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Rosetta
2020.11
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Rosetta
2020.11
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#include <KinaseMover.hh>
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... | |
| 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... | |
 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, 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... | |
| 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 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. <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::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 protocols::filters::Filters_map | Filters_map |
| typedef std::list< std::string > | Strings |
This Mover simulates the activity of a virtual kinase enzyme on a Pose by phosphorylating a residue at a biologically relevant sequon position.
| protocols::enzymatic_movers::KinaseMover::KinaseMover | ( | ) |
Default constructor.
References protocols::moves::Mover::type().
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default |
Copy constructor.
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overridedefault |
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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.
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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.
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overridevirtual |
Return the name of the Mover.
Implements protocols::enzymatic_movers::EnzymaticMover.
References mover_name().
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inlinestatic |
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overridevirtual |
Does this EnzymaticMover provide information about how to cite it?
Reimplemented from protocols::enzymatic_movers::EnzymaticMover.
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overrideprotectedvirtual |
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.
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.
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overridevirtual |
Provide a list of authors and their e-mail addresses, as strings.
Reimplemented from protocols::enzymatic_movers::EnzymaticMover.
References mover_name().
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static |
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static |
Register options with the option system.
References protocols::enzymatic_movers::EnzymaticMover::register_options().
1.8.7