designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...

#include <LoopLengthChange.hh>

Inheritance diagram for protocols::protein_interface_design::movers::LoopLengthChange:

[legend]

Public Types
typedef core::pose::Pose	Pose

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

Public Member Functions
	LoopLengthChange ()

void	apply (Pose &pose) override

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

virtual	~LoopLengthChange ()

void	loop_start (core::pose::ResidueIndexDescriptionCOP loop_start)

void	loop_end (core::pose::ResidueIndexDescriptionCOP loop_end)

void	loop_cut (core::pose::ResidueIndexDescriptionCOP loop_cut)

void	loop_start (core::Size const loop_start)

void	loop_end (core::Size const loop_end)

void	loop_cut (core::Size const loop_cut)

void	restype_char (char const restype_char)

core::Size	loop_start (core::pose::Pose const &) const

core::Size	loop_end (core::pose::Pose const &) const

core::Size	loop_cut (core::pose::Pose const &) const

char	restype_char () const

void	delta (int const d)

void	tail (bool b)

int	delta () const

bool	direction ()

void	direction (bool b)

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 ()

	~Mover () override

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...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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 void	set_current_tag (std::string const &new_tag)

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

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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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 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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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
core::pose::ResidueIndexDescriptionCOP	loop_start_

core::pose::ResidueIndexDescriptionCOP	loop_end_

core::pose::ResidueIndexDescriptionCOP	loop_cut_

int	delta_

bool	tail_segment_

char	restype_char_ = 'A'

bool	direction_

Additional Inherited Members
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

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines.

Member Typedef Documentation

typedef core::pose::Pose protocols::protein_interface_design::movers::LoopLengthChange::Pose

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::LoopLengthChange::LoopLengthChange ( )

protocols::protein_interface_design::movers::LoopLengthChange::~LoopLengthChange ( )

virtualdefault

Member Function Documentation

void protocols::protein_interface_design::movers::LoopLengthChange::apply ( Pose & pose )

overridevirtual

Implements protocols::moves::Mover.

References core::chemical::aa_from_oneletter_code(), core::conformation::Conformation::append_polymer_residue_after_seqpos(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::delete_polymer_residue(), core::conformation::Conformation::delete_polymer_residue(), core::pose::Pose::delete_residue_slow(), delta(), direction(), core::sequence::end, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_jump_point(), loop_end(), loop_start(), core::chemical::name_from_aa(), core::pose::Pose::pdb_info(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::pose::Pose::residue_type_set_for_pose(), restype_char(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), protocols::loops::start, tail_segment_, protocols::protein_interface_design::movers::TR(), and core::pose::Pose::update_residue_neighbors().

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopLengthChange::clone ( ) const

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.

Reimplemented from protocols::moves::Mover.

void protocols::protein_interface_design::movers::LoopLengthChange::delta ( int const d )

References delta_.

Referenced by protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), protocols::splice::SpliceIn::set_loop_length_change(), and protocols::splice::SpliceOut::set_loop_length_change().

int protocols::protein_interface_design::movers::LoopLengthChange::delta ( ) const

References delta_.

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::LoopLengthChange::direction ( )

inline

References direction_.

Referenced by apply(), protocols::splice::SpliceInTail::set_loop_length_change(), and protocols::splice::SpliceOutTail::set_loop_length_change().

void protocols::protein_interface_design::movers::LoopLengthChange::direction ( bool b )

References protocols::match::upstream::b, and direction_.

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopLengthChange::fresh_instance ( ) const

inlineoverridevirtual

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.

Reimplemented from protocols::moves::Mover.

std::string protocols::protein_interface_design::movers::LoopLengthChange::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References protocols::protein_interface_design::movers::LoopLengthChangeCreator::mover_name().

void protocols::protein_interface_design::movers::LoopLengthChange::loop_cut ( core::pose::ResidueIndexDescriptionCOP loop_cut )

References loop_cut_.

void protocols::protein_interface_design::movers::LoopLengthChange::loop_cut ( core::Size const loop_cut )

References loop_cut_, and core::pose::make_rid_posenum().

core::Size protocols::protein_interface_design::movers::LoopLengthChange::loop_cut ( core::pose::Pose const & p ) const

References loop_cut_.

void protocols::protein_interface_design::movers::LoopLengthChange::loop_end ( core::pose::ResidueIndexDescriptionCOP loop_end )

References loop_end_.

Referenced by apply(), parse_my_tag(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), protocols::splice::SpliceIn::set_loop_length_change(), and protocols::splice::SpliceOut::set_loop_length_change().

void protocols::protein_interface_design::movers::LoopLengthChange::loop_end ( core::Size const loop_end )

References loop_end_, and core::pose::make_rid_posenum().

core::Size protocols::protein_interface_design::movers::LoopLengthChange::loop_end ( core::pose::Pose const & p ) const

References loop_end_.

void protocols::protein_interface_design::movers::LoopLengthChange::loop_start ( core::pose::ResidueIndexDescriptionCOP loop_start )

References loop_start_.

Referenced by apply(), protocols::splice::Splice::copy_stretch(), parse_my_tag(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), protocols::splice::SpliceIn::set_loop_length_change(), and protocols::splice::SpliceOut::set_loop_length_change().

void protocols::protein_interface_design::movers::LoopLengthChange::loop_start ( core::Size const loop_start )

References loop_start_, and core::pose::make_rid_posenum().

core::Size protocols::protein_interface_design::movers::LoopLengthChange::loop_start ( core::pose::Pose const & p ) const

References loop_start_.

std::string protocols::protein_interface_design::movers::LoopLengthChange::mover_name ( )

static

Referenced by provide_xml_schema().

void protocols::protein_interface_design::movers::LoopLengthChange::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References delta(), loop_end(), loop_end_, loop_start(), loop_start_, core::chemical::oneletter_code_specifies_aa(), core::pose::parse_resnum(), restype_char(), and protocols::protein_interface_design::movers::TR().

void protocols::protein_interface_design::movers::LoopLengthChange::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::protein_interface_design::movers::LoopLengthChangeCreator::provide_xml_schema().

void protocols::protein_interface_design::movers::LoopLengthChange::restype_char ( char const restype_char )

References restype_char(), and restype_char_.

char protocols::protein_interface_design::movers::LoopLengthChange::restype_char ( ) const

References restype_char_.

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

void protocols::protein_interface_design::movers::LoopLengthChange::tail ( bool b )

References protocols::match::upstream::b, and tail_segment_.

Referenced by protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), and protocols::splice::SpliceIn::set_loop_length_change().

Member Data Documentation

int protocols::protein_interface_design::movers::LoopLengthChange::delta_

private

Referenced by delta().

bool protocols::protein_interface_design::movers::LoopLengthChange::direction_

private

Referenced by direction().

core::pose::ResidueIndexDescriptionCOP protocols::protein_interface_design::movers::LoopLengthChange::loop_cut_

private

Referenced by loop_cut().

core::pose::ResidueIndexDescriptionCOP protocols::protein_interface_design::movers::LoopLengthChange::loop_end_

private

Referenced by loop_end(), and parse_my_tag().

core::pose::ResidueIndexDescriptionCOP protocols::protein_interface_design::movers::LoopLengthChange::loop_start_

private

Referenced by loop_start(), and parse_my_tag().

char protocols::protein_interface_design::movers::LoopLengthChange::restype_char_ = 'A'

private

Referenced by restype_char().

bool protocols::protein_interface_design::movers::LoopLengthChange::tail_segment_

private

Referenced by apply(), and tail().

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

src/protocols/protein_interface_design/movers/LoopLengthChange.hh
src/protocols/protein_interface_design/movers/LoopLengthChange.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation