#include <SetupMetalsMover.hh>

Inheritance diagram for protocols::simple_moves::SetupMetalsMover:

[legend]

Public Member Functions
	SetupMetalsMover ()
	Constructs a SetupMetalsMover. More...

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	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. 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 (TagCOP, basic::datacache::DataMap &) override
	Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover's parsing. More...

bool	get_constraints_only () const

core::Real	get_metals_detection_LJ_multiplier () const

core::Real	get_metals_distance_constraint_multiplier () const

core::Real	get_metals_angle_constraint_multiplier () const

core::select::residue_selector::ResidueSelectorCOP	get_metal_selector () const

std::string	get_metal_resnums_string () const

bool	get_remove_hydrogens () const

bool	get_add_constraints () const

core::select::residue_selector::ResidueSelectorCOP	get_contact_selector () const

std::string	get_contact_resnums_string () const

void	set_constraints_only (bool)

void	set_metals_detection_LJ_multiplier (core::Real)

void	set_metals_distance_constraint_multiplier (core::Real)

void	set_metals_angle_constraint_multiplier (core::Real)

void	set_metal_selector (core::select::residue_selector::ResidueSelectorCOP)

void	set_metal_resnums_string (std::string)

void	set_remove_hydrogens (bool)

void	set_add_constraints (bool)

void	set_contact_selector (core::select::residue_selector::ResidueSelectorCOP)

void	set_contact_resnums_string (std::string)

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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 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...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	mover_name ()

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
utility::vector1< core::Size >	find_metal_resnums (core::pose::Pose const &)
	If a residue selector or resnum string is provided, returns any metal ions within the selection. Otherwise returns an empty vector. More...

std::set< core::Size >	find_contact_resnums (core::pose::Pose const &)

void	set_defaults_from_command_line ()

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...

Private Attributes
bool	remove_hydrogens_ = true

bool	constraints_only_ = false

bool	add_constraints_ = true

core::Real	metals_detection_LJ_multiplier_ = 1.0

core::Real	metals_distance_constraint_multiplier_ = 1.0

core::Real	metals_angle_constraint_multiplier_ = 1.0

core::select::residue_selector::ResidueSelectorCOP	metal_selector_ = nullptr

std::string	metal_resnums_string_ = ""

core::select::residue_selector::ResidueSelectorCOP	contact_selector_ = nullptr

std::string	contact_resnums_string_ = ""

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

Detailed Description

A protocols::moves::Mover that.

Constructor & Destructor Documentation

◆ SetupMetalsMover()

protocols::simple_moves::SetupMetalsMover::SetupMetalsMover ( )

Constructs a SetupMetalsMover.

References add_constraints_, constraints_only_, metal_resnums_string_, metal_selector_, metals_angle_constraint_multiplier_, metals_detection_LJ_multiplier_, metals_distance_constraint_multiplier_, remove_hydrogens_, and set_defaults_from_command_line().

Member Function Documentation

◆ apply()

void protocols::simple_moves::SetupMetalsMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References add_constraints_, core::util::add_constraints_to_metal(), core::util::add_covalent_linkages_to_metal(), core::util::auto_setup_all_metal_bonds(), core::util::auto_setup_all_metal_constraints(), constraints_only_, find_contact_resnums(), find_metal_resnums(), core::util::find_metalbinding_atoms(), metal_resnums_string_, metal_selector_, metals_angle_constraint_multiplier_, metals_detection_LJ_multiplier_, metals_distance_constraint_multiplier_, and remove_hydrogens_.

◆ clone()

protocols::moves::MoverOP protocols::simple_moves::SetupMetalsMover::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.

◆ find_contact_resnums()

std::set< core::Size > protocols::simple_moves::SetupMetalsMover::find_contact_resnums ( core::pose::Pose const & pose )

protected

References contact_resnums_string_, contact_selector_, core::pose::get_resnum_list(), core::pose::Pose::size(), and core::pose::Pose::total_residue().

Referenced by apply().

◆ find_metal_resnums()

utility::vector1< core::Size > protocols::simple_moves::SetupMetalsMover::find_metal_resnums ( core::pose::Pose const & pose )

protected

If a residue selector or resnum string is provided, returns any metal ions within the selection. Otherwise returns an empty vector.

If a residue selector or resnum string is provided, returns any metal ions within the selection. Otherwise returns an empty vector (it shouldn't be called in this situation, though)

References core::pose::get_resnum_list(), core::conformation::Residue::is_metal(), metal_resnums_string_, metal_selector_, core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::Pose::total_residue().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::simple_moves::SetupMetalsMover::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_add_constraints()

bool protocols::simple_moves::SetupMetalsMover::get_add_constraints ( ) const

References add_constraints_.

◆ get_constraints_only()

bool protocols::simple_moves::SetupMetalsMover::get_constraints_only ( ) const

References constraints_only_.

◆ get_contact_resnums_string()

std::string protocols::simple_moves::SetupMetalsMover::get_contact_resnums_string ( ) const

References contact_resnums_string_.

◆ get_contact_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::SetupMetalsMover::get_contact_selector ( ) const

References contact_selector_.

◆ get_metal_resnums_string()

std::string protocols::simple_moves::SetupMetalsMover::get_metal_resnums_string ( ) const

References metal_resnums_string_.

◆ get_metal_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::SetupMetalsMover::get_metal_selector ( ) const

References metal_selector_.

◆ get_metals_angle_constraint_multiplier()

core::Real protocols::simple_moves::SetupMetalsMover::get_metals_angle_constraint_multiplier ( ) const

References metals_angle_constraint_multiplier_.

◆ get_metals_detection_LJ_multiplier()

core::Real protocols::simple_moves::SetupMetalsMover::get_metals_detection_LJ_multiplier ( ) const

References metals_detection_LJ_multiplier_.

◆ get_metals_distance_constraint_multiplier()

core::Real protocols::simple_moves::SetupMetalsMover::get_metals_distance_constraint_multiplier ( ) const

References metals_distance_constraint_multiplier_.

◆ get_name()

std::string protocols::simple_moves::SetupMetalsMover::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_remove_hydrogens()

bool protocols::simple_moves::SetupMetalsMover::get_remove_hydrogens ( ) const

References remove_hydrogens_.

◆ mover_name()

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

static

Referenced by get_name(), protocols::simple_moves::SetupMetalsMoverCreator::keyname(), protocols::simple_moves::SetupMetalsMoverCreator::mover_name(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::simple_moves::SetupMetalsMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References add_constraints_, constraints_only_, contact_resnums_string_, contact_selector_, metal_resnums_string_, metal_selector_, metals_angle_constraint_multiplier_, metals_detection_LJ_multiplier_, metals_distance_constraint_multiplier_, core::select::residue_selector::parse_residue_selector(), and remove_hydrogens_.

◆ provide_citation_info()

void protocols::simple_moves::SetupMetalsMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References contact_selector_, and metal_selector_.

◆ provide_xml_schema()

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

static

References core::pose::attributes_for_get_resnum_selector(), core::select::residue_selector::attributes_for_parse_residue_selector(), protocols::moves::complex_type_name_for_mover(), and mover_name().

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

◆ set_add_constraints()

void protocols::simple_moves::SetupMetalsMover::set_add_constraints ( bool input )

References add_constraints_.

◆ set_constraints_only()

void protocols::simple_moves::SetupMetalsMover::set_constraints_only ( bool input )

References constraints_only_.

◆ set_contact_resnums_string()

void protocols::simple_moves::SetupMetalsMover::set_contact_resnums_string ( std::string input )

References contact_resnums_string_.

◆ set_contact_selector()

void protocols::simple_moves::SetupMetalsMover::set_contact_selector ( core::select::residue_selector::ResidueSelectorCOP input )

References contact_selector_.

◆ set_defaults_from_command_line()

void protocols::simple_moves::SetupMetalsMover::set_defaults_from_command_line ( )

protected

References metals_angle_constraint_multiplier_, metals_detection_LJ_multiplier_, and metals_distance_constraint_multiplier_.

Referenced by SetupMetalsMover().

◆ set_metal_resnums_string()

void protocols::simple_moves::SetupMetalsMover::set_metal_resnums_string ( std::string input )

References metal_resnums_string_.

◆ set_metal_selector()

void protocols::simple_moves::SetupMetalsMover::set_metal_selector ( core::select::residue_selector::ResidueSelectorCOP input )

References metal_selector_.

◆ set_metals_angle_constraint_multiplier()

void protocols::simple_moves::SetupMetalsMover::set_metals_angle_constraint_multiplier ( core::Real input )

References metals_angle_constraint_multiplier_.

◆ set_metals_detection_LJ_multiplier()

void protocols::simple_moves::SetupMetalsMover::set_metals_detection_LJ_multiplier ( core::Real input )

References metals_detection_LJ_multiplier_.

◆ set_metals_distance_constraint_multiplier()

void protocols::simple_moves::SetupMetalsMover::set_metals_distance_constraint_multiplier ( core::Real input )

References metals_distance_constraint_multiplier_.

◆ set_remove_hydrogens()

void protocols::simple_moves::SetupMetalsMover::set_remove_hydrogens ( bool input )

References remove_hydrogens_.

◆ show()

void protocols::simple_moves::SetupMetalsMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References constraints_only_, metal_resnums_string_, metal_selector_, metals_angle_constraint_multiplier_, metals_detection_LJ_multiplier_, metals_distance_constraint_multiplier_, remove_hydrogens_, and protocols::moves::Mover::show().

Referenced by protocols::simple_moves::operator<<().

Member Data Documentation

◆ add_constraints_

bool protocols::simple_moves::SetupMetalsMover::add_constraints_ = true

private

Referenced by apply(), get_add_constraints(), parse_my_tag(), set_add_constraints(), and SetupMetalsMover().

◆ constraints_only_

bool protocols::simple_moves::SetupMetalsMover::constraints_only_ = false

private

Referenced by apply(), get_constraints_only(), parse_my_tag(), set_constraints_only(), SetupMetalsMover(), and show().

◆ contact_resnums_string_

std::string protocols::simple_moves::SetupMetalsMover::contact_resnums_string_ = ""

private

Referenced by find_contact_resnums(), get_contact_resnums_string(), parse_my_tag(), and set_contact_resnums_string().

◆ contact_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::SetupMetalsMover::contact_selector_ = nullptr

private

Referenced by find_contact_resnums(), get_contact_selector(), parse_my_tag(), provide_citation_info(), and set_contact_selector().

◆ metal_resnums_string_

std::string protocols::simple_moves::SetupMetalsMover::metal_resnums_string_ = ""

private

Referenced by apply(), find_metal_resnums(), get_metal_resnums_string(), parse_my_tag(), set_metal_resnums_string(), SetupMetalsMover(), and show().

◆ metal_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::SetupMetalsMover::metal_selector_ = nullptr

private

Referenced by apply(), find_metal_resnums(), get_metal_selector(), parse_my_tag(), provide_citation_info(), set_metal_selector(), SetupMetalsMover(), and show().

◆ metals_angle_constraint_multiplier_

core::Real protocols::simple_moves::SetupMetalsMover::metals_angle_constraint_multiplier_ = 1.0

private

Referenced by apply(), get_metals_angle_constraint_multiplier(), parse_my_tag(), set_defaults_from_command_line(), set_metals_angle_constraint_multiplier(), SetupMetalsMover(), and show().

◆ metals_detection_LJ_multiplier_

core::Real protocols::simple_moves::SetupMetalsMover::metals_detection_LJ_multiplier_ = 1.0

private

Referenced by apply(), get_metals_detection_LJ_multiplier(), parse_my_tag(), set_defaults_from_command_line(), set_metals_detection_LJ_multiplier(), SetupMetalsMover(), and show().

◆ metals_distance_constraint_multiplier_

core::Real protocols::simple_moves::SetupMetalsMover::metals_distance_constraint_multiplier_ = 1.0

private

Referenced by apply(), get_metals_distance_constraint_multiplier(), parse_my_tag(), set_defaults_from_command_line(), set_metals_distance_constraint_multiplier(), SetupMetalsMover(), and show().

◆ remove_hydrogens_

bool protocols::simple_moves::SetupMetalsMover::remove_hydrogens_ = true

private

Referenced by apply(), get_remove_hydrogens(), parse_my_tag(), set_remove_hydrogens(), SetupMetalsMover(), and show().

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

src/protocols/simple_moves/SetupMetalsMover.hh
src/protocols/simple_moves/SetupMetalsMover.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SetupMetalsMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ find_contact_resnums()

◆ find_metal_resnums()

◆ fresh_instance()

◆ get_add_constraints()

◆ get_constraints_only()

◆ get_contact_resnums_string()

◆ get_contact_selector()

◆ get_metal_resnums_string()

◆ get_metal_selector()

◆ get_metals_angle_constraint_multiplier()

◆ get_metals_detection_LJ_multiplier()

◆ get_metals_distance_constraint_multiplier()

◆ get_name()

◆ get_remove_hydrogens()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ set_add_constraints()

◆ set_constraints_only()

◆ set_contact_resnums_string()

◆ set_contact_selector()

◆ set_defaults_from_command_line()

◆ set_metal_resnums_string()

◆ set_metal_selector()

◆ set_metals_angle_constraint_multiplier()

◆ set_metals_detection_LJ_multiplier()

◆ set_metals_distance_constraint_multiplier()

◆ set_remove_hydrogens()

◆ show()

Member Data Documentation

◆ add_constraints_

◆ constraints_only_

◆ contact_resnums_string_

◆ contact_selector_

◆ metal_resnums_string_

◆ metal_selector_

◆ metals_angle_constraint_multiplier_

◆ metals_detection_LJ_multiplier_

◆ metals_distance_constraint_multiplier_

◆ remove_hydrogens_