#include <ExplicitWaterMover.hh>

Inheritance diagram for protocols::simple_moves::ExplicitWaterMover:

[legend]

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 Strings &	info ()
	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...

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)

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

◆ ExplicitWaterMover() [1/2]

protocols::simple_moves::ExplicitWaterMover::ExplicitWaterMover ( )

inline

References init().

◆ ExplicitWaterMover() [2/2]

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

inline

References init().

Member Function Documentation

◆ add_point_water()

void protocols::simple_moves::ExplicitWaterMover::add_point_water	(	Pose &	pose,
		core::Vector	O,
		core::Size	resnum
	)

private

◆ apply()

void protocols::simple_moves::ExplicitWaterMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::motif::a(), core::pose::Pose::append_residue_by_jump(), protocols::match::upstream::b, core::conformation::ResidueFactory::create_residue(), core::membrane::find_closest(), core::chemical::FULL_ATOM_t, core::pose::Pose::pdb_info(), core::scoring::pointwater, core::pose::renumber_pdbinfo_based_on_conf_chains(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::total_residue(), protocols::simple_moves::TR(), and protocols::kinmatch::xyz().

Referenced by protocols::simple_ddg::ddG::calculate(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate().

◆ attach_rotamer_clouds_to_pose_and_rotset()

void protocols::simple_moves::ExplicitWaterMover::attach_rotamer_clouds_to_pose_and_rotset	(	core::pose::Pose &	pose,
		PWatRotamerCloud &	watercloud
	)

References core::pose::Pose::append_residue_by_jump(), core::pack::create_packer_graph(), core::conformation::ResidueFactory::create_residue(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::chemical::FULL_ATOM_t, core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

◆ build_backbone_rotamer_clouds()

void protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds	(	core::pose::Pose const &	pose,
		PWatRotamerCloud &	new_rotamers
	)

◆ build_lkboverlap_rotamer_clouds()

void protocols::simple_moves::ExplicitWaterMover::build_lkboverlap_rotamer_clouds	(	core::pose::Pose const &	pose,
		PWatRotamerCloud &	new_rotamers
	)

References protocols::simple_moves::AtomHash::add_point(), core::chemical::ResidueType::is_water(), protocols::simple_moves::AtomHash::npoints(), protocols::simple_moves::AtomHash::reset_and_get_clusters(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::simple_moves::TR(), and protocols::simple_moves::AtomHash::trim_to_heterogeneous_clusters().

◆ clone()

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.

◆ cluster_rotset()

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().

◆ define_explicit_water_mover_schema()

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::simple_moves::ExplicitWaterMover::define_explicit_water_mover_schema ( )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), and protocols::moves::complex_type_name_for_mover().

◆ delete_waters()

void protocols::simple_moves::ExplicitWaterMover::delete_waters	(	core::pose::Pose &	pose,
		bool	virt_only
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::conformation::Residue::name(), core::pose::renumber_pdbinfo_based_on_conf_chains(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

◆ find_closest()

core::Size protocols::simple_moves::ExplicitWaterMover::find_closest	(	Pose const &	pose,
		core::Vector	Ocoord
	)

find closest protein residue

References core::conformation::Residue::atom(), core::conformation::Residue::is_water(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::simple_moves::TR(), and core::conformation::Atom::xyz().

◆ fresh_instance()

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.

◆ get_name()

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().

◆ get_water_recovery()

void protocols::simple_moves::ExplicitWaterMover::get_water_recovery	(	core::pose::Pose const &	pose,
		bool	incl_vrt = `false`
	)

private

References protocols::mean_field::min(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::simple_moves::TR(), and core::conformation::Residue::xyz().

◆ init()

void protocols::simple_moves::ExplicitWaterMover::init ( void )

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), and core::io::StructFileRepOptions::set_ignore_waters().

Referenced by ExplicitWaterMover().

◆ mover_name()

std::string protocols::simple_moves::ExplicitWaterMover::mover_name ( )

static

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

◆ parse_my_tag()

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().

◆ provide_xml_schema()

void protocols::simple_moves::ExplicitWaterMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Referenced by protocols::simple_moves::ExplicitWaterMoverCreator::provide_xml_schema().

◆ run_pack()

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::pack::annealer::FixbbPwatSimAnnealer::get_dwell_times(), core::pack::annealer::FixbbPwatSimAnnealer::run(), core::pack::annealer::FixbbPwatSimAnnealer::set_min_dwell(), core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

◆ set_clust_cutoff()

void protocols::simple_moves::ExplicitWaterMover::set_clust_cutoff ( core::Real val )

inline

References clust_cutoff_, and protocols::hybridization::val.

◆ set_clust_radius()

void protocols::simple_moves::ExplicitWaterMover::set_clust_radius ( core::Real val )

inline

References clust_radius_, and protocols::hybridization::val.

◆ set_dwell_cutoff()

void protocols::simple_moves::ExplicitWaterMover::set_dwell_cutoff ( core::Real val )

inline

References dwell_cutoff_, and protocols::hybridization::val.

◆ set_gen_fixed() [1/2]

void protocols::simple_moves::ExplicitWaterMover::set_gen_fixed ( bool val )

inline

References gen_fixed_, and protocols::hybridization::val.

Referenced by protocols::simple_ddg::ddG::calculate().

◆ set_gen_fixed() [2/2]

void protocols::simple_moves::ExplicitWaterMover::set_gen_fixed ( utility::vector1< bool > val )

inline

References gen_fixed_byres_, and protocols::hybridization::val.

◆ set_lkb_clust_rad()

void protocols::simple_moves::ExplicitWaterMover::set_lkb_clust_rad ( core::Real val )

inline

References lkb_clust_rad_, and protocols::hybridization::val.

◆ set_lkb_overlap_dist()

void protocols::simple_moves::ExplicitWaterMover::set_lkb_overlap_dist ( core::Real val )

inline

References lkb_overlap_dist_, and protocols::hybridization::val.

◆ set_lkb_rotset_radius()

void protocols::simple_moves::ExplicitWaterMover::set_lkb_rotset_radius ( core::Real val )

inline

References lkb_rotset_radius_, and protocols::hybridization::val.

◆ set_mode()

void protocols::simple_moves::ExplicitWaterMover::set_mode ( std::string val )

inline

References mode_, and protocols::hybridization::val.

Referenced by protocols::simple_ddg::ddG::calculate().

◆ set_taskop()

void protocols::simple_moves::ExplicitWaterMover::set_taskop ( core::pack::task::PackerTaskCOP val )

inline

References task_, and protocols::hybridization::val.

Referenced by protocols::simple_ddg::ddG::calculate(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_solvate().

◆ set_watlim_scale()

void protocols::simple_moves::ExplicitWaterMover::set_watlim_scale ( core::Real val )

inline

References protocols::hybridization::val, and watlim_scale_.

◆ setup_pack()

void protocols::simple_moves::ExplicitWaterMover::setup_pack ( Pose & pose )

setup the initial packing step

References core::pack::create_packer_graph(), core::pack::task::TaskFactory::create_packer_task(), core::chemical::ResidueType::get_self_ptr(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), protocols::simple_moves::TR(), and core::pose::Pose::update_residue_neighbors().

◆ update_packer_task()

core::pack::task::PackerTaskOP protocols::simple_moves::ExplicitWaterMover::update_packer_task	(	core::pose::Pose const &	pose,
		core::pack::task::PackerTaskCOP &	packer_task
	)

update task to include all waters

References core::conformation::Residue::name(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Member Data Documentation

◆ clust_cutoff_

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

private

Referenced by set_clust_cutoff().

◆ clust_radius_

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

private

Referenced by set_clust_radius().

◆ dwell_cutoff_

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

private

Referenced by set_dwell_cutoff().

◆ gen_fixed_

bool protocols::simple_moves::ExplicitWaterMover::gen_fixed_

private

Referenced by set_gen_fixed().

◆ gen_fixed_byres_

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

private

Referenced by set_gen_fixed().

◆ ig_

core::pack::interaction_graph::AnnealableGraphBaseOP protocols::simple_moves::ExplicitWaterMover::ig_

private

◆ lkb_clust_rad_

core::Real protocols::simple_moves::ExplicitWaterMover::lkb_clust_rad_

private

Referenced by set_lkb_clust_rad().

◆ lkb_overlap_dist_

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

private

Referenced by set_lkb_overlap_dist().

◆ lkb_rotset_radius_

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

private

Referenced by set_lkb_rotset_radius().

◆ mode_

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

private

Referenced by set_mode().

◆ native_

core::pose::PoseOP protocols::simple_moves::ExplicitWaterMover::native_

private

◆ rotamer_sets_

core::pack::rotamer_set::RotamerSetsOP protocols::simple_moves::ExplicitWaterMover::rotamer_sets_

private

◆ sf_

core::scoring::ScoreFunctionOP protocols::simple_moves::ExplicitWaterMover::sf_

private

◆ task_

core::pack::task::PackerTaskCOP protocols::simple_moves::ExplicitWaterMover::task_

private

Referenced by set_taskop().

◆ task_factory_

core::pack::task::TaskFactoryCOP protocols::simple_moves::ExplicitWaterMover::task_factory_

private

◆ water_rots_db_

WaterRotsDB protocols::simple_moves::ExplicitWaterMover::water_rots_db_

staticprivate

◆ watlim_scale_

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:

src/protocols/simple_moves/ExplicitWaterMover.hh
src/protocols/simple_moves/ExplicitWaterMover.cc

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< bool >	gen_fixed_byres_

core::pose::PoseOP	native_

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ExplicitWaterMover() [1/2]

◆ ExplicitWaterMover() [2/2]

Member Function Documentation

◆ add_point_water()

◆ apply()

◆ attach_rotamer_clouds_to_pose_and_rotset()

◆ build_backbone_rotamer_clouds()

◆ build_lkboverlap_rotamer_clouds()

◆ clone()

◆ cluster_rotset()

◆ define_explicit_water_mover_schema()

◆ delete_waters()

◆ find_closest()

◆ fresh_instance()

◆ get_name()

◆ get_water_recovery()

◆ init()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ run_pack()

◆ set_clust_cutoff()

◆ set_clust_radius()

◆ set_dwell_cutoff()

◆ set_gen_fixed() [1/2]

◆ set_gen_fixed() [2/2]

◆ set_lkb_clust_rad()

◆ set_lkb_overlap_dist()

◆ set_lkb_rotset_radius()

◆ set_mode()

◆ set_taskop()

◆ set_watlim_scale()

◆ setup_pack()

◆ update_packer_task()

Member Data Documentation

◆ clust_cutoff_

◆ clust_radius_

◆ dwell_cutoff_

◆ gen_fixed_

◆ gen_fixed_byres_

◆ ig_

◆ lkb_clust_rad_

◆ lkb_overlap_dist_

◆ lkb_rotset_radius_

◆ mode_

◆ native_

◆ rotamer_sets_

◆ sf_

◆ task_

◆ task_factory_

◆ water_rots_db_

◆ watlim_scale_