A class for generating a pose from a sequence/fasta. More...

#include <PoseFromSequenceMover.hh>

Inheritance diagram for protocols::pose_creation::PoseFromSequenceMover:

[legend]

Public Member Functions
	PoseFromSequenceMover ()
	Constructors ///. More...

	PoseFromSequenceMover (std::string const &sequence, std::string const &residue_type_set="fa_standard", bool const extended=false)
	Default constructor. More...

	PoseFromSequenceMover (PoseFromSequenceMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~PoseFromSequenceMover () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	show (std::ostream &output=std::cout) const override
	Show the contents of the Mover. More...

void	set_sequence (std::string const &)
	Mover Methods ///. More...

std::string const &	get_sequence () const

void	set_residue_type_set (std::string const &)

std::string const &	get_residue_type_set () const

void	set_extended (bool const)

bool	get_extended () const

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. More...

PoseFromSequenceMover &	operator= (PoseFromSequenceMover const &src)

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...

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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 Attributes
std::string	sequence_

std::string	residue_type_set_

bool	extended_

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

A class for generating a pose from a sequence/fasta.

Constructor & Destructor Documentation

◆ PoseFromSequenceMover() [1/3]

protocols::pose_creation::PoseFromSequenceMover::PoseFromSequenceMover ( )

Constructors ///.

Default constructor

◆ PoseFromSequenceMover() [2/3]

protocols::pose_creation::PoseFromSequenceMover::PoseFromSequenceMover	(	std::string const &	sequence,
		std::string const &	residue_type_set = `"fa_standard"`,
		bool const	extended = `false`
	)

Default constructor.

◆ PoseFromSequenceMover() [3/3]

protocols::pose_creation::PoseFromSequenceMover::PoseFromSequenceMover ( PoseFromSequenceMover const & src )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~PoseFromSequenceMover()

protocols::pose_creation::PoseFromSequenceMover::~PoseFromSequenceMover ( )

override

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

Member Function Documentation

◆ apply()

void protocols::pose_creation::PoseFromSequenceMover::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

Implements protocols::moves::Mover.

References core::pose::Pose::clear(), get_extended(), get_residue_type_set(), get_sequence(), core::pose::make_pose_from_sequence(), protocols::loops::set_extended_torsions_and_idealize_loops(), show(), and protocols::pose_creation::TR().

◆ clone()

protocols::moves::MoverOP protocols::pose_creation::PoseFromSequenceMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::pose_creation::PoseFromSequenceMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_extended()

bool protocols::pose_creation::PoseFromSequenceMover::get_extended ( ) const

References extended_.

Referenced by apply(), operator=(), parse_my_tag(), and show().

◆ get_name()

std::string protocols::pose_creation::PoseFromSequenceMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_residue_type_set()

std::string const & protocols::pose_creation::PoseFromSequenceMover::get_residue_type_set ( ) const

References residue_type_set_.

Referenced by apply(), operator=(), parse_my_tag(), and show().

◆ get_sequence()

std::string const & protocols::pose_creation::PoseFromSequenceMover::get_sequence ( ) const

References sequence_.

Referenced by apply(), operator=(), parse_my_tag(), and show().

◆ mover_name()

std::string protocols::pose_creation::PoseFromSequenceMover::mover_name ( )

static

Referenced by get_name(), protocols::pose_creation::PoseFromSequenceMoverCreator::keyname(), and provide_xml_schema().

◆ operator=()

PoseFromSequenceMover & protocols::pose_creation::PoseFromSequenceMover::operator= ( PoseFromSequenceMover const & src )

References get_extended(), get_residue_type_set(), get_sequence(), set_extended(), set_residue_type_set(), and set_sequence().

◆ parse_my_tag()

void protocols::pose_creation::PoseFromSequenceMover::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 get_extended(), get_residue_type_set(), get_sequence(), core::sequence::read_fasta_file(), set_extended(), set_residue_type_set(), set_sequence(), and protocols::pose_creation::TR().

◆ provide_xml_schema()

void protocols::pose_creation::PoseFromSequenceMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::pose_creation::PoseFromSequenceMoverCreator::provide_xml_schema().

◆ set_extended()

void protocols::pose_creation::PoseFromSequenceMover::set_extended ( bool const extended )

References extended_.

Referenced by operator=(), and parse_my_tag().

◆ set_residue_type_set()

void protocols::pose_creation::PoseFromSequenceMover::set_residue_type_set ( std::string const & residue_type_set )

References residue_type_set_.

Referenced by operator=(), and parse_my_tag().

◆ set_sequence()

void protocols::pose_creation::PoseFromSequenceMover::set_sequence ( std::string const & sequence )

Mover Methods ///.

References sequence_.

Referenced by operator=(), and parse_my_tag().

◆ show()

void protocols::pose_creation::PoseFromSequenceMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References get_extended(), get_residue_type_set(), get_sequence(), and protocols::moves::Mover::show().

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

Member Data Documentation

◆ extended_

bool protocols::pose_creation::PoseFromSequenceMover::extended_

private

Referenced by get_extended(), and set_extended().

◆ residue_type_set_

std::string protocols::pose_creation::PoseFromSequenceMover::residue_type_set_

private

Referenced by get_residue_type_set(), and set_residue_type_set().

◆ sequence_

std::string protocols::pose_creation::PoseFromSequenceMover::sequence_

private

Referenced by get_sequence(), and set_sequence().

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

src/protocols/pose_creation/PoseFromSequenceMover.hh
src/protocols/pose_creation/PoseFromSequenceMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PoseFromSequenceMover() [1/3]

◆ PoseFromSequenceMover() [2/3]

◆ PoseFromSequenceMover() [3/3]

◆ ~PoseFromSequenceMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_extended()

◆ get_name()

◆ get_residue_type_set()

◆ get_sequence()

◆ mover_name()

◆ operator=()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_extended()

◆ set_residue_type_set()

◆ set_sequence()

◆ show()

Member Data Documentation

◆ extended_

◆ residue_type_set_

◆ sequence_