#include <EnzymaticMover.hh>

Inheritance diagram for protocols::enzymatic_movers::EnzymaticMover:

Public Member Functions
	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...

std::string	get_name () const override=0
	Return the name of the Mover. More...

moves::MoverOP	clone () const override=0
	Return a clone of the Mover object. More...

moves::MoverOP	fresh_instance () const override=0
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &, moves::Movers_map const &, core::pose::Pose const &pose) 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...

bool	mover_provides_citation_info () const override
	Does this EnzymaticMover provide information about how to cite it? More...

utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const override
	Provide a list of authors and their e-mail addresses, as strings. 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...

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...

Static Public Member Functions
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	set_enzyme_family (std::string const &family_name)
	Set the family name of this simulated enzyme. More...

virtual void	perform_reaction (core::pose::Pose &input_pose, core::uint const site, std::string const &cosubstrate="")=0
	Actually perform the virtual reaction for this specific EnzymaticMover. <input_pose>: The Pose to be acted on. <site>: An index for the reactive site to be acted on. <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::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 Member Functions
void	set_commandline_options ()

void	init (std::string const &enzyme_family)

void	set_efficiency ()

void	set_available_co_substrates ()

Private Attributes
std::string	enzyme_family_ = ""

std::string	species_name_ = ""

std::string	enzyme_name_ = ""

core::Real	efficiency_ = 1.0

utility::vector1< core::uint >	excluded_sites_

utility::vector1< core::uint >	ensured_sites_

utility::vector1< ReactionSite >	reaction_sites_

utility::vector1< std::string >	co_substrates_

bool	performs_major_reaction_only_ = false

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 protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Detailed Description

This is a base class for any Mover that modifies the sequence of a Pose in a way that simulates the action of an enzyme. Any Mover inheriting from this base class must provide an enzyme family corresponding to a directory of enzyme data and must implement the perform_reaction() method, which modifies, adds, or removes (a) Residue(s). The core machinery of this base class uses the enzymatic data to search for potential reaction sites.

Constructor & Destructor Documentation

protocols::enzymatic_movers::EnzymaticMover::EnzymaticMover ( )

Default constructor.

References init().

protocols::enzymatic_movers::EnzymaticMover::EnzymaticMover ( std::string const & enzyme_family )

Constructor with enzyme family provided.

References init().

protocols::enzymatic_movers::EnzymaticMover::EnzymaticMover ( EnzymaticMover const & )

default

Copy constructor.

protocols::enzymatic_movers::EnzymaticMover::~EnzymaticMover ( )

overridedefault

Member Function Documentation

void protocols::enzymatic_movers::EnzymaticMover::apply ( core::pose::Pose & input_pose )

overridevirtual

Apply the corresponding move to <input_pose>.

When applied, every EnzymaticMover first obtains a list of all possible reaction sites, using enzyme data. Next, it loops through the sites and checks if they are ensured. If not, it decides whether or not to modify the site based on the enzymes efficiency, as recorded in the database. Then it performs the specific "reaction" of the particular EnzymaticMover at that site.

Parameters

<input_pose> the structure to be post-translationally modified, i.e., "substrate 1"

Implements protocols::moves::Mover.

References protocols::sparta::contains(), protocols::moves::FAIL_DO_NOT_RETRY, get_co_substrate(), get_efficiency(), get_ensured_sites(), get_enzyme(), get_n_co_substrates(), get_n_reactive_sites(), get_reactive_site_sequence_position(), perform_reaction(), performs_major_reaction_only(), core::scoring::rg, protocols::moves::Mover::set_last_move_status(), set_pose_reactive_sites(), show(), and protocols::TR().

moves::MoverOP protocols::enzymatic_movers::EnzymaticMover::clone ( ) const

overridepure virtual

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.

Implemented in protocols::enzymatic_movers::DNAMethyltransferaseMover, protocols::enzymatic_movers::GlycosyltransferaseMover, protocols::enzymatic_movers::KinaseMover, and protocols::enzymatic_movers::NTerminalAcetyltransferaseMover.

void protocols::enzymatic_movers::EnzymaticMover::ensure_site ( core::uint seqpos )

Definitely modify this site, if it is within a consensus sequence match for this enzyme.

References ensured_sites_.

void protocols::enzymatic_movers::EnzymaticMover::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.

References excluded_sites_.

moves::MoverOP protocols::enzymatic_movers::EnzymaticMover::fresh_instance ( ) const

overridepure virtual

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.

Implemented in protocols::enzymatic_movers::DNAMethyltransferaseMover, protocols::enzymatic_movers::GlycosyltransferaseMover, protocols::enzymatic_movers::KinaseMover, and protocols::enzymatic_movers::NTerminalAcetyltransferaseMover.

std::string const& protocols::enzymatic_movers::EnzymaticMover::get_co_substrate ( core::uint const index ) const

inline

Return the requested cosubstrate of this enzymatic reaction.

References co_substrates_.

Referenced by apply().

core::Real protocols::enzymatic_movers::EnzymaticMover::get_efficiency ( ) const

inline

Get the efficiency of this enzyme.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of the time.

References efficiency_.

Referenced by apply().

utility::vector1< core::uint > protocols::enzymatic_movers::EnzymaticMover::get_ensured_sites ( ) const

inline

Return a list of sequence positions that are guaranteed to be modified, if they are within a consensus sequence match for this enzyme.

References ensured_sites_.

Referenced by apply().

std::string protocols::enzymatic_movers::EnzymaticMover::get_enzyme ( ) const

inline

Return the specific name of this simulated enzyme.

References enzyme_name_.

Referenced by apply().

std::string protocols::enzymatic_movers::EnzymaticMover::get_enzyme_family ( ) const

inline

Get the family name of this simulated enzyme.

This EnzymaticMover is a member of this enyzme family.

References enzyme_family_.

utility::vector1< core::uint > protocols::enzymatic_movers::EnzymaticMover::get_excluded_sites ( ) const

inline

Return a list of sequence positions that are forbidden from being modified, even if they are within a consensus sequence match for this enzyme.

References excluded_sites_.

core::Size protocols::enzymatic_movers::EnzymaticMover::get_n_co_substrates ( ) const

inline

Return the current number of reactive sites.

References co_substrates_.

Referenced by apply(), and show().

core::Size protocols::enzymatic_movers::EnzymaticMover::get_n_reactive_sites ( ) const

inline

Return the current number of reactive sites.

References reaction_sites_.

Referenced by apply().

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

overridepure virtual

Return the name of the Mover.

Implements protocols::moves::Mover.

Implemented in protocols::enzymatic_movers::DNAMethyltransferaseMover, protocols::enzymatic_movers::GlycosyltransferaseMover, protocols::enzymatic_movers::KinaseMover, and protocols::enzymatic_movers::NTerminalAcetyltransferaseMover.

Referenced by provide_authorship_info_for_unpublished().

std::string const& protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_atom_name ( core::uint const index ) const

inline

Return the atom name of the requested reactive site.

References reaction_sites_.

Referenced by protocols::enzymatic_movers::GlycosyltransferaseMover::perform_reaction().

core::uint protocols::enzymatic_movers::EnzymaticMover::get_reactive_site_sequence_position ( core::uint const index ) const

inline

Return the sequence position of the requested reactive site.

References reaction_sites_.

Referenced by apply(), protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::perform_reaction(), protocols::enzymatic_movers::DNAMethyltransferaseMover::perform_reaction(), protocols::enzymatic_movers::GlycosyltransferaseMover::perform_reaction(), and protocols::enzymatic_movers::KinaseMover::perform_reaction().

std::string protocols::enzymatic_movers::EnzymaticMover::get_species ( ) const

inline

Get the species name of this simulated enzyme.

This EnzymaticMover is limited to reactions known to occur in the returned species.

References species_name_.

void protocols::enzymatic_movers::EnzymaticMover::init ( std::string const & enzyme_family )

private

References set_commandline_options(), set_enzyme_family(), and protocols::TR().

Referenced by EnzymaticMover().

bool protocols::enzymatic_movers::EnzymaticMover::mover_provides_citation_info ( ) const

overridevirtual

Does this EnzymaticMover provide information about how to cite it?

Returns: true

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::enzymatic_movers::GlycosyltransferaseMover, and protocols::enzymatic_movers::KinaseMover.

void protocols::enzymatic_movers::EnzymaticMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	filters,
		moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References perform_all_reactions(), perform_major_reaction_only(), set_efficiency(), set_enzyme(), and set_species().

void protocols::enzymatic_movers::EnzymaticMover::perform_all_reactions ( )

inline

Allow this EnzymaticMover to be promiscuous, performing a random transfer from among its possible co-substrates.

References performs_major_reaction_only_.

Referenced by parse_my_tag().

void protocols::enzymatic_movers::EnzymaticMover::perform_major_reaction_only ( )

inline

Set this EnzymaticMover to perform only its major reaction.

References performs_major_reaction_only_.

Referenced by parse_my_tag().

virtual void protocols::enzymatic_movers::EnzymaticMover::perform_reaction	(	core::pose::Pose &	input_pose,
		core::uint const	site,
		std::string const &	cosubstrate = `""`
	)

protectedpure virtual

Actually perform the virtual reaction for this specific EnzymaticMover. <input_pose>: The Pose to be acted on. <site>: An index for the reactive site to be acted on. <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.

Implemented in protocols::enzymatic_movers::GlycosyltransferaseMover, protocols::enzymatic_movers::KinaseMover, protocols::enzymatic_movers::DNAMethyltransferaseMover, and protocols::enzymatic_movers::NTerminalAcetyltransferaseMover.

Referenced by apply().

bool protocols::enzymatic_movers::EnzymaticMover::performs_major_reaction_only ( ) const

inline

Does this enzyme only perform its major reaction?

References performs_major_reaction_only_.

Referenced by apply().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::enzymatic_movers::EnzymaticMover::provide_authorship_info_for_unpublished ( ) const

overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::enzymatic_movers::GlycosyltransferaseMover, and protocols::enzymatic_movers::KinaseMover.

References get_name().

void protocols::enzymatic_movers::EnzymaticMover::register_options ( )

static

Register options with the option system.

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

Referenced by protocols::enzymatic_movers::DNAMethyltransferaseMover::register_options(), protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::register_options(), protocols::enzymatic_movers::KinaseMover::register_options(), and protocols::enzymatic_movers::GlycosyltransferaseMover::register_options().

void protocols::enzymatic_movers::EnzymaticMover::set_available_co_substrates ( )

private

References co_substrates_, enzyme_family_, enzyme_name_, core::enzymes::EnzymeManager::get_second_substrates_or_byproducts(), and species_name_.

Referenced by set_enzyme(), and set_species().

void protocols::enzymatic_movers::EnzymaticMover::set_commandline_options ( )

private

References set_efficiency(), set_enzyme(), and set_species().

Referenced by init().

void protocols::enzymatic_movers::EnzymaticMover::set_efficiency ( core::Real setting )

inline

Directly set the efficiency of this enzyme, ignoring whatever is in the database.

An efficiency of 0.45 means that this enzyme will perform its reaction at any recognized site 45% of the time.

References efficiency_.

void protocols::enzymatic_movers::EnzymaticMover::set_efficiency ( )

private

References efficiency_, enzyme_family_, enzyme_name_, core::enzymes::EnzymeManager::get_efficiency(), and species_name_.

Referenced by parse_my_tag(), set_commandline_options(), set_enzyme(), and set_species().

void protocols::enzymatic_movers::EnzymaticMover::set_ensured_sites ( utility::vector1< core::uint > const & ensured_sites )

inline

Pass a list of sequence positions that are guaranteed to be modified, if they are within a consensus sequence match for this enzyme.

References ensured_sites_.

void protocols::enzymatic_movers::EnzymaticMover::set_enzyme ( std::string const & enzyme_name )

Set the specific name of this simulated enzyme.

If set, this EnzymaticMover will use specific enzymatic details for this reaction from the database. If the species name has not been set, an enzyme from "h_sapiens" is assumed.

Parameters

<setting> An enzyme name as listed in an appropriate enzyme file in "database/virtual_enzymes/glycosyltransferases/<species_name_>/"

References enzyme_name_, set_available_co_substrates(), set_efficiency(), and species_name_.

Referenced by parse_my_tag(), and set_commandline_options().

void protocols::enzymatic_movers::EnzymaticMover::set_enzyme_family ( std::string const & family_name )

protected

Set the family name of this simulated enzyme.

This method is protected; it should only ever be called by a derived class.

References enzyme_family_.

Referenced by init().

void protocols::enzymatic_movers::EnzymaticMover::set_excluded_sites ( utility::vector1< core::uint > const & excluded_sites )

inline

Pass a list of sequence positions that are forbidden from being modified, even if they are within a consensus sequence match for this enzyme.

References excluded_sites_.

void protocols::enzymatic_movers::EnzymaticMover::set_pose_reactive_sites ( core::pose::Pose const & pose )

References protocols::sparta::contains(), enzyme_family_, enzyme_name_, excluded_sites_, core::conformation::Residue::name3(), reaction_sites_, core::pose::Pose::residue(), core::pose::Pose::size(), species_name_, and protocols::TR().

Referenced by apply().

void protocols::enzymatic_movers::EnzymaticMover::set_species ( std::string const & species_name )

Set the species name of this simulated enzyme.

Setting the species name limits the behavior of this EnzymaticMover to reactions known to occur in the given species.

Parameters

<setting> A species name in the format "e_coli" or "h_sapiens", which must correspond to a directory in the Rosetta database, e.g., "database/virtual_enzymes/glycosyltransferases/h_sapiens/"

References enzyme_name_, set_available_co_substrates(), set_efficiency(), and species_name_.

Referenced by parse_my_tag(), and set_commandline_options().

void protocols::enzymatic_movers::EnzymaticMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Generate string representation of EnzymaticMover for debugging purposes.

Reimplemented from protocols::moves::Mover.

References co_substrates_, efficiency_, ensured_sites_, enzyme_name_, excluded_sites_, get_n_co_substrates(), performs_major_reaction_only_, protocols::moves::Mover::show(), and species_name_.

Referenced by apply(), and protocols::enzymatic_movers::operator<<().

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::enzymatic_movers::EnzymaticMover::xml_schema_complex_type_generator ( )

static

References protocols::moves::complex_type_name_for_mover().

Referenced by protocols::enzymatic_movers::DNAMethyltransferaseMover::provide_xml_schema(), protocols::enzymatic_movers::NTerminalAcetyltransferaseMover::provide_xml_schema(), protocols::enzymatic_movers::KinaseMover::provide_xml_schema(), and protocols::enzymatic_movers::GlycosyltransferaseMover::provide_xml_schema().