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

#include <StepWiseRNA_Minimizer.hh>

Public Member Functions

 StepWiseRNA_Minimizer (utility::vector1< core::pose::PoseOP > const &pose_list, stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP &working_parameters)
 
 ~StepWiseRNA_Minimizer ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_silent_file (std::string const &silent_file)
 
void set_move_map (core::kinematics::MoveMapOP move_map_)
 
void set_scorefxn (core::scoring::ScoreFunctionCOP const &scorefxn)
 
core::io::silent::SilentFileDataOPsilent_file_data ()
 
void set_base_centroid_checker (checker::RNA_BaseCentroidCheckerOP &checker)
 
void set_user_input_VDW_bin_checker (checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)
 
void output_pose_wrapper (std::string const &tag, core::pose::Pose &pose, std::string const &out_silent_file) const
 
void set_working_extra_minimize_res (utility::vector1< core::Size > setting)
 
void set_allow_variable_bond_geometry (bool const setting)
 
void set_vary_bond_geometry_frequency (core::Real const setting)
 
void set_allow_insert (toolbox::AllowInsertOP setting)
 
void set_options (protocols::stepwise::modeler::options::StepWiseModelerOptionsOP options)
 
utility::vector1
< core::pose::PoseOP > const & 
minimized_pose_list () 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
 
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 MoverOP clone () const
 Return a clone of the Mover object. More...
 
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

utility::vector1< core::Sizeget_working_moving_res (Size const &nres) const
 
core::kinematics::MoveMapOP get_default_movemap (core::pose::Pose const &pose)
 
bool pass_all_pose_screens (core::pose::Pose &pose, std::string const in_tag, core::io::silent::SilentFileData &silent_file_data) const
 
void freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const nres) const
 
void output_empty_minimizer_silent_file () const
 
void output_pose_wrapper (std::string &tag, char tag_first_char, core::pose::Pose &pose, core::io::silent::SilentFileData &silent_file_data, std::string const out_silent_file) const
 
bool native_edensity_score_checker (core::pose::Pose &pose, core::pose::Pose &native_pose) const
 
void output_minimized_pose_list ()
 
void output_parameters ()
 

Private Attributes

utility::vector1
< core::pose::PoseOP > const 
pose_list_
 
utility::vector1
< core::pose::PoseOP
minimized_pose_list_
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
core::io::silent::SilentFileDataOP sfd_
 
kinematics::MoveMapOP move_map_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
std::string silent_file_
 
bool perform_electron_density_screen_
 
protocols::stepwise::modeler::options::StepWiseModelerOptionsOP options_
 
std::map< core::id::AtomID,
core::id::AtomID
pose_to_native_map_
 
utility::vector1< core::Sizefixed_res_
 
checker::RNA_BaseCentroidCheckerOP base_centroid_checker_
 
checker::RNA_VDW_BinCheckerOP user_input_VDW_bin_checker_
 
core::Real vary_bond_geometry_frequency_
 
bool allow_variable_bond_geometry_
 
utility::vector1< core::Sizeworking_extra_minimize_res_
 
toolbox::AllowInsertOP allow_insert_
 
core::Real original_geometry_weight_
 

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...
 

Constructor & Destructor Documentation

protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::StepWiseRNA_Minimizer ( utility::vector1< core::pose::PoseOP > const &  pose_list,
stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters 
)
protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::~StepWiseRNA_Minimizer ( )

Member Function Documentation

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::apply ( core::pose::Pose pose_to_visualize)
virtual
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::freeze_sugar_torsions ( core::kinematics::MoveMap mm,
Size const  nres 
) const
private

References core::kinematics::MoveMap::set(), and protocols::TR.

Referenced by apply().

core::kinematics::MoveMapOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::get_default_movemap ( core::pose::Pose const &  pose)
private
std::string protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::get_working_moving_res ( Size const &  nres) const
private
utility::vector1< core::pose::PoseOP > const& protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::minimized_pose_list ( ) const
inline
bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::native_edensity_score_checker ( core::pose::Pose pose,
core::pose::Pose native_pose 
) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::output_empty_minimizer_silent_file ( ) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::output_minimized_pose_list ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::output_parameters ( )
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::output_pose_wrapper ( std::string const &  tag,
core::pose::Pose pose,
std::string const &  out_silent_file 
) const
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::output_pose_wrapper ( std::string tag,
char  tag_first_char,
core::pose::Pose pose,
core::io::silent::SilentFileData silent_file_data,
std::string const  out_silent_file 
) const
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::pass_all_pose_screens ( core::pose::Pose pose,
std::string const  in_tag,
core::io::silent::SilentFileData silent_file_data 
) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_allow_insert ( toolbox::AllowInsertOP  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_allow_variable_bond_geometry ( bool const  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_base_centroid_checker ( checker::RNA_BaseCentroidCheckerOP checker)
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_move_map ( core::kinematics::MoveMapOP  move_map_)

References move_map_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_options ( protocols::stepwise::modeler::options::StepWiseModelerOptionsOP  options)

References options_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_scorefxn ( core::scoring::ScoreFunctionCOP const &  scorefxn)

References scorefxn_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_silent_file ( std::string const &  silent_file)

References silent_file_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_user_input_VDW_bin_checker ( checker::RNA_VDW_BinCheckerOP const &  user_input_VDW_bin_checker)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_vary_bond_geometry_frequency ( core::Real const  setting)
inline
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::set_working_extra_minimize_res ( utility::vector1< core::Size setting)
inline
core::io::silent::SilentFileDataOP & protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::silent_file_data ( )

Member Data Documentation

toolbox::AllowInsertOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::allow_insert_
private

Referenced by apply(), and get_default_movemap().

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::allow_variable_bond_geometry_
private

Referenced by apply().

checker::RNA_BaseCentroidCheckerOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::base_centroid_checker_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::fixed_res_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::minimized_pose_list_
private
kinematics::MoveMapOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::move_map_
private

Referenced by apply(), and set_move_map().

protocols::stepwise::modeler::options::StepWiseModelerOptionsOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::options_
private
core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::original_geometry_weight_
private

Referenced by apply().

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::perform_electron_density_screen_
private
utility::vector1< core::pose::PoseOP > const protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::pose_list_
private

Referenced by apply(), and output_parameters().

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::pose_to_native_map_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::scorefxn_
private

Referenced by apply(), and set_scorefxn().

core::io::silent::SilentFileDataOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::sfd_
private

Referenced by silent_file_data().

std::string protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::silent_file_
private
checker::RNA_VDW_BinCheckerOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::user_input_VDW_bin_checker_
private
core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::vary_bond_geometry_frequency_
private

Referenced by apply().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::working_extra_minimize_res_
private

Referenced by get_default_movemap().

stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer::working_parameters_
private

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