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protocols::magnesium::MgScanner Class Reference

#include <MgScanner.hh>

Inheritance diagram for protocols::magnesium::MgScanner:
Inheritance graph
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Public Member Functions

 MgScanner ()
 
 ~MgScanner () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_minimize (bool const &setting)
 
bool minimize () const
 
void set_hydrate (bool const &setting)
 
bool hydrate () const
 
void set_minimize_during_scoring (bool const &setting)
 
bool minimize_during_scoring () const
 
void set_tether_to_closest_res (bool const &setting)
 
bool tether_to_closest_res () const
 
void set_integration_test (bool const &setting)
 
bool integration_test () const
 
void set_score_cut (core::Real const &setting)
 
core::Real score_cut () const
 
void set_score_cut_PDB (core::Real const &setting)
 
core::Real score_cut_PDB () const
 
void set_xyz_step (core::Real const &setting)
 
core::Real xyz_step () const
 
void set_scorefxn (core::scoring::ScoreFunctionOP const &setting)
 
core::scoring::ScoreFunctionOP scorefxn () const
 
void set_silent_file (std::string const &setting)
 
std::string silent_file () const
 
void set_output_pdb (std::string const &setting)
 
std::string output_pdb () const
 
void set_input_scan_res (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizeinput_scan_res () const
 
void set_minimize_mg_coord_constraint_distance (core::Distance const &setting)
 
core::Distance minimize_mg_coord_constraint_distance () 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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...
 

Private Member Functions

void scan_magnesiums (core::pose::Pose &pose)
 
core::Real get_score (core::pose::Pose &pose, core::Vector const &mg_position, core::scoring::ScoreFunctionCOP scorefxn, bool const hydrate_magnesium=false, bool const keep_waters=false, bool const minimize=false)
 
void cluster_mg ()
 
void output_mg_to_silent_file (std::string const &silent_file)
 
void output_mg_into_one_PDB (core::pose::Pose const &pose)
 
core::Size get_unique_mg_res (core::pose::Pose const &mg_pose)
 
core::pose::PoseOP get_single_mg_pose ()
 
core::Distance distance_to_closest_magnesium (core::Vector const &mg_position, core::pose::Pose const &reference_pose)
 

Private Attributes

utility::vector1
< core::pose::PoseOP
mg_poses
 
bool hydrate_
 
bool minimize_
 
bool minimize_during_scoring_
 
bool tether_to_closest_res_
 
bool integration_test_
 
core::Real score_cut_
 
core::Real score_cut_PDB_
 
core::Real xyz_step_
 
std::string silent_file_
 
std::string output_pdb_
 
utility::vector1< core::Sizeinput_scan_res_
 
core::Distance minimize_mg_coord_constraint_distance_
 
core::scoring::ScoreFunctionOP scorefxn_
 
utility::vector1
< core::pose::PoseOP
mg_poses_
 

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
 
- 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::magnesium::MgScanner::MgScanner ( )
protocols::magnesium::MgScanner::~MgScanner ( )
overridedefault

Member Function Documentation

void protocols::magnesium::MgScanner::apply ( core::pose::Pose )
overridevirtual
void protocols::magnesium::MgScanner::cluster_mg ( )
private
Distance protocols::magnesium::MgScanner::distance_to_closest_magnesium ( core::Vector const &  mg_position,
core::pose::Pose const &  reference_pose 
)
private
std::string protocols::magnesium::MgScanner::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

Real protocols::magnesium::MgScanner::get_score ( core::pose::Pose pose,
core::Vector const &  mg_position,
core::scoring::ScoreFunctionCOP  scorefxn,
bool const  hydrate_magnesium = false,
bool const  keep_waters = false,
bool const  minimize = false 
)
private
core::pose::PoseOP protocols::magnesium::MgScanner::get_single_mg_pose ( )
private
Size protocols::magnesium::MgScanner::get_unique_mg_res ( core::pose::Pose const &  mg_pose)
private
bool protocols::magnesium::MgScanner::hydrate ( ) const
inline

References hydrate_.

utility::vector1< core::Size > protocols::magnesium::MgScanner::input_scan_res ( ) const
inline

References input_scan_res_.

bool protocols::magnesium::MgScanner::integration_test ( ) const
inline

References integration_test_.

bool protocols::magnesium::MgScanner::minimize ( ) const
inline

References minimize_.

bool protocols::magnesium::MgScanner::minimize_during_scoring ( ) const
inline
core::Distance protocols::magnesium::MgScanner::minimize_mg_coord_constraint_distance ( ) const
inline
void protocols::magnesium::MgScanner::output_mg_into_one_PDB ( core::pose::Pose const &  pose)
private
void protocols::magnesium::MgScanner::output_mg_to_silent_file ( std::string const &  silent_file)
private
std::string protocols::magnesium::MgScanner::output_pdb ( ) const
inline

References output_pdb_.

void protocols::magnesium::MgScanner::scan_magnesiums ( core::pose::Pose pose)
private
core::Real protocols::magnesium::MgScanner::score_cut ( ) const
inline

References score_cut_.

core::Real protocols::magnesium::MgScanner::score_cut_PDB ( ) const
inline

References score_cut_PDB_.

core::scoring::ScoreFunctionOP protocols::magnesium::MgScanner::scorefxn ( ) const
inline

References scorefxn_.

void protocols::magnesium::MgScanner::set_hydrate ( bool const &  setting)
inline

References hydrate_.

void protocols::magnesium::MgScanner::set_input_scan_res ( utility::vector1< core::Size > const &  setting)
inline

References input_scan_res_.

void protocols::magnesium::MgScanner::set_integration_test ( bool const &  setting)
inline

References integration_test_.

void protocols::magnesium::MgScanner::set_minimize ( bool const &  setting)
inline

References minimize_.

void protocols::magnesium::MgScanner::set_minimize_during_scoring ( bool const &  setting)
inline
void protocols::magnesium::MgScanner::set_minimize_mg_coord_constraint_distance ( core::Distance const &  setting)
inline
void protocols::magnesium::MgScanner::set_output_pdb ( std::string const &  setting)
inline

References output_pdb_.

void protocols::magnesium::MgScanner::set_score_cut ( core::Real const &  setting)
inline

References score_cut_.

void protocols::magnesium::MgScanner::set_score_cut_PDB ( core::Real const &  setting)
inline

References score_cut_PDB_.

void protocols::magnesium::MgScanner::set_scorefxn ( core::scoring::ScoreFunctionOP const &  setting)
inline

References scorefxn_.

void protocols::magnesium::MgScanner::set_silent_file ( std::string const &  setting)
inline

References silent_file_.

void protocols::magnesium::MgScanner::set_tether_to_closest_res ( bool const &  setting)
inline
void protocols::magnesium::MgScanner::set_xyz_step ( core::Real const &  setting)
inline

References xyz_step_.

std::string protocols::magnesium::MgScanner::silent_file ( ) const
inline

References silent_file_.

bool protocols::magnesium::MgScanner::tether_to_closest_res ( ) const
inline
core::Real protocols::magnesium::MgScanner::xyz_step ( ) const
inline

References xyz_step_.

Member Data Documentation

bool protocols::magnesium::MgScanner::hydrate_
private
utility::vector1< core::Size > protocols::magnesium::MgScanner::input_scan_res_
private
bool protocols::magnesium::MgScanner::integration_test_
private
utility::vector1< core::pose::PoseOP > protocols::magnesium::MgScanner::mg_poses
private
utility::vector1< core::pose::PoseOP > protocols::magnesium::MgScanner::mg_poses_
private
bool protocols::magnesium::MgScanner::minimize_
private

Referenced by apply(), minimize(), and set_minimize().

bool protocols::magnesium::MgScanner::minimize_during_scoring_
private
core::Distance protocols::magnesium::MgScanner::minimize_mg_coord_constraint_distance_
private
std::string protocols::magnesium::MgScanner::output_pdb_
private
core::Real protocols::magnesium::MgScanner::score_cut_
private
core::Real protocols::magnesium::MgScanner::score_cut_PDB_
private
core::scoring::ScoreFunctionOP protocols::magnesium::MgScanner::scorefxn_
private
std::string protocols::magnesium::MgScanner::silent_file_
private

Referenced by apply(), set_silent_file(), and silent_file().

bool protocols::magnesium::MgScanner::tether_to_closest_res_
private
core::Real protocols::magnesium::MgScanner::xyz_step_
private

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