::RNA_LoopCloserOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_loop_closer_
private
protocols::rna::movers::RNA_LoopCloserOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_loop_closer_init_
private
movers::RNA_MinimizerOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_minimizer_
private
movers::RNA_RelaxerOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rna_relaxer_
private

Referenced by apply(), and initialize_movers().

movers::RNP_HighResMoverOP protocols::rna::denovo::RNA_FragmentMonteCarlo::rnp_high_res_mover_
private

Referenced by apply(), and initialize_movers().

core::Size protocols::rna::denovo::RNA_FragmentMonteCarlo::rounds_
private
core::import_pose::libraries::RNA_ChunkLibraryCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::user_input_rna_chunk_initialization_library_
private
core::import_pose::libraries::RNA_ChunkLibraryCOP protocols::rna::denovo::RNA_FragmentMonteCarlo::user_input_rna_chunk_library_
private
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP protocols::rna::denovo::RNA_FragmentMonteCarlo::vdw_grid_
private

Referenced by apply(), and set_vdw_grid().

core::scoring::ScoreFunctionOP protocols::rna::denovo::RNA_FragmentMonteCarlo::working_denovo_scorefxn_
private

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