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protocols::rna::RNA_Minimizer Class Reference

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

#include <RNA_Minimizer.hh>

Inheritance diagram for protocols::rna::RNA_Minimizer:
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Public Member Functions

 RNA_Minimizer ()
 Construct the protocol object given the RNA fragment library to use. More...
 
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 deriv_check (bool const setting)
 
void use_coordinate_constraints (bool const setting)
 
void skip_o2star_trials (bool const setting)
 
void set_perform_minimizer_run (bool const setting)
 
void vary_bond_geometry (bool const setting)
 
void set_include_default_linear_chainbreak (bool const setting)
 
void set_verbose (bool const setting)
 
void set_do_dump_pdb (bool const setting)
 
void set_move_first_rigid_body (bool const setting)
 
void set_min_type (std::string const setting)
 
void set_allow_insert (toolbox::AllowInsertOP allow_insert)
 
void set_extra_minimize_res (utility::vector1< core::Size > setting)
 
void set_score_function (core::scoring::ScoreFunctionOP const &scorefxn)
 
core::scoring::ScoreFunctionOP
const & 
score_function () const
 
core::scoring::ScoreFunctionOP clone_scorefxn () const
 
- 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 o2star_trials (core::pose::Pose &pose, core::scoring::ScoreFunctionOP const &scorefxn) const
 
void setup_movemap (core::kinematics::MoveMap &mm, core::pose::Pose &pose)
 
void update_allow_insert_with_extra_minimize_res (core::pose::Pose const &pose)
 

Private Attributes

bool deriv_check_
 
bool use_coordinate_constraints_
 
core::Real const coord_sdev_
 
core::Real const coord_cst_weight_
 
core::Size const rounds_
 
bool skip_o2star_trials_
 
bool perform_minimizer_run_
 
bool vary_bond_geometry_
 
bool include_default_linear_chainbreak_
 
bool verbose_
 
bool do_dump_pdb_
 
bool move_first_rigid_body_
 
std::string min_type_
 
toolbox::AllowInsertOP allow_insert_
 
utility::vector1< core::Sizeextra_minimize_res_
 
core::scoring::ScoreFunctionOP scorefxn_
 

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::rna::RNA_Minimizer::RNA_Minimizer ( )

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

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::RNA_HIRES_WTS, and scorefxn_.

Referenced by clone().

Member Function Documentation

void protocols::rna::RNA_Minimizer::apply ( core::pose::Pose pose)
virtual
virtual protocols::moves::MoverOP protocols::rna::RNA_Minimizer::clone ( ) const
inlinevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References RNA_Minimizer().

core::scoring::ScoreFunctionOP protocols::rna::RNA_Minimizer::clone_scorefxn ( ) const
inline

References scorefxn_.

void protocols::rna::RNA_Minimizer::deriv_check ( bool const  setting)
inline

References deriv_check_.

std::string protocols::rna::RNA_Minimizer::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::rna::RNA_Minimizer::o2star_trials ( core::pose::Pose pose,
core::scoring::ScoreFunctionOP const &  scorefxn 
) const
private
core::scoring::ScoreFunctionOP const& protocols::rna::RNA_Minimizer::score_function ( ) const
inline

References scorefxn_.

void protocols::rna::RNA_Minimizer::set_allow_insert ( toolbox::AllowInsertOP  allow_insert)

References allow_insert_.

void protocols::rna::RNA_Minimizer::set_do_dump_pdb ( bool const  setting)
inline

References do_dump_pdb_.

void protocols::rna::RNA_Minimizer::set_extra_minimize_res ( utility::vector1< core::Size setting)

References extra_minimize_res_.

void protocols::rna::RNA_Minimizer::set_include_default_linear_chainbreak ( bool const  setting)
inline
void protocols::rna::RNA_Minimizer::set_min_type ( std::string const  setting)
inline

References min_type_.

void protocols::rna::RNA_Minimizer::set_move_first_rigid_body ( bool const  setting)
inline
void protocols::rna::RNA_Minimizer::set_perform_minimizer_run ( bool const  setting)
inline
void protocols::rna::RNA_Minimizer::set_score_function ( core::scoring::ScoreFunctionOP const &  scorefxn)

References scorefxn_.

void protocols::rna::RNA_Minimizer::set_verbose ( bool const  setting)
inline

References verbose_.

void protocols::rna::RNA_Minimizer::setup_movemap ( core::kinematics::MoveMap mm,
core::pose::Pose pose 
)
private
void protocols::rna::RNA_Minimizer::skip_o2star_trials ( bool const  setting)
inline

References skip_o2star_trials_.

void protocols::rna::RNA_Minimizer::update_allow_insert_with_extra_minimize_res ( core::pose::Pose const &  pose)
private
void protocols::rna::RNA_Minimizer::use_coordinate_constraints ( bool const  setting)
inline
void protocols::rna::RNA_Minimizer::vary_bond_geometry ( bool const  setting)
inline

References vary_bond_geometry_.

Member Data Documentation

toolbox::AllowInsertOP protocols::rna::RNA_Minimizer::allow_insert_
private
core::Real const protocols::rna::RNA_Minimizer::coord_cst_weight_
private

Referenced by apply().

core::Real const protocols::rna::RNA_Minimizer::coord_sdev_
private

Referenced by apply().

bool protocols::rna::RNA_Minimizer::deriv_check_
private

Referenced by apply(), and deriv_check().

bool protocols::rna::RNA_Minimizer::do_dump_pdb_
private

Referenced by apply(), and set_do_dump_pdb().

utility::vector1< core::Size > protocols::rna::RNA_Minimizer::extra_minimize_res_
private
bool protocols::rna::RNA_Minimizer::include_default_linear_chainbreak_
private
std::string protocols::rna::RNA_Minimizer::min_type_
private

Referenced by apply(), and set_min_type().

bool protocols::rna::RNA_Minimizer::move_first_rigid_body_
private
bool protocols::rna::RNA_Minimizer::perform_minimizer_run_
private

Referenced by apply(), and set_perform_minimizer_run().

core::Size const protocols::rna::RNA_Minimizer::rounds_
private

Referenced by apply().

core::scoring::ScoreFunctionOP protocols::rna::RNA_Minimizer::scorefxn_
private
bool protocols::rna::RNA_Minimizer::skip_o2star_trials_
private

Referenced by apply(), and skip_o2star_trials().

bool protocols::rna::RNA_Minimizer::use_coordinate_constraints_
private
bool protocols::rna::RNA_Minimizer::vary_bond_geometry_
private
bool protocols::rna::RNA_Minimizer::verbose_
private

Referenced by apply(), and set_verbose().


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