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protocols::rna::denovo::RNA_DeNovoProtocol Class Reference

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

#include <RNA_DeNovoProtocol.hh>

Inheritance diagram for protocols::rna::denovo::RNA_DeNovoProtocol:
Inheritance graph
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Public Member Functions

 RNA_DeNovoProtocol (core::import_pose::options::RNA_DeNovoProtocolOptionsCOP options=nullptr, core::import_pose::RNA_DeNovoParametersCOP params=nullptr)
 Construct the protocol object given the RNA fragment library to use. More...
 
 ~RNA_DeNovoProtocol () override
 
protocols::moves::MoverOP clone () const override
 Clone this object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void apply (core::pose::Pose &pose) override
 Apply the RNA denovo modeling protocol to the input pose. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
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_refine_pose_list (utility::vector1< core::pose::PoseOP > const &setting)
 
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP options () const
 
RNA_FragmentMonteCarloCOP rna_fragment_monte_carlo () 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 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...
 
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...
 
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
 
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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static void register_options ()
 
- 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...
 

Private Member Functions

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 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 check_for_loop_modeling_case (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, core::pose::Pose const &pose) const
 
void calc_rmsds (core::io::silent::SilentStruct &s, core::pose::Pose &pose, std::string const &out_file_tag) const
 
void add_chem_shift_info (core::io::silent::SilentStruct &silent_struct, core::pose::Pose const &const_pose) const
 

Private Attributes

core::import_pose::options::RNA_DeNovoProtocolOptionsCOP options_
 
core::import_pose::RNA_DeNovoParametersCOP rna_params_
 
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP vdw_grid_
 
std::string lores_silent_file_
 
RNA_FragmentMonteCarloOP rna_fragment_monte_carlo_
 
std::map< std::string, booltag_is_done_
 
core::scoring::ScoreFunctionOP denovo_scorefxn_
 
core::scoring::ScoreFunctionOP hires_scorefxn_
 
utility::vector1
< core::pose::PoseOP
refine_pose_list_
 
core::Size refine_pose_id_ = 1
 

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
 
- 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::rna::denovo::RNA_DeNovoProtocol::RNA_DeNovoProtocol ( core::import_pose::options::RNA_DeNovoProtocolOptionsCOP  options = nullptr,
core::import_pose::RNA_DeNovoParametersCOP  params = nullptr 
)

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

References rna_params_.

protocols::rna::denovo::RNA_DeNovoProtocol::~RNA_DeNovoProtocol ( )
overridedefault

Member Function Documentation

void protocols::rna::denovo::RNA_DeNovoProtocol::add_chem_shift_info ( core::io::silent::SilentStruct silent_struct,
core::pose::Pose const &  const_pose 
) const
private
void protocols::rna::denovo::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::rna::denovo::RNA_DeNovoProtocol::apply ( core::pose::Pose pose)
overridevirtual
void protocols::rna::denovo::RNA_DeNovoProtocol::calc_rmsds ( core::io::silent::SilentStruct s,
core::pose::Pose pose,
std::string const &  out_file_tag 
) const
private
void protocols::rna::denovo::RNA_DeNovoProtocol::check_for_loop_modeling_case ( std::map< core::id::AtomID, core::id::AtomID > &  atom_id_map,
core::pose::Pose const &  pose 
) const
private
protocols::moves::MoverOP protocols::rna::denovo::RNA_DeNovoProtocol::clone ( ) const
overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

moves::MoverOP protocols::rna::denovo::RNA_DeNovoProtocol::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::rna::denovo::RNA_DeNovoProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::rna::denovo::RNA_DeNovoProtocol::initialize_constraints ( core::pose::Pose pose)
private
void protocols::rna::denovo::RNA_DeNovoProtocol::initialize_lores_silent_file ( )
private
void protocols::rna::denovo::RNA_DeNovoProtocol::initialize_scorefxn ( core::pose::Pose pose)
private
void protocols::rna::denovo::RNA_DeNovoProtocol::initialize_tag_is_done ( )
private
std::string protocols::rna::denovo::RNA_DeNovoProtocol::mover_name ( )
static
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP protocols::rna::denovo::RNA_DeNovoProtocol::options ( ) const
inline

References options_.

void protocols::rna::denovo::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::rna::denovo::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
void protocols::rna::denovo::RNA_DeNovoProtocol::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

void protocols::rna::denovo::RNA_DeNovoProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::rna::denovo::RNA_DeNovoProtocol::register_options ( )
static
RNA_FragmentMonteCarloCOP protocols::rna::denovo::RNA_DeNovoProtocol::rna_fragment_monte_carlo ( ) const
inline
void protocols::rna::denovo::RNA_DeNovoProtocol::set_refine_pose_list ( utility::vector1< core::pose::PoseOP > const &  setting)
inline

References refine_pose_list_.

void protocols::rna::denovo::RNA_DeNovoProtocol::show ( std::ostream &  output = std::cout) 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 options_.

Referenced by protocols::rna::denovo::operator<<().

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::rna::denovo::RNA_DeNovoProtocol::denovo_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::rna::denovo::RNA_DeNovoProtocol::hires_scorefxn_
private

Referenced by apply(), and initialize_scorefxn().

std::string protocols::rna::denovo::RNA_DeNovoProtocol::lores_silent_file_
private
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP protocols::rna::denovo::RNA_DeNovoProtocol::options_
private
core::Size protocols::rna::denovo::RNA_DeNovoProtocol::refine_pose_id_ = 1
private
utility::vector1<core::pose::PoseOP> protocols::rna::denovo::RNA_DeNovoProtocol::refine_pose_list_
private

Referenced by apply(), and set_refine_pose_list().

RNA_FragmentMonteCarloOP protocols::rna::denovo::RNA_DeNovoProtocol::rna_fragment_monte_carlo_
private
core::import_pose::RNA_DeNovoParametersCOP protocols::rna::denovo::RNA_DeNovoProtocol::rna_params_
private
std::map< std::string, bool > protocols::rna::denovo::RNA_DeNovoProtocol::tag_is_done_
private

Referenced by apply(), and initialize_tag_is_done().

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP protocols::rna::denovo::RNA_DeNovoProtocol::vdw_grid_
private

Referenced by apply().


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