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protocols::swa::rna::StepWiseRNA_Minimizer Class Reference

#include <StepWiseRNA_Minimizer.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_Minimizer:
Inheritance graph
Collaboration diagram for protocols::swa::rna::StepWiseRNA_Minimizer:
Collaboration graph

Public Member Functions

 StepWiseRNA_Minimizer (utility::vector1< pose_data_struct2 > const &pose_data_list, StepWiseRNA_JobParametersCOP &job_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_list (utility::vector1< core::kinematics::MoveMap > const &move_map_list)
void set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
core::io::silent::SilentFileDataOPsilent_file_data ()
void set_base_centroid_screener (StepWiseRNA_BaseCentroidScreenerOP &screener)
void set_native_edensity_score_cutoff (core::Real const &setting)
void set_verbose (bool const setting)
void set_centroid_screen (bool const setting)
void set_perform_o2star_pack (bool const setting)
void set_output_before_o2star_pack (bool const setting)
void set_rm_virt_phosphate (bool const setting)
void set_perform_minimize (bool const setting)
void set_num_pose_minimize (Size const setting)
void set_minimize_and_score_sugar (bool const setting)
void set_native_rmsd_screen (bool const setting)
void set_native_screen_rmsd_cutoff (core::Real const setting)
void set_user_input_VDW_bin_screener (StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)
void set_rename_tag (bool const setting)
- 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 MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
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

< core::kinematics::MoveMap
Get_default_movemap (core::pose::Pose const &pose) const
void Figure_out_moving_residues (core::kinematics::MoveMap &mm, core::pose::Pose const &pose) const
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_data_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
core::Size figure_out_actual_five_prime_chain_break_res (core::pose::Pose const &pose) const
bool native_edensity_score_screener (core::pose::Pose &pose, core::pose::Pose &native_pose) const

Private Attributes

< pose_data_struct2 > const 
StepWiseRNA_JobParametersCOP job_parameters_
core::io::silent::SilentFileDataOP sfd_
< core::kinematics::MoveMap
core::scoring::ScoreFunctionOP scorefxn_
std::string silent_file_
bool verbose_
bool screen_verbose_
bool native_screen_
core::Real native_screen_rmsd_cutoff_
bool perform_electron_density_screen_
bool rm_virt_phosphate_
core::Real native_edensity_score_cutoff_
bool centroid_screen_
bool perform_o2star_pack_
bool output_before_o2star_pack_
bool perform_minimize_
core::Size num_pose_minimize_
bool minimize_and_score_sugar_
bool rename_tag_
std::map< core::id::AtomID,
utility::vector1< core::Sizefixed_res_
StepWiseRNA_BaseCentroidScreenerOP base_centroid_screener_
StepWiseRNA_VDW_Bin_ScreenerOP user_input_VDW_bin_screener_

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 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...

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_Minimizer::StepWiseRNA_Minimizer ( utility::vector1< pose_data_struct2 > const &  pose_data_list,
StepWiseRNA_JobParametersCOP job_parameters 
protocols::swa::rna::StepWiseRNA_Minimizer::~StepWiseRNA_Minimizer ( )

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_Minimizer::apply ( core::pose::Pose pose_to_visualize)
core::Size protocols::swa::rna::StepWiseRNA_Minimizer::figure_out_actual_five_prime_chain_break_res ( core::pose::Pose const &  pose) const
void protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues ( core::kinematics::MoveMap mm,
core::pose::Pose const &  pose 
) const
void protocols::swa::rna::StepWiseRNA_Minimizer::Freeze_sugar_torsions ( core::kinematics::MoveMap mm,
Size const  nres 
) const
utility::vector1< core::kinematics::MoveMap > protocols::swa::rna::StepWiseRNA_Minimizer::Get_default_movemap ( core::pose::Pose const &  pose) const

References Figure_out_moving_residues().

Referenced by apply().

std::string protocols::swa::rna::StepWiseRNA_Minimizer::get_name ( ) const

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

Implements protocols::moves::Mover.

bool protocols::swa::rna::StepWiseRNA_Minimizer::native_edensity_score_screener ( core::pose::Pose pose,
core::pose::Pose native_pose 
) const
void protocols::swa::rna::StepWiseRNA_Minimizer::output_empty_minimizer_silent_file ( ) const

References protocols::swa::rna::file_exists(), and silent_file_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_Minimizer::output_pose_data_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 protocols::swa::rna::StepWiseRNA_Minimizer::pass_all_pose_screens ( core::pose::Pose pose,
std::string const  in_tag,
core::io::silent::SilentFileData silent_file_data 
) const
void protocols::swa::rna::StepWiseRNA_Minimizer::set_base_centroid_screener ( StepWiseRNA_BaseCentroidScreenerOP screener)
void protocols::swa::rna::StepWiseRNA_Minimizer::set_centroid_screen ( bool const  setting)

References centroid_screen_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_minimize_and_score_sugar ( bool const  setting)
void protocols::swa::rna::StepWiseRNA_Minimizer::set_move_map_list ( utility::vector1< core::kinematics::MoveMap > const &  move_map_list)

References move_map_list_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_native_edensity_score_cutoff ( core::Real const &  setting)
void protocols::swa::rna::StepWiseRNA_Minimizer::set_native_rmsd_screen ( bool const  setting)

References native_screen_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_native_screen_rmsd_cutoff ( core::Real const  setting)
void protocols::swa::rna::StepWiseRNA_Minimizer::set_num_pose_minimize ( Size const  setting)

References num_pose_minimize_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_output_before_o2star_pack ( bool const  setting)
void protocols::swa::rna::StepWiseRNA_Minimizer::set_perform_minimize ( bool const  setting)

References perform_minimize_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_perform_o2star_pack ( bool const  setting)

References perform_o2star_pack_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_rename_tag ( bool const  setting)

References rename_tag_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_rm_virt_phosphate ( bool const  setting)

References rm_virt_phosphate_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References scorefxn_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_silent_file ( std::string const &  silent_file)

References silent_file_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_user_input_VDW_bin_screener ( StepWiseRNA_VDW_Bin_ScreenerOP const &  user_input_VDW_bin_screener)
void protocols::swa::rna::StepWiseRNA_Minimizer::set_verbose ( bool const  setting)

References verbose_.

core::io::silent::SilentFileDataOP & protocols::swa::rna::StepWiseRNA_Minimizer::silent_file_data ( )

References sfd_.

Referenced by apply().

Member Data Documentation

StepWiseRNA_BaseCentroidScreenerOP protocols::swa::rna::StepWiseRNA_Minimizer::base_centroid_screener_
bool protocols::swa::rna::StepWiseRNA_Minimizer::centroid_screen_
utility::vector1< core::Size > protocols::swa::rna::StepWiseRNA_Minimizer::fixed_res_
StepWiseRNA_JobParametersCOP protocols::swa::rna::StepWiseRNA_Minimizer::job_parameters_
bool protocols::swa::rna::StepWiseRNA_Minimizer::minimize_and_score_sugar_
utility::vector1<core::kinematics::MoveMap> protocols::swa::rna::StepWiseRNA_Minimizer::move_map_list_

Referenced by apply(), and set_move_map_list().

core::Real protocols::swa::rna::StepWiseRNA_Minimizer::native_edensity_score_cutoff_
bool protocols::swa::rna::StepWiseRNA_Minimizer::native_screen_
core::Real protocols::swa::rna::StepWiseRNA_Minimizer::native_screen_rmsd_cutoff_
core::Size protocols::swa::rna::StepWiseRNA_Minimizer::num_pose_minimize_

Referenced by apply(), and set_num_pose_minimize().

bool protocols::swa::rna::StepWiseRNA_Minimizer::output_before_o2star_pack_
bool protocols::swa::rna::StepWiseRNA_Minimizer::perform_electron_density_screen_
bool protocols::swa::rna::StepWiseRNA_Minimizer::perform_minimize_

Referenced by apply(), and set_perform_minimize().

bool protocols::swa::rna::StepWiseRNA_Minimizer::perform_o2star_pack_

Referenced by apply(), and set_perform_o2star_pack().

utility::vector1<pose_data_struct2> const protocols::swa::rna::StepWiseRNA_Minimizer::pose_data_list_

Referenced by apply().

std::map< core::id::AtomID, core::id::AtomID > protocols::swa::rna::StepWiseRNA_Minimizer::pose_to_native_map_
bool protocols::swa::rna::StepWiseRNA_Minimizer::rename_tag_

Referenced by apply(), and set_rename_tag().

bool protocols::swa::rna::StepWiseRNA_Minimizer::rm_virt_phosphate_

Referenced by apply(), and set_rm_virt_phosphate().

core::scoring::ScoreFunctionOP protocols::swa::rna::StepWiseRNA_Minimizer::scorefxn_

Referenced by apply(), and set_scorefxn().

bool protocols::swa::rna::StepWiseRNA_Minimizer::screen_verbose_
core::io::silent::SilentFileDataOP protocols::swa::rna::StepWiseRNA_Minimizer::sfd_

Referenced by silent_file_data().

std::string protocols::swa::rna::StepWiseRNA_Minimizer::silent_file_
StepWiseRNA_VDW_Bin_ScreenerOP protocols::swa::rna::StepWiseRNA_Minimizer::user_input_VDW_bin_screener_
bool protocols::swa::rna::StepWiseRNA_Minimizer::verbose_

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