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protocols::magnesium::MgWaterHydrogenPacker Class Reference

#include <MgWaterHydrogenPacker.hh>

Inheritance diagram for protocols::magnesium::MgWaterHydrogenPacker:
Inheritance graph

Public Member Functions

 MgWaterHydrogenPacker ()
 MgWaterHydrogenPacker (utility::vector1< core::Size > const &mg_res_list)
 ~MgWaterHydrogenPacker () override
void apply (core::pose::Pose &pose) override
 Main Method. More...
void apply (core::pose::Pose &pose, std::pair< core::Size, core::Size > const &mg_water)
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void remove_waters_except_mg_bound (core::pose::Pose &pose) const
void set_excise_mini_pose (bool const &setting)
bool excise_mini_pose () const
void set_use_fast_heuristic (bool const &setting)
bool use_fast_heuristic () 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions

void pack_mg_water_hydrogens_in_pose (core::pose::Pose &pose, std::pair< core::Size, core::Size > const &mg_water_pair)
core::Real get_heuristic_water_hydrogen_score (utility::vector1< core::Vector > const &acc_vecs, utility::vector1< core::Vector > const &rep_vecs, core::Vector const &mg_vec, core::Vector const &OH1c, core::Vector const &OH2c, numeric::xyzMatrix< core::Real > const &R) const
void find_water_neighbor_vecs (core::pose::Pose const &pose, core::Size const water_res, core::Size const mg_res, utility::vector1< core::Vector > &acc_vecs, utility::vector1< core::Vector > &rep_vecs, core::Vector &mg_vec) const
bool rotate_water_away_from_magnesium (core::pose::Pose &pose, core::Size const seqpos, core::Vector const &O, core::Vector const &OH1c, core::Vector const &OH2c, core::Vector const &MG, numeric::xyzMatrix< core::Real > const &R) const

Private Attributes

utility::vector1< core::Sizemg_res_list_
utility::vector1< std::pair
< core::Size, core::Size > > 
bool excise_mini_pose_
bool use_fast_heuristic_
numeric::UniformRotationSamplerCOP urs_

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::MgWaterHydrogenPacker::MgWaterHydrogenPacker ( )
protocols::magnesium::MgWaterHydrogenPacker::MgWaterHydrogenPacker ( utility::vector1< core::Size > const &  mg_res_list)
protocols::magnesium::MgWaterHydrogenPacker::~MgWaterHydrogenPacker ( )

Member Function Documentation

void protocols::magnesium::MgWaterHydrogenPacker::apply ( core::pose::Pose )
void protocols::magnesium::MgWaterHydrogenPacker::apply ( core::pose::Pose pose,
std::pair< core::Size, core::Size > const &  mg_water 
bool protocols::magnesium::MgWaterHydrogenPacker::excise_mini_pose ( ) const

References excise_mini_pose_.

void protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs ( core::pose::Pose const &  pose,
core::Size const  water_res,
core::Size const  mg_res,
utility::vector1< core::Vector > &  acc_vecs,
utility::vector1< core::Vector > &  rep_vecs,
core::Vector mg_vec 
) const
Real protocols::magnesium::MgWaterHydrogenPacker::get_heuristic_water_hydrogen_score ( utility::vector1< core::Vector > const &  acc_vecs,
utility::vector1< core::Vector > const &  rep_vecs,
core::Vector const &  mg_vec,
core::Vector const &  OH1c,
core::Vector const &  OH2c,
numeric::xyzMatrix< core::Real > const &  R 
) const
std::string protocols::magnesium::MgWaterHydrogenPacker::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose ( core::pose::Pose pose,
std::pair< core::Size, core::Size > const &  mg_water_pair 
void protocols::magnesium::MgWaterHydrogenPacker::remove_waters_except_mg_bound ( core::pose::Pose pose) const
bool protocols::magnesium::MgWaterHydrogenPacker::rotate_water_away_from_magnesium ( core::pose::Pose pose,
core::Size const  seqpos,
core::Vector const &  O,
core::Vector const &  OH1c,
core::Vector const &  OH2c,
core::Vector const &  MG,
numeric::xyzMatrix< core::Real > const &  R 
) const
void protocols::magnesium::MgWaterHydrogenPacker::set_excise_mini_pose ( bool const &  setting)

References excise_mini_pose_.

void protocols::magnesium::MgWaterHydrogenPacker::set_use_fast_heuristic ( bool const &  setting)

References use_fast_heuristic_.

bool protocols::magnesium::MgWaterHydrogenPacker::use_fast_heuristic ( ) const

References use_fast_heuristic_.

Member Data Documentation

bool protocols::magnesium::MgWaterHydrogenPacker::excise_mini_pose_
utility::vector1< core::Size > protocols::magnesium::MgWaterHydrogenPacker::mg_res_list_

Referenced by apply().

utility::vector1< std::pair< core::Size, core::Size > > protocols::magnesium::MgWaterHydrogenPacker::mg_water_pairs_

Referenced by apply().

numeric::UniformRotationSamplerCOP protocols::magnesium::MgWaterHydrogenPacker::urs_
bool protocols::magnesium::MgWaterHydrogenPacker::use_fast_heuristic_

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