#include <PolarHydrogenPacker.hh>

Inheritance diagram for protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker:

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Public Member Functions
	PolarHydrogenPacker ()

	~PolarHydrogenPacker () override

void	apply (core::pose::Pose &pose) override
	Apply the corresponding move to <pose>. More...

std::string	get_name () const override
	Return the name of the Mover. More...

void	set_allow_virtual_o2prime_hydrogens (bool const setting)

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 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...

Private Member Functions
void	init ()

void	check_hbond_score (core::Vector const &H_xyz, core::Vector const &D_xyz, core::Real &best_score, core::Vector &best_hydrogen_xyz)

void	get_best_hxyz (core::conformation::Residue const &residue, utility::vector1< core::Vector > const &ideal_hydrogen_xyz_positions, core::Size const abase, core::Size const abase2, core::Vector const &donor_xyz, core::Real &best_score, core::Vector &best_hydrogen_xyz)

utility::vector1< core::Vector >	get_ideal_hxyz_positions (core::conformation::Residue const &residue, core::conformation::Residue const &ideal_res, core::Size const j, core::kinematics::Stub const &current_input_stub, core::kinematics::Stub const &ideal_input_stub)

void	virtualize_poor_scoring_o2prime_hydrogens (core::pose::Pose &pose, core::Size const i, core::Size const j, core::Real const best_score)

void	get_possible_hbond_acceptors (core::pose::Pose const &pose, core::Size const moving_res, core::Size const atomno)

Private Attributes
core::scoring::hbonds::HBondOptionsOP	hbond_options_

core::scoring::hbonds::HBondDatabaseCOP	hbond_database_

utility::vector1< utility::vector1< core::Vector > >	possible_hbond_acceptors_

utility::vector1< core::scoring::hbonds::HBEvalTuple >	hb_eval_tuples_

bool	allow_virtual_o2prime_hydrogens_

bool	disallow_vary_geometry_proton_chi_

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

◆ PolarHydrogenPacker()

protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::PolarHydrogenPacker ( )

References init().

◆ ~PolarHydrogenPacker()

protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::~PolarHydrogenPacker ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply ( core::pose::Pose & pose )

overridevirtual

Apply the corresponding move to <pose>.

Implements protocols::moves::Mover.

References allow_virtual_o2prime_hydrogens_, core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), check_hbond_score(), disallow_vary_geometry_proton_chi_, get_best_hxyz(), get_ideal_hxyz_positions(), get_possible_hbond_acceptors(), core::conformation::Residue::Hpos_polar(), core::conformation::Residue::natoms(), core::pose::remove_variant_type_from_residue(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::total_residue(), core::conformation::Residue::type(), core::chemical::VIRTUAL_O2PRIME_HYDROGEN, virtualize_poor_scoring_o2prime_hydrogens(), and core::conformation::Residue::xyz().

Referenced by protocols::stepwise::modeler::polar_hydrogens::pack_polar_hydrogens().

◆ check_hbond_score()

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::check_hbond_score	(	core::Vector const &	H_xyz,
		core::Vector const &	D_xyz,
		core::Real &	best_score,
		core::Vector &	best_hydrogen_xyz
	)

private

References protocols::buns::energy, core::scoring::hbonds::hb_energy_deriv(), hb_eval_tuples_, hbond_database_, hbond_options_, possible_hbond_acceptors_, and core::scoring::total_score.

Referenced by apply(), and get_best_hxyz().

◆ get_best_hxyz()

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_best_hxyz	(	core::conformation::Residue const &	residue,
		utility::vector1< core::Vector > const &	ideal_hydrogen_xyz_positions,
		core::Size const	abase,
		core::Size const	abase2,
		core::Vector const &	donor_xyz,
		core::Real &	best_score,
		core::Vector &	best_hydrogen_xyz
	)

private

References check_hbond_score(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::scoring::packstat::old::nphi, core::scoring::packstat::old::ntheta, possible_hbond_acceptors_, core::chemical::rings::q, and core::conformation::Residue::xyz().

Referenced by apply().

◆ get_ideal_hxyz_positions()

utility::vector1< Vector > protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions	(	core::conformation::Residue const &	residue,
		core::conformation::Residue const &	ideal_res,
		core::Size const	j,
		core::kinematics::Stub const &	current_input_stub,
		core::kinematics::Stub const &	ideal_input_stub
	)

private

References protocols::stepwise::modeler::polar_hydrogens::check_if_proton_chi_atom(), disallow_vary_geometry_proton_chi_, core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ get_name()

std::string protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_name ( ) const

inlineoverridevirtual

Return the name of the Mover.

Implements protocols::moves::Mover.

◆ get_possible_hbond_acceptors()

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors	(	core::pose::Pose const &	pose,
		core::Size const	moving_res,
		core::Size const	atomno
	)

private

References core::conformation::Residue::abase2(), core::conformation::Residue::atom_base(), core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), hb_eval_tuples_, core::chemical::ResidueType::heavyatom_has_polar_hydrogens(), core::chemical::ResidueType::heavyatom_is_an_acceptor(), core::chemical::ResidueType::is_virtual(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), possible_hbond_acceptors_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ init()

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::init ( void )

private

References hbond_database_, and hbond_options_.

Referenced by PolarHydrogenPacker().

◆ set_allow_virtual_o2prime_hydrogens()

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::set_allow_virtual_o2prime_hydrogens ( bool const setting )

inline

References allow_virtual_o2prime_hydrogens_.

Referenced by protocols::stepwise::modeler::polar_hydrogens::pack_polar_hydrogens().

◆ virtualize_poor_scoring_o2prime_hydrogens()

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::virtualize_poor_scoring_o2prime_hydrogens	(	core::pose::Pose &	pose,
		core::Size const	i,
		core::Size const	j,
		core::Real const	best_score
	)

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::rna::RNA_Info::ho2prime_index(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::RNA_info(), and core::chemical::VIRTUAL_O2PRIME_HYDROGEN.

Referenced by apply().

Member Data Documentation

◆ allow_virtual_o2prime_hydrogens_

bool protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::allow_virtual_o2prime_hydrogens_

private

Referenced by apply(), and set_allow_virtual_o2prime_hydrogens().

◆ disallow_vary_geometry_proton_chi_

bool protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::disallow_vary_geometry_proton_chi_

private

Referenced by apply(), and get_ideal_hxyz_positions().

◆ hb_eval_tuples_

utility::vector1< core::scoring::hbonds::HBEvalTuple > protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::hb_eval_tuples_

private

Referenced by check_hbond_score(), and get_possible_hbond_acceptors().

◆ hbond_database_

core::scoring::hbonds::HBondDatabaseCOP protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::hbond_database_

private

Referenced by check_hbond_score(), and init().

◆ hbond_options_

core::scoring::hbonds::HBondOptionsOP protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::hbond_options_

private

Referenced by check_hbond_score(), and init().

◆ possible_hbond_acceptors_

utility::vector1< utility::vector1< core::Vector > > protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::possible_hbond_acceptors_

private

Referenced by check_hbond_score(), get_best_hxyz(), and get_possible_hbond_acceptors().

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

src/protocols/stepwise/modeler/polar_hydrogens/PolarHydrogenPacker.hh
src/protocols/stepwise/modeler/polar_hydrogens/PolarHydrogenPacker.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ PolarHydrogenPacker()

◆ ~PolarHydrogenPacker()

Member Function Documentation

◆ apply()

◆ check_hbond_score()

◆ get_best_hxyz()

◆ get_ideal_hxyz_positions()

◆ get_name()

◆ get_possible_hbond_acceptors()

◆ init()

◆ set_allow_virtual_o2prime_hydrogens()

◆ virtualize_poor_scoring_o2prime_hydrogens()

Member Data Documentation

◆ allow_virtual_o2prime_hydrogens_

◆ disallow_vary_geometry_proton_chi_

◆ hb_eval_tuples_

◆ hbond_database_

◆ hbond_options_

◆ possible_hbond_acceptors_