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:

[legend]

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...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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 Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor 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.

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. FOr example [POLAR] is totally cool. Separate these by commas.

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 )

References set_residue_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

Mover Methods ///.

Apply the mover.

Apply the mover

Implements protocols::moves::Mover.

References protocols::minimization_packing::PackRotamersMover::apply(), initialize_objects(), protocols::minimization_packing::PackRotamersMover::nloop(), pack_rounds_, scorefxn_, protocols::minimization_packing::PackRotamersMover::task_factory(), tf_, and protocols::calc_taskop_movers::TR().

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

Referenced by get_name(), protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator::keyname(), provide_citation_info(), and provide_xml_schema().

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_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References mover_name(), and selector_.

void protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_get_score_function_name(), core::select::residue_selector::attributes_for_parse_residue_selector(), core::sequence::get_design_sequence_motif_syntax(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::calc_taskop_movers::CreateSequenceMotifMoverCreator::provide_xml_schema().

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

Referenced by initialize_objects(), parse_my_tag(), and set_design_neighbors().

std::string protocols::calc_taskop_movers::CreateSequenceMotifMover::motif_

private

Referenced by initialize_objects(), parse_my_tag(), and set_motif().

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

Referenced by CreateSequenceMotifMover(), initialize_objects(), set_design_neighbors(), set_motif(), set_neighbor_distance(), set_pack_neighbors(), and set_residue_selector().

core::Real protocols::calc_taskop_movers::CreateSequenceMotifMover::pack_distance_ = 6.0

private

Referenced by initialize_objects(), parse_my_tag(), and set_neighbor_distance().

bool protocols::calc_taskop_movers::CreateSequenceMotifMover::pack_neighbors_ = true

private

Referenced by initialize_objects(), parse_my_tag(), and set_pack_neighbors().

core::Size protocols::calc_taskop_movers::CreateSequenceMotifMover::pack_rounds_ = 5

private

Referenced by apply(), parse_my_tag(), and set_pack_rounds().

core::scoring::ScoreFunctionCOP protocols::calc_taskop_movers::CreateSequenceMotifMover::scorefxn_ = nullptr

private

Referenced by apply(), CreateSequenceMotifMover(), initialize_objects(), parse_my_tag(), and set_score_function().

core::select::residue_selector::ResidueSelectorCOP protocols::calc_taskop_movers::CreateSequenceMotifMover::selector_ = nullptr

private

Referenced by CreateSequenceMotifMover(), initialize_objects(), parse_my_tag(), provide_citation_info(), and set_residue_selector().

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:

src/protocols/calc_taskop_movers/CreateSequenceMotifMover.hh
src/protocols/calc_taskop_movers/CreateSequenceMotifMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation