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protocols::coarse_rna::CoarseRNA_DeNovoProtocol Class Reference

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

#include <CoarseRNA_DeNovoProtocol.hh>

Inheritance diagram for protocols::coarse_rna::CoarseRNA_DeNovoProtocol:
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Public Member Functions

 CoarseRNA_DeNovoProtocol (Size const nstruct, Size const monte_carlo_cycles, std::string const silent_file)
 Construct the protocol object given the RNA fragment library to use. More...
 
 ~CoarseRNA_DeNovoProtocol ()
 
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...
 
void set_dump_pdb (bool const setting)
 
void set_force_ideal_chainbreak (bool const &setting)
 
void set_check_pairing_dists (bool const &setting)
 
void set_add_base_pair_constraints (bool const &setting)
 
void set_jump_library_file (std::string const jump_library_file)
 
void set_rna_params_file (std::string const file)
 
void set_rna_data_file (std::string const file)
 
void set_chunk_silent_files (utility::vector1< std::string > const &chunk_silent_files)
 
void set_input_res (utility::vector1< core::Size > const &setting)
 
void set_lores_scorefxn (std::string const &lores_scorefxn)
 
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 set_temperature (core::Real const &setting)
 
void set_staged_constraints (bool const &setting)
 
void set_sim_anneal (bool const &setting)
 
void set_close_loops (bool const &setting)
 
void set_choose_best_solution (bool const &setting)
 
void set_freeze_domains (bool 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
 
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 (TagPtr const tag, 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
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). 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 initialize_tag_is_done ()
 
core::Real get_temperature (Size const &r, Size const &rounds) const
 
void do_random_fragment_insertions (core::pose::Pose &pose)
 
void RNA_move_trial (core::pose::Pose &pose)
 
void random_fragment_trial (core::pose::Pose &pose)
 
void random_domain_move_trial (core::pose::Pose &pose)
 
void initialize_constraints (core::pose::Pose &pose)
 
Size figure_out_constraint_separation_cutoff (Size const &r, Size const &rounds, Size const &max_dist)
 
void update_pose_constraints (Size const &r, Size const &rounds, core::pose::Pose &pose)
 
void update_domain_rot_trans_mag (Size const &r, Size const &rounds)
 
void fill_pairing_dists (core::pose::Pose &pose)
 
void check_new_pairing_dists (core::pose::Pose &pose, Size const &frag_pos)
 

Private Attributes

Size const nstruct_
 
Size const monte_carlo_cycles_
 
Size const rounds_
 
std::string const silent_file_
 
bool freeze_domains_
 
bool dump_pdb_
 
core::Real domain_move_frequency_
 
core::Real m_Temperature_
 
bool sim_anneal_
 
core::scoring::constraints::ConstraintSetOP constraint_set_
 
bool staged_constraints_
 
Size frag_size_
 
protocols::moves::MonteCarloOP monte_carlo_
 
std::string rna_params_file_
 
std::string rna_data_file_
 
std::string all_rna_fragments_file_
 
std::string jump_library_file_
 
std::map< std::string, booltag_is_done_
 
std::string lores_scorefxn_
 
core::scoring::ScoreFunctionOP denovo_scorefxn_
 
protocols::rna::RNA_FragmentMoverOP frag_mover_
 
protocols::rna::RNA_StructureParametersOP rna_structure_parameters_
 
protocols::rna::RNA_DataReaderOP rna_data_reader_
 
protocols::rna::RNA_ChunkLibraryOP rna_chunk_library_
 
protocols::coarse_rna::CoarseRNA_LoopCloserOP rna_loop_closer_
 
protocols::rna::MultipleDomainMoverOP multiple_domain_mover_
 
utility::vector1< std::string > chunk_silent_files_
 
utility::vector1< core::Sizeinput_res_
 
bool close_loops_
 
bool choose_best_solution_
 
bool force_ideal_chainbreak_
 
bool add_base_pair_constraints_
 
bool check_pairing_dists_
 
bool view_monte_carlo_
 
utility::vector1< core::Realpairing_dists_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::coarse_rna::CoarseRNA_DeNovoProtocol::CoarseRNA_DeNovoProtocol ( Size const  nstruct,
Size const  monte_carlo_cycles,
std::string const  silent_file 
)

Construct the protocol object given the RNA fragment library to use.

Referenced by clone().

protocols::coarse_rna::CoarseRNA_DeNovoProtocol::~CoarseRNA_DeNovoProtocol ( )

Member Function Documentation

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::apply ( core::pose::Pose pose)
virtual
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::check_new_pairing_dists ( core::pose::Pose pose,
Size const &  frag_pos 
)
private
protocols::moves::MoverOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::clone ( ) const
virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References CoarseRNA_DeNovoProtocol().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::do_random_fragment_insertions ( core::pose::Pose pose)
private
Size protocols::coarse_rna::CoarseRNA_DeNovoProtocol::figure_out_constraint_separation_cutoff ( Size const &  r,
Size const &  rounds,
Size const &  max_dist 
)
private

Referenced by update_pose_constraints().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::fill_pairing_dists ( core::pose::Pose pose)
private
std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

core::Real protocols::coarse_rna::CoarseRNA_DeNovoProtocol::get_temperature ( Size const &  r,
Size const &  rounds 
) const
private

References m_Temperature_, and sim_anneal_.

Referenced by apply().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::initialize_constraints ( core::pose::Pose pose)
private
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::initialize_movers ( core::pose::Pose pose)
private
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::initialize_tag_is_done ( )
private
void protocols::coarse_rna::CoarseRNA_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
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::random_domain_move_trial ( core::pose::Pose pose)
private
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::random_fragment_trial ( core::pose::Pose pose)
private
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::RNA_move_trial ( core::pose::Pose pose)
private
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_add_base_pair_constraints ( bool const &  setting)
inline
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_check_pairing_dists ( bool const &  setting)
inline

References check_pairing_dists_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_choose_best_solution ( bool const &  setting)
inline

References choose_best_solution_.

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

References chunk_silent_files_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_close_loops ( bool const &  setting)
inline

References close_loops_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_dump_pdb ( bool const  setting)
inline

References dump_pdb_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_force_ideal_chainbreak ( bool const &  setting)
inline
void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_freeze_domains ( bool const &  setting)
inline

References freeze_domains_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_input_res ( utility::vector1< core::Size > const &  setting)
inline

References input_res_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_jump_library_file ( std::string const  jump_library_file)
inline

References jump_library_file_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_lores_scorefxn ( std::string const &  lores_scorefxn)
inline

References lores_scorefxn_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_rna_data_file ( std::string const  file)
inline

References rna_data_file_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_rna_params_file ( std::string const  file)
inline

References rna_params_file_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_sim_anneal ( bool const &  setting)
inline

References sim_anneal_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_staged_constraints ( bool const &  setting)
inline

References staged_constraints_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::set_temperature ( core::Real const &  setting)
inline

References m_Temperature_.

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::update_domain_rot_trans_mag ( Size const &  r,
Size const &  rounds 
)
private

References multiple_domain_mover_.

Referenced by apply().

void protocols::coarse_rna::CoarseRNA_DeNovoProtocol::update_pose_constraints ( Size const &  r,
Size const &  rounds,
core::pose::Pose pose 
)
private

Member Data Documentation

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::add_base_pair_constraints_
private
std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::all_rna_fragments_file_
private

Referenced by apply().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::check_pairing_dists_
private
bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::choose_best_solution_
private

Referenced by apply(), and set_choose_best_solution().

utility::vector1< std::string > protocols::coarse_rna::CoarseRNA_DeNovoProtocol::chunk_silent_files_
private

Referenced by apply(), and set_chunk_silent_files().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::close_loops_
private
core::scoring::constraints::ConstraintSetOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::constraint_set_
private
core::scoring::ScoreFunctionOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::denovo_scorefxn_
private

Referenced by apply(), and initialize_constraints().

core::Real protocols::coarse_rna::CoarseRNA_DeNovoProtocol::domain_move_frequency_
private

Referenced by apply(), and RNA_move_trial().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::dump_pdb_
private

Referenced by apply(), and set_dump_pdb().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::force_ideal_chainbreak_
private
protocols::rna::RNA_FragmentMoverOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::frag_mover_
private

Referenced by apply(), and random_fragment_trial().

Size protocols::coarse_rna::CoarseRNA_DeNovoProtocol::frag_size_
private

Referenced by apply(), and random_fragment_trial().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::freeze_domains_
private
utility::vector1< core::Size > protocols::coarse_rna::CoarseRNA_DeNovoProtocol::input_res_
private

Referenced by apply(), and set_input_res().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::jump_library_file_
private

Referenced by apply(), and set_jump_library_file().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::lores_scorefxn_
private

Referenced by apply(), and set_lores_scorefxn().

core::Real protocols::coarse_rna::CoarseRNA_DeNovoProtocol::m_Temperature_
private
protocols::moves::MonteCarloOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::monte_carlo_
private
Size const protocols::coarse_rna::CoarseRNA_DeNovoProtocol::monte_carlo_cycles_
private

Referenced by apply().

protocols::rna::MultipleDomainMoverOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::multiple_domain_mover_
private
Size const protocols::coarse_rna::CoarseRNA_DeNovoProtocol::nstruct_
private

Referenced by apply().

utility::vector1< core::Real > protocols::coarse_rna::CoarseRNA_DeNovoProtocol::pairing_dists_
private
protocols::rna::RNA_ChunkLibraryOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_chunk_library_
private

Referenced by apply().

std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_data_file_
private

Referenced by apply(), and set_rna_data_file().

protocols::rna::RNA_DataReaderOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_data_reader_
private

Referenced by apply().

protocols::coarse_rna::CoarseRNA_LoopCloserOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_loop_closer_
private
std::string protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_params_file_
private

Referenced by apply(), and set_rna_params_file().

protocols::rna::RNA_StructureParametersOP protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rna_structure_parameters_
private
Size const protocols::coarse_rna::CoarseRNA_DeNovoProtocol::rounds_
private

Referenced by apply().

std::string const protocols::coarse_rna::CoarseRNA_DeNovoProtocol::silent_file_
private

Referenced by apply(), and initialize_tag_is_done().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::sim_anneal_
private

Referenced by get_temperature(), and set_sim_anneal().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::staged_constraints_
private
std::map< std::string, bool > protocols::coarse_rna::CoarseRNA_DeNovoProtocol::tag_is_done_
private

Referenced by apply(), and initialize_tag_is_done().

bool protocols::coarse_rna::CoarseRNA_DeNovoProtocol::view_monte_carlo_
private

Referenced by apply().


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