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protocols::enzymatic_movers::EnzymaticMover Class Referenceabstract

#include <EnzymaticMover.hh>

Inheritance diagram for protocols::enzymatic_movers::EnzymaticMover:
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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) 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::uintget_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::uintget_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 Stringsinfo ()
 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::uintexcluded_sites_
 
utility::vector1< core::uintensured_sites_
 
utility::vector1< ReactionSitereaction_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 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
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
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
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 
)
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 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
void protocols::enzymatic_movers::EnzymaticMover::set_available_co_substrates ( )
private
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
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)
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
utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::enzymatic_movers::EnzymaticMover::xml_schema_complex_type_generator ( )
static

Member Data Documentation

utility::vector1< std::string > protocols::enzymatic_movers::EnzymaticMover::co_substrates_
private
core::Real protocols::enzymatic_movers::EnzymaticMover::efficiency_ = 1.0
private
utility::vector1< core::uint > protocols::enzymatic_movers::EnzymaticMover::ensured_sites_
private
std::string protocols::enzymatic_movers::EnzymaticMover::enzyme_family_ = ""
private
std::string protocols::enzymatic_movers::EnzymaticMover::enzyme_name_ = ""
private
utility::vector1< core::uint > protocols::enzymatic_movers::EnzymaticMover::excluded_sites_
private
bool protocols::enzymatic_movers::EnzymaticMover::performs_major_reaction_only_ = false
private
utility::vector1< ReactionSite > protocols::enzymatic_movers::EnzymaticMover::reaction_sites_
private
std::string protocols::enzymatic_movers::EnzymaticMover::species_name_ = ""
private

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