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protocols::simple_moves::ExplicitWaterMover Class Reference

#include <ExplicitWaterMover.hh>

Inheritance diagram for protocols::simple_moves::ExplicitWaterMover:
Inheritance graph
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Public Member Functions

 ExplicitWaterMover ()
 
 ExplicitWaterMover (core::scoring::ScoreFunctionOP sfin)
 
void init ()
 
void apply (Pose &pose) override
 Main Method. More...
 
void delete_waters (core::pose::Pose &pose, bool virt_only)
 
void build_backbone_rotamer_clouds (core::pose::Pose const &pose, PWatRotamerCloud &new_rotamers)
 
void build_lkboverlap_rotamer_clouds (core::pose::Pose const &pose, PWatRotamerCloud &new_rotamers)
 
void attach_rotamer_clouds_to_pose_and_rotset (core::pose::Pose &pose, PWatRotamerCloud &watercloud)
 
void setup_pack (Pose &pose)
 setup the initial packing step More...
 
void run_pack (Pose &pose, utility::vector0< int > rot_to_pack, utility::vector1< core::pack::annealer::PointDwell > &all_rot)
 run packing trajectory More...
 
core::pack::task::PackerTaskOP update_packer_task (core::pose::Pose const &pose, core::pack::task::PackerTaskCOP &packer_task)
 update task to include all waters More...
 
void cluster_rotset (utility::vector1< core::pack::annealer::PointDwell > &rotset)
 cluster water clouds More...
 
core::Size find_closest (Pose const &pose, core::Vector Ocoord)
 find closest protein residue More...
 
void set_mode (std::string val)
 
void set_lkb_overlap_dist (core::Real val)
 
void set_lkb_clust_rad (core::Real val)
 
void set_lkb_rotset_radius (core::Real val)
 
void set_dwell_cutoff (core::Real val)
 
void set_clust_radius (core::Real val)
 
void set_clust_cutoff (core::Real val)
 
void set_watlim_scale (core::Real val)
 
void set_gen_fixed (bool val)
 
void set_gen_fixed (utility::vector1< bool > val)
 
void set_taskop (core::pack::task::PackerTaskCOP val)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
- 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 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...
 
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
 
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...
 

Static Public Member Functions

static std::string mover_name ()
 
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
define_explicit_water_mover_schema ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

void add_point_water (Pose &pose, core::Vector O, core::Size resnum)
 
void get_water_recovery (core::pose::Pose const &pose, bool incl_vrt=false)
 

Private Attributes

core::scoring::ScoreFunctionOP sf_
 
core::pack::task::PackerTaskCOP task_
 
core::pack::task::TaskFactoryCOP task_factory_
 
core::pack::rotamer_set::RotamerSetsOP rotamer_sets_
 
core::pack::interaction_graph::AnnealableGraphBaseOP ig_
 
std::string mode_
 
core::Real lkb_overlap_dist_
 
core::Real lkb_clust_rad_
 
core::Real lkb_rotset_radius_
 
core::Real dwell_cutoff_
 
core::Real clust_radius_
 
core::Real clust_cutoff_
 
core::Real watlim_scale_
 
bool gen_fixed_
 
utility::vector1< boolgen_fixed_byres_
 
core::pose::PoseOP native_
 

Static Private Attributes

static WaterRotsDB water_rots_db_
 

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
 
- 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::simple_moves::ExplicitWaterMover::ExplicitWaterMover ( )
inline

References init().

protocols::simple_moves::ExplicitWaterMover::ExplicitWaterMover ( core::scoring::ScoreFunctionOP  sfin)
inline

References init().

Member Function Documentation

void protocols::simple_moves::ExplicitWaterMover::add_point_water ( Pose pose,
core::Vector  O,
core::Size  resnum 
)
private
void protocols::simple_moves::ExplicitWaterMover::apply ( Pose )
overridevirtual
void protocols::simple_moves::ExplicitWaterMover::attach_rotamer_clouds_to_pose_and_rotset ( core::pose::Pose pose,
PWatRotamerCloud watercloud 
)
void protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds ( core::pose::Pose const &  pose,
PWatRotamerCloud new_rotamers 
)
void protocols::simple_moves::ExplicitWaterMover::build_lkboverlap_rotamer_clouds ( core::pose::Pose const &  pose,
PWatRotamerCloud new_rotamers 
)
protocols::moves::MoverOP protocols::simple_moves::ExplicitWaterMover::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

void protocols::simple_moves::ExplicitWaterMover::cluster_rotset ( utility::vector1< core::pack::annealer::PointDwell > &  rotset)

cluster water clouds

cluster water clouds inefficient but probably okay (there should not be many waters passing filters else rotatible waters would take excessively long)

References core::pack::annealer::PointDwell::dwell, protocols::simple_moves::TR(), core::pack::annealer::PointDwell::xyz, and protocols::kinmatch::xyz().

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::simple_moves::ExplicitWaterMover::define_explicit_water_mover_schema ( )
static
void protocols::simple_moves::ExplicitWaterMover::delete_waters ( core::pose::Pose pose,
bool  virt_only 
)
core::Size protocols::simple_moves::ExplicitWaterMover::find_closest ( Pose const &  pose,
core::Vector  Ocoord 
)
protocols::moves::MoverOP protocols::simple_moves::ExplicitWaterMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::simple_moves::ExplicitWaterMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References protocols::simple_moves::ExplicitWaterMoverCreator::mover_name().

void protocols::simple_moves::ExplicitWaterMover::get_water_recovery ( core::pose::Pose const &  pose,
bool  incl_vrt = false 
)
private
void protocols::simple_moves::ExplicitWaterMover::init ( void  )
std::string protocols::simple_moves::ExplicitWaterMover::mover_name ( )
static
void protocols::simple_moves::ExplicitWaterMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), core::io::StructFileRepOptions::set_ignore_waters(), and core::pack::task::TASK_OPERATIONS_TAG().

void protocols::simple_moves::ExplicitWaterMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_moves::ExplicitWaterMover::run_pack ( Pose pose,
utility::vector0< int >  rot_to_pack,
utility::vector1< core::pack::annealer::PointDwell > &  all_rot 
)

run packing trajectory

References core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

void protocols::simple_moves::ExplicitWaterMover::set_clust_cutoff ( core::Real  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_clust_radius ( core::Real  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_dwell_cutoff ( core::Real  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_gen_fixed ( bool  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_gen_fixed ( utility::vector1< bool val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_lkb_clust_rad ( core::Real  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_lkb_overlap_dist ( core::Real  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_lkb_rotset_radius ( core::Real  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_mode ( std::string  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_taskop ( core::pack::task::PackerTaskCOP  val)
inline
void protocols::simple_moves::ExplicitWaterMover::set_watlim_scale ( core::Real  val)
inline
void protocols::simple_moves::ExplicitWaterMover::setup_pack ( Pose pose)
core::pack::task::PackerTaskOP protocols::simple_moves::ExplicitWaterMover::update_packer_task ( core::pose::Pose const &  pose,
core::pack::task::PackerTaskCOP packer_task 
)

Member Data Documentation

core::Real protocols::simple_moves::ExplicitWaterMover::clust_cutoff_
private

Referenced by set_clust_cutoff().

core::Real protocols::simple_moves::ExplicitWaterMover::clust_radius_
private

Referenced by set_clust_radius().

core::Real protocols::simple_moves::ExplicitWaterMover::dwell_cutoff_
private

Referenced by set_dwell_cutoff().

bool protocols::simple_moves::ExplicitWaterMover::gen_fixed_
private

Referenced by set_gen_fixed().

utility::vector1<bool> protocols::simple_moves::ExplicitWaterMover::gen_fixed_byres_
private

Referenced by set_gen_fixed().

core::pack::interaction_graph::AnnealableGraphBaseOP protocols::simple_moves::ExplicitWaterMover::ig_
private
core::Real protocols::simple_moves::ExplicitWaterMover::lkb_clust_rad_
private

Referenced by set_lkb_clust_rad().

core::Real protocols::simple_moves::ExplicitWaterMover::lkb_overlap_dist_
private

Referenced by set_lkb_overlap_dist().

core::Real protocols::simple_moves::ExplicitWaterMover::lkb_rotset_radius_
private

Referenced by set_lkb_rotset_radius().

std::string protocols::simple_moves::ExplicitWaterMover::mode_
private

Referenced by set_mode().

core::pose::PoseOP protocols::simple_moves::ExplicitWaterMover::native_
private
core::pack::rotamer_set::RotamerSetsOP protocols::simple_moves::ExplicitWaterMover::rotamer_sets_
private
core::scoring::ScoreFunctionOP protocols::simple_moves::ExplicitWaterMover::sf_
private
core::pack::task::PackerTaskCOP protocols::simple_moves::ExplicitWaterMover::task_
private

Referenced by set_taskop().

core::pack::task::TaskFactoryCOP protocols::simple_moves::ExplicitWaterMover::task_factory_
private
WaterRotsDB protocols::simple_moves::ExplicitWaterMover::water_rots_db_
staticprivate
core::Real protocols::simple_moves::ExplicitWaterMover::watlim_scale_
private

Referenced by set_watlim_scale().


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