#include <KinaseMover.hh>

Inheritance diagram for protocols::enzymatic_movers::KinaseMover:

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Public Member Functions
	KinaseMover ()
	Default constructor. More...

	KinaseMover (KinaseMover const &)=default
	Copy constructor. More...

	~KinaseMover () override=default

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

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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

Public Member Functions inherited from protocols::enzymatic_movers::EnzymaticMover
	EnzymaticMover ()
	Default constructor. More...

	EnzymaticMover (std::string const &enzyme_family)
	Constructor with enzyme family provided. More...

	EnzymaticMover (EnzymaticMover const &)=default
	Copy constructor. More...

	~EnzymaticMover () override=default

void	show (std::ostream &output=std::cout) const override
	Generate string representation of EnzymaticMover for debugging purposes. More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

std::string	get_enzyme_family () const
	Get the family name of this simulated enzyme. More...

void	set_species (std::string const &species_name)
	Set the species name of this simulated enzyme. More...

std::string	get_species () const
	Get the species name of this simulated enzyme. More...

void	set_enzyme (std::string const &enzyme_name)
	Set the specific name of this simulated enzyme. More...

std::string	get_enzyme () const
	Return the specific name of this simulated enzyme. More...

void	set_efficiency (core::Real setting)
	Directly set the efficiency of this enzyme, ignoring whatever is in the database. More...

core::Real	get_efficiency () const
	Get the efficiency of this enzyme. More...

void	exclude_site (core::uint seqpos)
	Do not perform a reaction at this site, even if it is within a consensus sequence match for this enzyme. More...

void	set_excluded_sites (utility::vector1< core::uint > const &excluded_sites)
	Pass a list of sequence positions that are forbidden from being modified, even if they are within a consensus sequence match for this enzyme. More...

utility::vector1< core::uint >	get_excluded_sites () const
	Return a list of sequence positions that are forbidden from being modified, even if they are within a consensus sequence match for this enzyme. More...

void	ensure_site (core::uint seqpos)
	Definitely modify this site, if it is within a consensus sequence match for this enzyme. More...

void	set_ensured_sites (utility::vector1< core::uint > const &ensured_sites)
	Pass a list of sequence positions that are guaranteed to be modified, if they are within a consensus sequence match for this enzyme. More...

utility::vector1< core::uint >	get_ensured_sites () const
	Return a list of sequence positions that are guaranteed to be modified, if they are within a consensus sequence match for this enzyme. More...

core::Size	get_n_reactive_sites () const
	Return the current number of reactive sites. More...

core::uint	get_reactive_site_sequence_position (core::uint const index) const
	Return the sequence position of the requested reactive site. More...

std::string const &	get_reactive_site_atom_name (core::uint const index) const
	Return the atom name of the requested reactive site. More...

core::Size	get_n_co_substrates () const
	Return the current number of reactive sites. More...

std::string const &	get_co_substrate (core::uint const index) const
	Return the requested cosubstrate of this enzymatic reaction. More...

void	perform_major_reaction_only ()
	Set this EnzymaticMover to perform only its major reaction. More...

void	perform_all_reactions ()
	Allow this EnzymaticMover to be promiscuous, performing a random transfer from among its possible co-substrates. More...

bool	performs_major_reaction_only () const
	Does this enzyme only perform its major reaction? More...

void	set_pose_reactive_sites (core::pose::Pose const &pose)

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	register_options ()
	Register options with the option system. More...

static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::enzymatic_movers::EnzymaticMover
static void	register_options ()
	Register options with the option system. More...

static utility::tag::XMLSchemaComplexTypeGeneratorOP	xml_schema_complex_type_generator ()

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
void	perform_reaction (core::pose::Pose &input_pose, core::uint const site, std::string const &cosubstrate) override
	Actually perform the virtual reaction for this specific EnzymaticMover. @params <input_pose>: The Pose to be acted on. @params <site>: An index for the reactive site to be acted on. @params <cosubstrate>: A string providing information to the Enzymatic Mover to add or subtract the proper atoms or Residues from the Pose. How this parameter is handled is specific to each distinct EnzymaticMover. More...

Protected Member Functions inherited from protocols::enzymatic_movers::EnzymaticMover
void	set_enzyme_family (std::string const &family_name)
	Set the family name of this simulated enzyme. 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...

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

This Mover simulates the activity of a virtual kinase enzyme on a Pose by phosphorylating a residue at a biologically relevant sequon position.

Constructor & Destructor Documentation

◆ KinaseMover() [1/2]

protocols::enzymatic_movers::KinaseMover::KinaseMover ( )

Default constructor.

References protocols::moves::Mover::type().

◆ KinaseMover() [2/2]

protocols::enzymatic_movers::KinaseMover::KinaseMover ( KinaseMover const & )

default

Copy constructor.

◆ ~KinaseMover()

protocols::enzymatic_movers::KinaseMover::~KinaseMover ( )

overridedefault

Member Function Documentation

◆ clone()

moves::MoverOP protocols::enzymatic_movers::KinaseMover::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.

Implements protocols::enzymatic_movers::EnzymaticMover.

◆ fresh_instance()

moves::MoverOP protocols::enzymatic_movers::KinaseMover::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.

Implements protocols::enzymatic_movers::EnzymaticMover.

◆ get_name()

std::string protocols::enzymatic_movers::KinaseMover::get_name ( ) const

overridevirtual

Return the name of the Mover.

Implements protocols::enzymatic_movers::EnzymaticMover.

References mover_name().

◆ mover_name()

static std::string protocols::enzymatic_movers::KinaseMover::mover_name ( )

inlinestatic

Referenced by get_name(), protocols::enzymatic_movers::KinaseMoverCreator::keyname(), provide_citation_info(), and provide_xml_schema().

◆ perform_reaction()

void protocols::enzymatic_movers::KinaseMover::perform_reaction	(	core::pose::Pose &	input_pose,
		core::uint const	site,
		std::string const &	cosubstrate
	)

overrideprotectedvirtual

Actually perform the virtual reaction for this specific EnzymaticMover. @params <input_pose>: The Pose to be acted on. @params <site>: An index for the reactive site to be acted on. @params <cosubstrate>: A string providing information to the Enzymatic Mover to add or subtract the proper atoms or Residues from the Pose. How this parameter is handled is specific to each distinct EnzymaticMover.

Implements protocols::enzymatic_movers::EnzymaticMover.

References core::pose::add_variant_type_to_pose_residue(), protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_sequence_position(), and core::chemical::PHOSPHORYLATION.