Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently). More...

#include <DockingInitialPerturbation.hh>

Inheritance diagram for protocols::docking::DockingSlideIntoContact:

[legend]

Public Member Functions
	DockingSlideIntoContact ()

	DockingSlideIntoContact (core::Size const rb_jump)

	DockingSlideIntoContact (core::Size const rb_jump, core::Vector const &slide_axis)

	DockingSlideIntoContact (core::Size const rb_jump, core::Vector const &slide_axis, core::scoring::ScoreFunctionCOP scorefxn, core::scoring::ScoreType scoretype_for_contact)

	DockingSlideIntoContact (core::Size const rb_jump, core::Vector const &slide_axis, core::scoring::ScoreFunctionCOP scorefxn, core::scoring::ScoreType scoretype_for_contact, core::Real threshold)

	~DockingSlideIntoContact () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

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 &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

void	set_use_delta (bool setting)

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

core::Size	get_jump_num () const

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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. 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...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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
bool	is_there_contact (core::Real current_score, core::Real last_score)

Private Attributes
core::Size	rb_jump_

core::Vector	slide_axis_

core::scoring::ScoreFunctionCOP	scorefxn_

core::scoring::ScoreType	scoretype_for_contact_

core::Real	threshold_

bool	use_delta_

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 protocols::filters::Filters_map	Filters_map

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

Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently).

Constructor & Destructor Documentation

protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact ( )

References core::scoring::CENTROID_WTS, core::scoring::DOCK_LOW_PATCH, core::scoring::interchain_vdw, rb_jump_, scorefxn_, scoretype_for_contact_, threshold_, and use_delta_.

protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact ( core::Size const rb_jump )

References core::scoring::CENTROID_WTS, core::scoring::DOCK_LOW_PATCH, core::scoring::interchain_vdw, scorefxn_, scoretype_for_contact_, threshold_, and use_delta_.

protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact	(	core::Size const	rb_jump,
		core::Vector const &	slide_axis
	)

References core::scoring::CENTROID_WTS, core::scoring::DOCK_LOW_PATCH, core::scoring::interchain_vdw, scorefxn_, scoretype_for_contact_, threshold_, and use_delta_.

protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact	(	core::Size const	rb_jump,
		core::Vector const &	slide_axis,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::scoring::ScoreType	scoretype_for_contact
	)

References threshold_, and use_delta_.

protocols::docking::DockingSlideIntoContact::DockingSlideIntoContact	(	core::Size const	rb_jump,
		core::Vector const &	slide_axis,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::scoring::ScoreType	scoretype_for_contact,
		core::Real	threshold
	)

References use_delta_.

protocols::docking::DockingSlideIntoContact::~DockingSlideIntoContact ( )

overridedefault

Member Function Documentation

void protocols::docking::DockingSlideIntoContact::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::membrane::geometry::EmbeddingDef::center(), core::pose::Pose::conformation(), core::pose::Pose::energies(), core::conformation::Conformation::is_membrane(), is_there_contact(), protocols::membrane::membrane_axis(), rb_jump_, scoretype_for_contact_, protocols::moves::Mover::set_current_tag(), slide_axis_, core::scoring::Energies::total_energies(), protocols::docking::TR(), and protocols::membrane::update_partner_embeddings().

Referenced by protocols::docking::DockingInitialPerturbation::apply_body(), and protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation().

protocols::moves::MoverOP protocols::docking::DockingSlideIntoContact::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.

protocols::moves::MoverOP protocols::docking::DockingSlideIntoContact::fresh_instance ( ) const

overridevirtual

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.

core::Size protocols::docking::DockingSlideIntoContact::get_jump_num ( ) const

inline

References rb_jump_.

Referenced by show().

std::string protocols::docking::DockingSlideIntoContact::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::docking::DockingSlideIntoContact::is_there_contact	(	core::Real	current_score,
		core::Real	last_score
	)

private

References threshold_, and use_delta_.

Referenced by apply().

std::string protocols::docking::DockingSlideIntoContact::mover_name ( )

static

Referenced by protocols::docking::DockingSlideIntoContactCreator::keyname(), and provide_xml_schema().

void protocols::docking::DockingSlideIntoContact::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 rb_jump_, and slide_axis_.

void protocols::docking::DockingSlideIntoContact::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::docking::DockingSlideIntoContactCreator::provide_xml_schema().

void protocols::docking::DockingSlideIntoContact::set_use_delta ( bool setting )

inline

References use_delta_.

void protocols::docking::DockingSlideIntoContact::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.