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

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

#include <RNA_DeNovoProtocol.hh>

Public Member Functions

 RNA_DeNovoProtocol (Size const nstruct, std::string const silent_file, bool const heat_structure=true, bool const minimize_structure=false, bool const relax_structure=false, bool const allow_bulge=false)
 Construct the protocol object given the RNA fragment library to use. More...
 
 ~RNA_DeNovoProtocol ()
 
virtual protocols::moves::MoverOP clone () const
 Clone this object. More...
 
void apply (core::pose::Pose &pose)
 Apply the RNA denovo modeling protocol to the input pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
void set_dump_pdb (bool const setting)
 
void set_temperature (core::Real const setting)
 
void set_jump_library_file (std::string const jump_library_file)
 
void set_all_rna_fragments_file (std::string const file)
 
void set_vall_torsions_file (std::string const file)
 
void set_rna_params_file (std::string const file)
 
void set_rna_data_file (std::string const file)
 
void set_chunk_pdb_files (utility::vector1< std::string > const &chunk_pdb_files)
 
void set_chunk_silent_files (utility::vector1< std::string > const &chunk_silent_files)
 
void set_input_res (utility::vector1< Size > const &input_res)
 
void ignore_secstruct (bool const setting)
 
void jump_change_frequency (core::Real const value)
 
void set_close_loops (bool const setting)
 
void set_close_loops_after_each_move (bool const setting)
 
void simple_rmsd_cutoff_relax (bool const setting)
 
void output_lores_silent_file (bool const setting)
 
void set_filter_lores_base_pairs (bool const setting)
 
void set_filter_lores_base_pairs_early (bool const setting)
 
void set_filter_chain_closure (bool const setting)
 
void set_filter_chain_closure_distance (core::Real const setting)
 
void set_filter_chain_closure_halfway (bool const setting)
 
void set_binary_rna_output (bool const setting)
 
void set_suppress_bp_constraint (core::Real const setting)
 
void set_lores_scorefxn (std::string const &lores_scorefxn)
 
void set_vary_bond_geometry (bool const setting)
 
void output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag, bool const score_only=false) const
 
void align_and_output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag) const
 
void set_staged_constraints (bool const setting)
 
void set_allow_consecutive_bulges (bool const setting)
 
void set_chainbreak_weight (core::Real setting)
 
void set_linear_chainbreak_weight (core::Real setting)
 
void set_allowed_bulge_res (utility::vector1< core::Size > const &setting)
 
void set_move_first_rigid_body (bool const setting)
 
void set_root_at_first_rigid_body (bool const setting)
 
void set_output_filters (bool const setting)
 
void set_autofilter (bool const setting)
 
void set_monte_carlo_cycles (Size const setting)
 
void set_rounds (Size const setting)
 
void set_extra_minimize_res (utility::vector1< core::Size > setting)
 
void set_extra_minimize_chi_res (utility::vector1< core::Size > setting)
 
void set_refine_pose_list (utility::vector1< core::pose::PoseOP > const &setting)
 
void set_refine_pose (Size const setting)
 
void set_bps_moves (Size const setting)
 
void set_minimizer_use_coordinate_constraints (Size const setting)
 
- 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
 

Private Member Functions

void initialize_movers (core::pose::Pose &pose)
 
void setup_monte_carlo_cycles (core::pose::Pose const &pose)
 
utility::vector1< Sizeget_moving_res (core::pose::Pose const &pose) const
 
void initialize_lores_silent_file ()
 
void initialize_constraints (core::pose::Pose &pose)
 
void initialize_scorefxn (core::pose::Pose &pose)
 
void initialize_tag_is_done ()
 
void setup_rigid_body_mover (core::pose::Pose const &pose, core::Size const r)
 
void final_score (core::pose::Pose &pose)
 
void output_silent_struct (core::io::silent::SilentStruct &s, core::io::silent::SilentFileData &silent_file_data, std::string const &silent_file, core::pose::Pose &pose, std::string const out_file_tag, bool const score_only=false) const
 
void do_random_moves (core::pose::Pose &pose)
 
void randomize_rigid_body_orientations (core::pose::Pose &pose)
 
void update_denovo_scorefxn_weights (Size const r)
 
Size figure_out_constraint_separation_cutoff (Size const r, Size const max_dist)
 
void update_pose_constraints (Size const r, core::pose::Pose &pose)
 
void update_frag_size (Size const r)
 
void random_fragment_trial (core::pose::Pose &pose)
 
bool random_chunk_trial (core::pose::Pose &pose)
 
void random_jump_trial (core::pose::Pose &pose)
 
void RNA_move_trial (core::pose::Pose &pose)
 
void add_number_base_pairs (core::pose::Pose const &pose_input, core::io::silent::SilentStruct &s) const
 
void add_number_native_base_pairs (core::pose::Pose &pose, core::io::silent::SilentStruct &s) const
 
void calc_rmsds (core::io::silent::SilentStruct &s, core::pose::Pose &pose, std::string const &out_file_tag) 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, std::string const out_file_tag)
 
void add_chem_shift_info (core::io::silent::SilentStruct &silent_struct, core::pose::Pose const &const_pose) const
 

Private Attributes

Size const nstruct_
 
Size rounds_
 
Size monte_carlo_cycles_
 
Size const monte_carlo_cycles_max_default_
 
bool user_defined_cycles_
 
std::string all_rna_fragments_file_
 
std::string const silent_file_
 
std::string lores_silent_file_
 
bool const heat_structure_
 
bool dump_pdb_
 
bool const minimize_structure_
 
bool const relax_structure_
 
bool ignore_secstruct_
 
bool do_close_loops_
 
bool close_loops_at_end_
 
bool close_loops_in_last_round_
 
bool close_loops_after_each_move_
 
bool simple_rmsd_cutoff_relax_
 
bool allow_bulge_
 
bool allow_consecutive_bulges_
 
bool const use_chem_shift_data_
 
core::Real m_Temperature_
 
Size frag_size_
 
protocols::moves::MonteCarloOP monte_carlo_
 
protocols::farna::RNA_FragmentsOP all_rna_fragments_
 
protocols::farna::RNA_FragmentMoverOP rna_fragment_mover_
 
protocols::farna::RNA_LoopCloserOP rna_loop_closer_
 
protocols::farna::RNA_ChunkLibraryOP rna_chunk_library_
 
protocols::farna::RNA_MinimizerOP rna_minimizer_
 
protocols::farna::RNA_RelaxerOP rna_relaxer_
 
protocols::rigid::RigidBodyPerturbMoverOP rigid_body_mover_
 
std::string rna_params_file_
 
std::string rna_data_file_
 
std::string jump_library_file_
 
RNA_StructureParametersOP rna_structure_parameters_
 
core::io::rna::RNA_DataReaderOP rna_data_reader_
 
bool output_lores_silent_file_
 
bool filter_lores_base_pairs_
 
bool filter_lores_base_pairs_early_
 
bool filter_chain_closure_
 
core::Real filter_chain_closure_distance_
 
bool filter_chain_closure_halfway_
 
bool vary_bond_geometry_
 
bool binary_rna_output_
 
core::scoring::constraints::ConstraintSetOP constraint_set_
 
core::Real jump_change_frequency_
 
std::map< std::string, booltag_is_done_
 
std::string lores_scorefxn_
 
core::scoring::ScoreFunctionOP denovo_scorefxn_
 
core::scoring::ScoreFunctionOP hires_scorefxn_
 
core::scoring::ScoreFunctionOP chem_shift_scorefxn_
 
core::scoring::ScoreFunctionOP initial_denovo_scorefxn_
 
core::scoring::ScoreFunctionOP final_scorefxn_
 
core::scoring::rna::RNA_LowResolutionPotential local_rna_low_resolution_potential_
 
utility::vector1< std::stringchunk_pdb_files_
 
utility::vector1< std::stringchunk_silent_files_
 
utility::vector1< core::Sizeinput_res_
 
utility::vector1< core::Sizeallowed_bulge_res_
 
utility::vector1< core::Sizeextra_minimize_res_
 
utility::vector1< core::Sizeextra_minimize_chi_res_
 
core::Real chunk_coverage_
 
bool staged_constraints_
 
core::Real chainbreak_weight_
 
core::Real linear_chainbreak_weight_
 
bool titrate_stack_bonus_
 
bool move_first_rigid_body_
 
bool root_at_first_rigid_body_
 
core::Real suppress_bp_constraint_
 
bool output_filters_
 
core::Real lores_score_early_
 
core::Real lores_score_final_
 
bool autofilter_
 
core::Real autofilter_score_quantile_
 
std::list< core::Realall_lores_score_final_
 
bool refine_from_silent_
 
utility::vector1
< core::pose::PoseOP
refine_pose_list_
 
bool refine_pose_
 
bool bps_moves_
 
bool minimizer_use_coordinate_constraints_
 

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::RNA_DeNovoProtocol::RNA_DeNovoProtocol ( Size const  nstruct,
std::string const  silent_file,
bool const  heat_structure = true,
bool const  minimize_structure = false,
bool const  relax_structure = false,
bool const  allow_bulge = false 
)
protocols::farna::RNA_DeNovoProtocol::~RNA_DeNovoProtocol ( )

Member Function Documentation

void protocols::farna::RNA_DeNovoProtocol::add_chem_shift_info ( core::io::silent::SilentStruct silent_struct,
core::pose::Pose const &  const_pose 
) const
private
void protocols::farna::RNA_DeNovoProtocol::add_number_base_pairs ( core::pose::Pose const &  pose_input,
core::io::silent::SilentStruct s 
) const
private
void protocols::farna::RNA_DeNovoProtocol::add_number_native_base_pairs ( core::pose::Pose pose,
core::io::silent::SilentStruct s 
) const
private
void protocols::farna::RNA_DeNovoProtocol::align_and_output_to_silent_file ( core::pose::Pose pose,
std::string const &  silent_file,
std::string const &  out_file_tag 
) const
void protocols::farna::RNA_DeNovoProtocol::apply ( core::pose::Pose pose)
virtual

Apply the RNA denovo modeling protocol to the input pose.

Apply the RNA de novo modeling protocol to a pose.

Implements protocols::moves::Mover.

References align_and_output_to_silent_file(), all_atom_rmsd(), all_lores_score_final_, allow_bulge_, allow_consecutive_bulges_, protocols::farna::RNA_StructureParameters::allow_insert(), allowed_bulge_res_, protocols::farna::RNA_Minimizer::apply(), protocols::farna::RNA_LoopCloser::apply(), protocols::farna::RNA_Relaxer::apply(), apply_chem_shift_data(), autofilter_, protocols::farna::RNA_StructureParameters::check_base_pairs(), protocols::farna::RNA_LoopCloser::check_closure(), check_score_filter(), close_loops_after_each_move_, close_loops_at_end_, close_loops_in_last_round_, protocols::farna::RNA_StructureParameters::connections(), core::pose::copydofs::copy_dofs_match_atom_names(), denovo_scorefxn_, do_close_loops_, do_random_moves(), core::pose::Pose::dump_pdb(), dump_pdb, dump_pdb_, filter_chain_closure_, filter_chain_closure_distance_, filter_chain_closure_halfway_, filter_lores_base_pairs_, filter_lores_base_pairs_early_, final_score(), final_scorefxn_, frag_size_, protocols::moves::Mover::get_native_pose(), heat_structure_, hires_scorefxn_, initialize_constraints(), initialize_lores_silent_file(), initialize_movers(), protocols::farna::RNA_ChunkLibrary::initialize_random_chunks(), initialize_scorefxn(), initialize_tag_is_done(), lores_score_early_, lores_score_final_, lores_silent_file_, protocols::moves::MonteCarlo::lowest_score_pose(), m_Temperature_, minimize_structure_, monte_carlo_, monte_carlo_cycles_, nstruct_, output_lores_silent_file_, protocols::moves::MonteCarlo::recover_low(), refine_from_silent_, refine_pose_, refine_pose_list_, relax_structure_, protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), rmsd, rna_chunk_library_, rna_loop_closer_, rna_minimizer_, RNA_move_trial(), rna_relaxer_, rna_structure_parameters_, rounds_, protocols::moves::MonteCarlo::score_function(), protocols::farna::RNA_Minimizer::set_allow_insert(), protocols::farna::RNA_StructureParameters::setup_base_pair_constraints(), protocols::farna::RNA_StructureParameters::setup_fold_tree_and_jumps_and_variants(), setup_monte_carlo_cycles(), setup_rigid_body_mover(), protocols::moves::MonteCarlo::show_counters(), silent_file_, tag_is_done_, protocols::farna::TR, update_denovo_scorefxn_weights(), update_frag_size(), update_pose_constraints(), use_chem_shift_data_, and protocols::farna::virtualize_bulges().

void protocols::farna::RNA_DeNovoProtocol::apply_chem_shift_data ( core::pose::Pose pose,
std::string const  out_file_tag 
)
private
void protocols::farna::RNA_DeNovoProtocol::calc_rmsds ( core::io::silent::SilentStruct s,
core::pose::Pose pose,
std::string const &  out_file_tag 
) const
private
bool protocols::farna::RNA_DeNovoProtocol::check_score_filter ( core::Real const  lores_score_,
std::list< core::Real > &  all_lores_score_ 
)
private

References autofilter_score_quantile_, and protocols::farna::TR.

Referenced by apply().

protocols::moves::MoverOP protocols::farna::RNA_DeNovoProtocol::clone ( ) const
virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References RNA_DeNovoProtocol().

void protocols::farna::RNA_DeNovoProtocol::do_random_moves ( core::pose::Pose pose)
private
Size protocols::farna::RNA_DeNovoProtocol::figure_out_constraint_separation_cutoff ( Size const  r,
Size const  max_dist 
)
private

References rounds_.

Referenced by update_pose_constraints().

void protocols::farna::RNA_DeNovoProtocol::final_score ( core::pose::Pose pose)
private

References final_scorefxn_, core::scoring::rna_chem_map, and size().

Referenced by apply().

utility::vector1< Size > protocols::farna::RNA_DeNovoProtocol::get_moving_res ( core::pose::Pose const &  pose) const
private
std::string protocols::farna::RNA_DeNovoProtocol::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::farna::RNA_DeNovoProtocol::ignore_secstruct ( bool const  setting)
inline

References ignore_secstruct_.

void protocols::farna::RNA_DeNovoProtocol::initialize_constraints ( core::pose::Pose pose)
private
void protocols::farna::RNA_DeNovoProtocol::initialize_lores_silent_file ( )
private
void protocols::farna::RNA_DeNovoProtocol::initialize_movers ( core::pose::Pose pose)
private
void protocols::farna::RNA_DeNovoProtocol::initialize_scorefxn ( core::pose::Pose pose)
private
void protocols::farna::RNA_DeNovoProtocol::initialize_tag_is_done ( )
private
void protocols::farna::RNA_DeNovoProtocol::jump_change_frequency ( core::Real const  value)
inline
void protocols::farna::RNA_DeNovoProtocol::output_lores_silent_file ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::output_silent_struct ( core::io::silent::SilentStruct s,
core::io::silent::SilentFileData silent_file_data,
std::string const &  silent_file,
core::pose::Pose pose,
std::string const  out_file_tag,
bool const  score_only = false 
) const
private
void protocols::farna::RNA_DeNovoProtocol::output_to_silent_file ( core::pose::Pose pose,
std::string const &  silent_file,
std::string const &  out_file_tag,
bool const  score_only = false 
) const
bool protocols::farna::RNA_DeNovoProtocol::random_chunk_trial ( core::pose::Pose pose)
private
void protocols::farna::RNA_DeNovoProtocol::random_fragment_trial ( core::pose::Pose pose)
private
void protocols::farna::RNA_DeNovoProtocol::random_jump_trial ( core::pose::Pose pose)
private
void protocols::farna::RNA_DeNovoProtocol::randomize_rigid_body_orientations ( core::pose::Pose pose)
private
void protocols::farna::RNA_DeNovoProtocol::RNA_move_trial ( core::pose::Pose pose)
private
void protocols::farna::RNA_DeNovoProtocol::set_all_rna_fragments_file ( std::string const  file)
inline
void protocols::farna::RNA_DeNovoProtocol::set_allow_consecutive_bulges ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_allowed_bulge_res ( utility::vector1< core::Size > const &  setting)
inline

References allowed_bulge_res_.

void protocols::farna::RNA_DeNovoProtocol::set_autofilter ( bool const  setting)
inline

References autofilter_.

void protocols::farna::RNA_DeNovoProtocol::set_binary_rna_output ( bool const  setting)
inline

References binary_rna_output_.

void protocols::farna::RNA_DeNovoProtocol::set_bps_moves ( Size const  setting)
inline

References bps_moves_.

void protocols::farna::RNA_DeNovoProtocol::set_chainbreak_weight ( core::Real  setting)
inline

References chainbreak_weight_.

void protocols::farna::RNA_DeNovoProtocol::set_chunk_pdb_files ( utility::vector1< std::string > const &  chunk_pdb_files)
inline

References chunk_pdb_files_.

void protocols::farna::RNA_DeNovoProtocol::set_chunk_silent_files ( utility::vector1< std::string > const &  chunk_silent_files)
inline

References chunk_silent_files_.

void protocols::farna::RNA_DeNovoProtocol::set_close_loops ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_close_loops_after_each_move ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_dump_pdb ( bool const  setting)
inline

References dump_pdb_.

void protocols::farna::RNA_DeNovoProtocol::set_extra_minimize_chi_res ( utility::vector1< core::Size setting)
void protocols::farna::RNA_DeNovoProtocol::set_extra_minimize_res ( utility::vector1< core::Size setting)

References extra_minimize_res_.

void protocols::farna::RNA_DeNovoProtocol::set_filter_chain_closure ( bool const  setting)
inline

References filter_chain_closure_.

void protocols::farna::RNA_DeNovoProtocol::set_filter_chain_closure_distance ( core::Real const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_filter_chain_closure_halfway ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_filter_lores_base_pairs ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_filter_lores_base_pairs_early ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_input_res ( utility::vector1< Size > const &  input_res)
inline

References input_res_.

void protocols::farna::RNA_DeNovoProtocol::set_jump_library_file ( std::string const  jump_library_file)
inline

References jump_library_file_.

void protocols::farna::RNA_DeNovoProtocol::set_linear_chainbreak_weight ( core::Real  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_lores_scorefxn ( std::string const &  lores_scorefxn)
inline

References lores_scorefxn_.

void protocols::farna::RNA_DeNovoProtocol::set_minimizer_use_coordinate_constraints ( Size const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_monte_carlo_cycles ( Size const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_move_first_rigid_body ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_output_filters ( bool const  setting)
inline

References output_filters_.

void protocols::farna::RNA_DeNovoProtocol::set_refine_pose ( Size const  setting)
inline

References refine_pose_.

void protocols::farna::RNA_DeNovoProtocol::set_refine_pose_list ( utility::vector1< core::pose::PoseOP > const &  setting)
void protocols::farna::RNA_DeNovoProtocol::set_rna_data_file ( std::string const  file)
inline

References rna_data_file_.

void protocols::farna::RNA_DeNovoProtocol::set_rna_params_file ( std::string const  file)
inline

References rna_params_file_.

void protocols::farna::RNA_DeNovoProtocol::set_root_at_first_rigid_body ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_rounds ( Size const  setting)
inline

References rounds_.

void protocols::farna::RNA_DeNovoProtocol::set_staged_constraints ( bool const  setting)
inline

References staged_constraints_.

void protocols::farna::RNA_DeNovoProtocol::set_suppress_bp_constraint ( core::Real const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::set_temperature ( core::Real const  setting)
inline

References m_Temperature_.

void protocols::farna::RNA_DeNovoProtocol::set_vall_torsions_file ( std::string const  file)
inline
void protocols::farna::RNA_DeNovoProtocol::set_vary_bond_geometry ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::setup_monte_carlo_cycles ( core::pose::Pose const &  pose)
private
void protocols::farna::RNA_DeNovoProtocol::setup_rigid_body_mover ( core::pose::Pose const &  pose,
core::Size const  r 
)
private
void protocols::farna::RNA_DeNovoProtocol::show ( std::ostream &  output = std::cout) const
virtual
void protocols::farna::RNA_DeNovoProtocol::simple_rmsd_cutoff_relax ( bool const  setting)
inline
void protocols::farna::RNA_DeNovoProtocol::update_denovo_scorefxn_weights ( Size const  r)
private
void protocols::farna::RNA_DeNovoProtocol::update_frag_size ( Size const  r)
private

References frag_size_, rounds_, and protocols::farna::TR.

Referenced by apply().

void protocols::farna::RNA_DeNovoProtocol::update_pose_constraints ( Size const  r,
core::pose::Pose pose 
)
private

Member Data Documentation

std::list< core::Real > protocols::farna::RNA_DeNovoProtocol::all_lores_score_final_
private

Referenced by apply().

protocols::farna::RNA_FragmentsOP protocols::farna::RNA_DeNovoProtocol::all_rna_fragments_
private

Referenced by initialize_movers().

std::string protocols::farna::RNA_DeNovoProtocol::all_rna_fragments_file_
private
bool protocols::farna::RNA_DeNovoProtocol::allow_bulge_
private

Referenced by apply(), and show().

bool protocols::farna::RNA_DeNovoProtocol::allow_consecutive_bulges_
private
utility::vector1< core::Size > protocols::farna::RNA_DeNovoProtocol::allowed_bulge_res_
private

Referenced by apply(), and set_allowed_bulge_res().

bool protocols::farna::RNA_DeNovoProtocol::autofilter_
private

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

core::Real protocols::farna::RNA_DeNovoProtocol::autofilter_score_quantile_
private

Referenced by check_score_filter(), and show().

bool protocols::farna::RNA_DeNovoProtocol::binary_rna_output_
private
bool protocols::farna::RNA_DeNovoProtocol::bps_moves_
private

Referenced by initialize_movers(), and set_bps_moves().

core::Real protocols::farna::RNA_DeNovoProtocol::chainbreak_weight_
private
core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::chem_shift_scorefxn_
private
core::Real protocols::farna::RNA_DeNovoProtocol::chunk_coverage_
private
utility::vector1< std::string > protocols::farna::RNA_DeNovoProtocol::chunk_pdb_files_
private
utility::vector1< std::string > protocols::farna::RNA_DeNovoProtocol::chunk_silent_files_
private
bool protocols::farna::RNA_DeNovoProtocol::close_loops_after_each_move_
private
bool protocols::farna::RNA_DeNovoProtocol::close_loops_at_end_
private
bool protocols::farna::RNA_DeNovoProtocol::close_loops_in_last_round_
private

Referenced by apply(), and show().

core::scoring::constraints::ConstraintSetOP protocols::farna::RNA_DeNovoProtocol::constraint_set_
private
core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::denovo_scorefxn_
private
bool protocols::farna::RNA_DeNovoProtocol::do_close_loops_
private
bool protocols::farna::RNA_DeNovoProtocol::dump_pdb_
private
utility::vector1< core::Size > protocols::farna::RNA_DeNovoProtocol::extra_minimize_chi_res_
private
utility::vector1< core::Size > protocols::farna::RNA_DeNovoProtocol::extra_minimize_res_
private
bool protocols::farna::RNA_DeNovoProtocol::filter_chain_closure_
private
core::Real protocols::farna::RNA_DeNovoProtocol::filter_chain_closure_distance_
private
bool protocols::farna::RNA_DeNovoProtocol::filter_chain_closure_halfway_
private
bool protocols::farna::RNA_DeNovoProtocol::filter_lores_base_pairs_
private
bool protocols::farna::RNA_DeNovoProtocol::filter_lores_base_pairs_early_
private
core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::final_scorefxn_
private
Size protocols::farna::RNA_DeNovoProtocol::frag_size_
private
bool const protocols::farna::RNA_DeNovoProtocol::heat_structure_
private

Referenced by apply(), and show().

core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::hires_scorefxn_
private
bool protocols::farna::RNA_DeNovoProtocol::ignore_secstruct_
private
core::scoring::ScoreFunctionOP protocols::farna::RNA_DeNovoProtocol::initial_denovo_scorefxn_
private
utility::vector1< core::Size > protocols::farna::RNA_DeNovoProtocol::input_res_
private
core::Real protocols::farna::RNA_DeNovoProtocol::jump_change_frequency_
private
std::string protocols::farna::RNA_DeNovoProtocol::jump_library_file_
private
core::Real protocols::farna::RNA_DeNovoProtocol::linear_chainbreak_weight_
private
core::scoring::rna::RNA_LowResolutionPotential protocols::farna::RNA_DeNovoProtocol::local_rna_low_resolution_potential_
private

Referenced by RNA_DeNovoProtocol().

core::Real protocols::farna::RNA_DeNovoProtocol::lores_score_early_
private

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

core::Real protocols::farna::RNA_DeNovoProtocol::lores_score_final_
private

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

std::string protocols::farna::RNA_DeNovoProtocol::lores_scorefxn_
private
std::string protocols::farna::RNA_DeNovoProtocol::lores_silent_file_
private
core::Real protocols::farna::RNA_DeNovoProtocol::m_Temperature_
private

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

bool const protocols::farna::RNA_DeNovoProtocol::minimize_structure_
private
bool protocols::farna::RNA_DeNovoProtocol::minimizer_use_coordinate_constraints_
private
protocols::moves::MonteCarloOP protocols::farna::RNA_DeNovoProtocol::monte_carlo_
private
Size protocols::farna::RNA_DeNovoProtocol::monte_carlo_cycles_
private
Size const protocols::farna::RNA_DeNovoProtocol::monte_carlo_cycles_max_default_
private

Referenced by setup_monte_carlo_cycles(), and show().

bool protocols::farna::RNA_DeNovoProtocol::move_first_rigid_body_
private
Size const protocols::farna::RNA_DeNovoProtocol::nstruct_
private

Referenced by apply(), and show().

bool protocols::farna::RNA_DeNovoProtocol::output_filters_
private
bool protocols::farna::RNA_DeNovoProtocol::output_lores_silent_file_
private
bool protocols::farna::RNA_DeNovoProtocol::refine_from_silent_
private

Referenced by apply(), and set_refine_pose_list().

bool protocols::farna::RNA_DeNovoProtocol::refine_pose_
private

Referenced by apply(), and set_refine_pose().

utility::vector1<core::pose::PoseOP> protocols::farna::RNA_DeNovoProtocol::refine_pose_list_
private

Referenced by apply(), and set_refine_pose_list().

bool const protocols::farna::RNA_DeNovoProtocol::relax_structure_
private

Referenced by apply(), and show().

protocols::rigid::RigidBodyPerturbMoverOP protocols::farna::RNA_DeNovoProtocol::rigid_body_mover_
private
protocols::farna::RNA_ChunkLibraryOP protocols::farna::RNA_DeNovoProtocol::rna_chunk_library_
private
std::string protocols::farna::RNA_DeNovoProtocol::rna_data_file_
private
core::io::rna::RNA_DataReaderOP protocols::farna::RNA_DeNovoProtocol::rna_data_reader_
private

Referenced by initialize_movers().

protocols::farna::RNA_FragmentMoverOP protocols::farna::RNA_DeNovoProtocol::rna_fragment_mover_
private
protocols::farna::RNA_LoopCloserOP protocols::farna::RNA_DeNovoProtocol::rna_loop_closer_
private
protocols::farna::RNA_MinimizerOP protocols::farna::RNA_DeNovoProtocol::rna_minimizer_
private
std::string protocols::farna::RNA_DeNovoProtocol::rna_params_file_
private
protocols::farna::RNA_RelaxerOP protocols::farna::RNA_DeNovoProtocol::rna_relaxer_
private

Referenced by apply(), and initialize_movers().

RNA_StructureParametersOP protocols::farna::RNA_DeNovoProtocol::rna_structure_parameters_
private
bool protocols::farna::RNA_DeNovoProtocol::root_at_first_rigid_body_
private
Size protocols::farna::RNA_DeNovoProtocol::rounds_
private
std::string const protocols::farna::RNA_DeNovoProtocol::silent_file_
private
bool protocols::farna::RNA_DeNovoProtocol::simple_rmsd_cutoff_relax_
private
bool protocols::farna::RNA_DeNovoProtocol::staged_constraints_
private
core::Real protocols::farna::RNA_DeNovoProtocol::suppress_bp_constraint_
private
std::map< std::string, bool > protocols::farna::RNA_DeNovoProtocol::tag_is_done_
private

Referenced by apply(), and initialize_tag_is_done().

bool protocols::farna::RNA_DeNovoProtocol::titrate_stack_bonus_
private
bool const protocols::farna::RNA_DeNovoProtocol::use_chem_shift_data_
private
bool protocols::farna::RNA_DeNovoProtocol::user_defined_cycles_
private
bool protocols::farna::RNA_DeNovoProtocol::vary_bond_geometry_
private

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