Realign poses to sequences after losing pdb_info. More...

#include <AlignPDBInfoToSequences.hh>

Inheritance diagram for protocols::pdbinfo_manipulations::AlignPDBInfoToSequences:

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

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

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

AlignPDBInfoToSequences &	operator= (AlignPDBInfoToSequences const &src)
	= operator 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_target_sequences (utility::vector1< SequenceSpecification > const &target_sequences)

utility::vector1 < SequenceSpecification > const &	get_target_sequences () const

utility::vector1 < SequenceSpecification > &	get_target_sequences ()

void	set_mode (AlignPDBInfoToSequencesMode const &mode)

void	set_mode_from_string (std::string const &mode)

AlignPDBInfoToSequencesMode const &	get_mode () const

std::string	get_mode_as_string () const

void	set_throw_on_fail (bool const throw_on_fail)

bool	get_throw_on_fail () const

void	set_sequence_alignment_cut_max (core::Size const sequence_alignment_cut_max)

core::Size	get_sequence_alignment_cut_max () const

SequenceSpecification	parse_target_tag (utility::tag::TagCOP const &tag) const
	Rosetta Scripts Support ///. More...

void	load_json_file (std::string const &json_fn)
	Rosetta Scripts Support ///. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	parse XML tag (to use this Mover in Rosetta Scripts) 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...

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 Member Functions
void	apply_multi_sequence (core::pose::Pose &pose)
	This method tries to align every sequence of the pose to every target sequence by applying a SWAligner to them, and if we find a perfect alignment we use that target sequence as the reference. More...

void	apply_single_sequence (core::pose::Pose &pose)
	This method tries to align the pose to a target sequence that is generated by appending all target_sequences_ together. This allows for more residue-level control of the residue numbers/chainIDs but uses more memory (larger SWAligner). Most of the time you should probably use apply_multi_sequence, but sometimes you just crave that control!!! More...

Private Attributes
utility::vector1 < SequenceSpecification >	target_sequences_

AlignPDBInfoToSequencesMode	mode_

bool	throw_on_fail_ = false

core::Size	sequence_alignment_cut_max_ = 10

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

Realign poses to sequences after losing pdb_info.

Constructor & Destructor Documentation

protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::AlignPDBInfoToSequences ( )

Constructors ///.

Default constructor

protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::AlignPDBInfoToSequences ( AlignPDBInfoToSequences const & src )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::~AlignPDBInfoToSequences ( )

override

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

Member Function Documentation

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

Implements protocols::moves::Mover.

References apply_multi_sequence(), apply_single_sequence(), get_mode(), get_target_sequences(), protocols::pdbinfo_manipulations::multiple, core::pose::Pose::pdb_info(), protocols::pdbinfo_manipulations::single, throw_on_fail_, and protocols::TR().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence ( core::pose::Pose & pose )

private

This method tries to align every sequence of the pose to every target sequence by applying a SWAligner to them, and if we find a perfect alignment we use that target sequence as the reference.

Referenced by apply().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_single_sequence ( core::pose::Pose & pose )

private

This method tries to align the pose to a target sequence that is generated by appending all target_sequences_ together. This allows for more residue-level control of the residue numbers/chainIDs but uses more memory (larger SWAligner). Most of the time you should probably use apply_multi_sequence, but sometimes you just crave that control!!!

Mover Methods ///.

References core::sequence::SWAligner::align(), protocols::pdbinfo_manipulations::pad_sequences(), core::pose::Pose::pdb_info(), core::pose::Pose::sequence(), target_sequences_, and protocols::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

AlignPDBInfoToSequencesMode const& protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_mode ( ) const

inline

References mode_.

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

std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_mode_as_string ( ) const

References protocols::pdbinfo_manipulations::alignpdbinfotosequencesmode_to_string(), and get_mode().

std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_sequence_alignment_cut_max ( ) const

inline

References sequence_alignment_cut_max_.

utility::vector1<SequenceSpecification> const& protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_target_sequences ( ) const

inline

References target_sequences_.

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

utility::vector1<SequenceSpecification>& protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_target_sequences ( )

inline

References target_sequences_.

bool protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_throw_on_fail ( ) const

inline

References throw_on_fail_.

Referenced by operator=().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::load_json_file ( std::string const & json_fn )

Rosetta Scripts Support ///.

References core::sequence::end, and get_target_sequences().

Referenced by parse_my_tag().

std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::mover_name ( )

static

Referenced by get_name(), protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesCreator::keyname(), and provide_xml_schema().

AlignPDBInfoToSequences & protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::operator= ( AlignPDBInfoToSequences const & src )

= operator

References get_mode(), get_target_sequences(), get_throw_on_fail(), set_mode(), set_target_sequences(), and set_throw_on_fail().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References protocols::pdbinfo_manipulations::get_alignpdbinfotosequencesmode_from_string(), get_mode(), get_target_sequences(), load_json_file(), protocols::pdbinfo_manipulations::multiple, parse_target_tag(), set_mode(), set_sequence_alignment_cut_max(), set_throw_on_fail(), and protocols::pdbinfo_manipulations::single.

SequenceSpecification protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::parse_target_tag ( utility::tag::TagCOP const & tag ) const

Rosetta Scripts Support ///.

References protocols::kinmatch::str().

Referenced by parse_my_tag().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::pdbinfo_manipulations::AlignPDBInfoToSequences_namer(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesCreator::provide_xml_schema().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_mode ( AlignPDBInfoToSequencesMode const & mode )

inline

References mode_.

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

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_mode_from_string ( std::string const & mode )

References protocols::pdbinfo_manipulations::get_alignpdbinfotosequencesmode_from_string(), and set_mode().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_sequence_alignment_cut_max ( core::Size const sequence_alignment_cut_max )

inline

References sequence_alignment_cut_max_.

Referenced by parse_my_tag().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_target_sequences ( utility::vector1< SequenceSpecification > const & target_sequences )

inline

References target_sequences_.

Referenced by operator=().

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_throw_on_fail ( bool const throw_on_fail )

inline

References throw_on_fail_.

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

void protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::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::pdbinfo_manipulations::operator<<().

Member Data Documentation

AlignPDBInfoToSequencesMode protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::mode_

private

Referenced by get_mode(), and set_mode().

core::Size protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::sequence_alignment_cut_max_ = 10

private

Referenced by apply_multi_sequence(), get_sequence_alignment_cut_max(), and set_sequence_alignment_cut_max().

utility::vector1<SequenceSpecification> protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::target_sequences_

private

Referenced by apply_multi_sequence(), apply_single_sequence(), get_target_sequences(), and set_target_sequences().

bool protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::throw_on_fail_ = false

private

Referenced by apply(), apply_multi_sequence(), get_throw_on_fail(), and set_throw_on_fail().

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

src/protocols/pdbinfo_manipulations/AlignPDBInfoToSequences.hh
src/protocols/pdbinfo_manipulations/AlignPDBInfoToSequences.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