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protocols::calc_taskop_movers::CreateSequenceMotifMover Class Reference

Simple mover to Create a sequence motif in a region of protein using the SequenceMotifTaskOperation. Uses psueo-regular expressions to define the motif. More...

#include <CreateSequenceMotifMover.hh>

Inheritance diagram for protocols::calc_taskop_movers::CreateSequenceMotifMover:
Inheritance graph
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Public Member Functions

 CreateSequenceMotifMover ()
 Constructors ///. More...
 
 CreateSequenceMotifMover (core::select::residue_selector::ResidueSelectorCOP selector)
 
 CreateSequenceMotifMover (CreateSequenceMotifMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~CreateSequenceMotifMover () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
void set_motif (std::string motif)
 Set a string that tells this operation how to design. More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 Set a residue selector where each position returned from the selector is a place in which we create the motif. More...
 
void set_pack_neighbors (bool pack_neighbors)
 Should we pack neighbors? Default True. More...
 
void set_design_neighbors (bool design_neighbors)
 Should we design neighbors? Default False. More...
 
void set_neighbor_distance (core::Real neighbor_distance)
 Set the distance for any neighbor packing set. Default is 6A. More...
 
void set_score_function (core::scoring::ScoreFunctionCOP scorefxn)
 
void set_pack_rounds (core::Size pack_rounds)
 Set the number of packing/design rounds. Default is 5! More...
 
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Rosetta Scripts Support ///. More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool mover_provides_citation_info () const override
 Does this mover 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...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Although this mover is unpublished and provides no citation info of its own, it can provide citation info for modules that it calls. 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor 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 std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

void initialize_objects (core::pose::Pose &pose)
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_ = nullptr
 
std::string motif_
 
bool pack_neighbors_ = true
 
bool design_neighbors_ = false
 
core::Real pack_distance_ = 6.0
 
core::pack::task::TaskFactoryOP tf_ = nullptr
 
utility::vector1
< core::pack::task::operation::OperateOnResidueSubsetOP
neighbor_operations_
 
core::pack::task::operation::InitializeFromCommandlineOP cmd_line_operation_ = nullptr
 
protocols::task_operations::SequenceMotifTaskOperationOP motif_operation_ = nullptr
 
core::scoring::ScoreFunctionCOP scorefxn_ = nullptr
 
core::Size pack_rounds_ = 5
 

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
 
- 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...
 

Detailed Description

Simple mover to Create a sequence motif in a region of protein using the SequenceMotifTaskOperation. Uses psueo-regular expressions to define the motif.

Simply calls the packer using the operation, optionally packing neighbor residues as it does so. If you need something more complex, use the SequenceMotifTaskOperation directly.

MOTIF:

This is slightly similar to a regex, but not quite. We are not matching a sequence, we are designing in a motif regardless of the current sequence, anywhere in a protein.

EXAMPLE: Glycosylation N-Linked motif design: N[^P][ST]

Constructor & Destructor Documentation

protocols::calc_taskop_movers::CreateSequenceMotifMover::CreateSequenceMotifMover ( )

Constructors ///.

Default constructor

protocols::calc_taskop_movers::CreateSequenceMotifMover::CreateSequenceMotifMover ( core::select::residue_selector::ResidueSelectorCOP  selector)
protocols::calc_taskop_movers::CreateSequenceMotifMover::CreateSequenceMotifMover ( CreateSequenceMotifMover const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References neighbor_operations_, scorefxn_, and selector_.

protocols::calc_taskop_movers::CreateSequenceMotifMover::~CreateSequenceMotifMover ( )
override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::calc_taskop_movers::CreateSequenceMotifMover::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::calc_taskop_movers::CreateSequenceMotifMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::calc_taskop_movers::CreateSequenceMotifMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::calc_taskop_movers::CreateSequenceMotifMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::calc_taskop_movers::CreateSequenceMotifMover::initialize_objects ( core::pose::Pose pose)
private
std::string protocols::calc_taskop_movers::CreateSequenceMotifMover::mover_name ( )
static
bool protocols::calc_taskop_movers::CreateSequenceMotifMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Reimplemented from protocols::moves::Mover.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References design_neighbors_, motif_, pack_distance_, pack_neighbors_, pack_rounds_, core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), scorefxn_, and selector_.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

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

Reimplemented from protocols::moves::Mover.

References mover_name(), and selector_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_citation_info ( ) const
overridevirtual

Although this mover is unpublished and provides no citation info of its own, it can provide citation info for modules that it calls.

Reimplemented from protocols::moves::Mover.

References selector_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::calc_taskop_movers::CreateSequenceMotifMover::set_design_neighbors ( bool  design_neighbors)

Should we design neighbors? Default False.

References design_neighbors_, and neighbor_operations_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::set_motif ( std::string  motif)

Set a string that tells this operation how to design.

This is slightly similar to a regex, but not quite. We are not matching a sequence, we are designing in a motif regardless of the current sequence, anywhere in a protein.

  • Each letter corresponds to a position. Using [ ] indicates a more complicated expression for that position.
  • An X indicates it can be anything, and that we are designing here.
  • An AA Letter, like V, indicates that that position will be designed to a V.
  • A - charactor indicates that that position stays with whatever it is currently. We essentially skip this position.
  • An expression like: [^PAV] indicates that we will design anything except Proline, Alanine, and Valine
  • An expression like: [NTS] indicates that that position can be Asparigine, Threonine, or Serine and only of these will be enabled during the design.
  • RESFILE commands are accepted as well. A % is required in front of them. For example [POLAR] is totally cool. These are the same as in a resfile line.

EXAMPLE: Glycosylation N-Linked motif design: N[^P][ST]

References motif_, and neighbor_operations_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::set_neighbor_distance ( core::Real  neighbor_distance)

Set the distance for any neighbor packing set. Default is 6A.

References neighbor_operations_, and pack_distance_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::set_pack_neighbors ( bool  pack_neighbors)

Should we pack neighbors? Default True.

References neighbor_operations_, and pack_neighbors_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::set_pack_rounds ( core::Size  pack_rounds)

Set the number of packing/design rounds. Default is 5!

References pack_rounds_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

Set a residue selector where each position returned from the selector is a place in which we create the motif.

Mover Methods ///.

References neighbor_operations_, and selector_.

Referenced by CreateSequenceMotifMover().

void protocols::calc_taskop_movers::CreateSequenceMotifMover::set_score_function ( core::scoring::ScoreFunctionCOP  scorefxn)

References scorefxn_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

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

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

Member Data Documentation

core::pack::task::operation::InitializeFromCommandlineOP protocols::calc_taskop_movers::CreateSequenceMotifMover::cmd_line_operation_ = nullptr
private

Referenced by initialize_objects().

bool protocols::calc_taskop_movers::CreateSequenceMotifMover::design_neighbors_ = false
private
std::string protocols::calc_taskop_movers::CreateSequenceMotifMover::motif_
private
protocols::task_operations::SequenceMotifTaskOperationOP protocols::calc_taskop_movers::CreateSequenceMotifMover::motif_operation_ = nullptr
private

Referenced by initialize_objects().

utility::vector1< core::pack::task::operation::OperateOnResidueSubsetOP > protocols::calc_taskop_movers::CreateSequenceMotifMover::neighbor_operations_
private
core::Real protocols::calc_taskop_movers::CreateSequenceMotifMover::pack_distance_ = 6.0
private
bool protocols::calc_taskop_movers::CreateSequenceMotifMover::pack_neighbors_ = true
private
core::Size protocols::calc_taskop_movers::CreateSequenceMotifMover::pack_rounds_ = 5
private
core::scoring::ScoreFunctionCOP protocols::calc_taskop_movers::CreateSequenceMotifMover::scorefxn_ = nullptr
private
core::select::residue_selector::ResidueSelectorCOP protocols::calc_taskop_movers::CreateSequenceMotifMover::selector_ = nullptr
private
core::pack::task::TaskFactoryOP protocols::calc_taskop_movers::CreateSequenceMotifMover::tf_ = nullptr
private

Referenced by apply(), and initialize_objects().


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