Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler Class Reference

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

#include <RNA_HelixAssembler.hh>

Public Member Functions

 RNA_HelixAssembler ()
 Construct the protocol object. More...
 ~RNA_HelixAssembler ()
 Destroy the protocol object. More...
virtual protocols::moves::MoverOP clone () const
 Clone this object. More...
void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void apply (core::pose::Pose &pose, std::string const &sequence)
 Apply the loop-rebuild protocol to the input pose. More...
void random_perturbation (bool const &setting)
void set_dump (bool const &setting)
void set_minimize_all (bool const &setting)
void set_scorefxn (core::scoring::ScoreFunctionOP setting)
void set_finish_scorefxn (core::scoring::ScoreFunctionOP setting)
void use_phenix_geo (bool const setting)
void set_model_and_remove_capping_residues (bool setting)
void build_helix (core::pose::Pose &pose, std::string const &full_sequence)
core::pose::PoseOP build_init_pose (std::string const &seq1, std::string const &seq2)
- 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
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...

Private Member Functions

void initialize_minimizer ()
void set_Aform_torsions (core::pose::Pose &pose, Size const &n) const
void build_on_base_pair (core::pose::Pose &pose, Size const &n, char const &seq1, char const &seq2) const
void minimize_base_step (core::pose::Pose &pose, Size const n, core::scoring::ScoreFunctionOP scorefxn) const
void put_constraints_on_base_step (core::pose::Pose &pose, Size const &n) const
void get_rid_of_capping_base_pairs (core::pose::Pose &pose) const
std::string figure_out_and_remove_dangling_ends (std::string const &full_sequence)
void build_dangling_ends (core::pose::Pose &pose) const
void build_dangle_seq1_5prime (core::pose::Pose &pose, std::string const &dangle_seq) const
void build_dangle_seq2_5prime (core::pose::Pose &pose, std::string const &dangle_seq) const
void build_dangle_seq1_3prime (core::pose::Pose &pose, std::string const &dangle_seq) const
void build_dangle_seq2_3prime (core::pose::Pose &pose, std::string const &dangle_seq) const
core::Size get_cutpoint (core::pose::Pose const &pose) const
void append_Aform_residue (core::pose::Pose &pose, Size const &n, char const &nt) const
void prepend_Aform_residue (core::pose::Pose &pose, Size const &n, char const &nt) const
void perturb_torsion (core::pose::Pose &pose, utility::vector1< core::id::TorsionID > const &id_list) const
void minimize_append_res (core::pose::Pose &pose, Size const n) const
void minimize_prepend_res (core::pose::Pose &pose, Size const n) const
void fill_chain_info (core::pose::Pose &pose, std::string const &full_sequence)

Private Attributes

bool dump_
bool random_perturbation_
bool minimize_all_
bool minimize_jump_
bool use_phenix_geo_
core::chemical::ResidueTypeSetCAP rsd_set_
core::Real perturb_amplitude_
core::scoring::ScoreFunctionOP scorefxn_
core::scoring::ScoreFunctionOP finish_scorefxn_
bool model_and_remove_capping_residues_
std::string const capping_residues_
core::optimization::AtomTreeMinimizerOP minimizer_
core::optimization::MinimizerOptionsOP minimizer_options_
std::string dangle_seq1_5prime_
std::string dangle_seq1_3prime_
std::string dangle_seq2_5prime_
std::string dangle_seq2_3prime_

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::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::stepwise::modeler::rna::helix::RNA_HelixAssembler::RNA_HelixAssembler ( )

Construct the protocol object.

References chemical, FA_RNA, initialize_minimizer(), residue_type_set, and scoring.

Referenced by clone().

protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::~RNA_HelixAssembler ( )

Destroy the protocol object.

Member Function Documentation

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::append_Aform_residue ( core::pose::Pose pose,
Size const &  n,
char const &  nt 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::apply ( core::pose::Pose pose)

Apply the RNA HelixAssembler

Implements protocols::moves::Mover.

References core::pose::Pose::sequence().

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::apply ( core::pose::Pose pose,
std::string const &  sequence 

Apply the loop-rebuild protocol to the input pose.

References build_dangling_ends(), build_helix(), figure_out_and_remove_dangling_ends(), fill_chain_info(), and protocols::TR.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq1_3prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq1_5prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq2_3prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq2_5prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangling_ends ( core::pose::Pose pose) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_helix ( core::pose::Pose pose,
std::string const &  full_sequence 
pose::PoseOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_init_pose ( std::string const &  seq1,
std::string const &  seq2 
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_on_base_pair ( core::pose::Pose pose,
Size const &  n,
char const &  seq1,
char const &  seq2 
) const
protocols::moves::MoverOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::clone ( ) const

Clone this object.

Reimplemented from protocols::moves::Mover.

References RNA_HelixAssembler().

std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::figure_out_and_remove_dangling_ends ( std::string const &  full_sequence)
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::fill_chain_info ( core::pose::Pose pose,
std::string const &  full_sequence 
Size protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::get_cutpoint ( core::pose::Pose const &  pose) const
std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::get_rid_of_capping_base_pairs ( core::pose::Pose pose) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::initialize_minimizer ( )
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_append_res ( core::pose::Pose pose,
Size const  n 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_base_step ( core::pose::Pose pose,
Size const  n,
core::scoring::ScoreFunctionOP  scorefxn 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_prepend_res ( core::pose::Pose pose,
Size const  n 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::perturb_torsion ( core::pose::Pose pose,
utility::vector1< core::id::TorsionID > const &  id_list 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::prepend_Aform_residue ( core::pose::Pose pose,
Size const &  n,
char const &  nt 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::put_constraints_on_base_step ( core::pose::Pose pose,
Size const &  n 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::random_perturbation ( bool const &  setting)

References random_perturbation_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_Aform_torsions ( core::pose::Pose pose,
Size const &  n 
) const
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_dump ( bool const &  setting)

References dump_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_finish_scorefxn ( core::scoring::ScoreFunctionOP  setting)

References finish_scorefxn_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_minimize_all ( bool const &  setting)

References minimize_all_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_model_and_remove_capping_residues ( bool  setting)
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_scorefxn ( core::scoring::ScoreFunctionOP  setting)

References scorefxn_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::use_phenix_geo ( bool const  setting)

Member Data Documentation

std::string const protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::capping_residues_

Referenced by build_helix().

std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dangle_seq1_3prime_
std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dangle_seq1_5prime_
std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dangle_seq2_3prime_
std::string protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dangle_seq2_5prime_
bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::dump_

Referenced by build_helix(), and set_dump().

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::finish_scorefxn_
bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_all_
bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimize_jump_

Referenced by minimize_base_step().

core::optimization::AtomTreeMinimizerOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimizer_
core::optimization::MinimizerOptionsOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::minimizer_options_
bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::model_and_remove_capping_residues_
core::Real protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::perturb_amplitude_

Referenced by perturb_torsion().

bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::random_perturbation_
core::chemical::ResidueTypeSetCAP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::rsd_set_
core::scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::scorefxn_
core::chemical::rna::RNA_FittedTorsionInfo const protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::torsion_info_
bool protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::use_phenix_geo_

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