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::chemical::rna::RNA_FittedTorsionInfo
const 
torsion_info_
 
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
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::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
private
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::apply ( core::pose::Pose pose)
virtual

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
private
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq1_5prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
private
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq2_3prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
private
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangle_seq2_5prime ( core::pose::Pose pose,
std::string const &  dangle_seq 
) const
private
void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::build_dangling_ends ( core::pose::Pose pose) const
private
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
private
protocols::moves::MoverOP protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::clone ( ) const
virtual

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

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

References random_perturbation_.

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

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)
inline

References minimize_all_.

void protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::set_model_and_remove_capping_residues ( bool  setting)
inline
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_
private

Referenced by build_helix().

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

Referenced by build_helix(), and set_dump().

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

Referenced by minimize_base_step().

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

Referenced by perturb_torsion().

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

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