Setup for MPDocking. More...

#include <MPDockingSetupMover.hh>

Inheritance diagram for protocols::docking::membrane::MPDockingSetupMover:

[legend]

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

	MPDockingSetupMover (MPDockingSetupMover const &src)
	Copy Constructor. More...

	~MPDockingSetupMover () override
	Destructor. More...

protocols::moves::MoverOP	clone () const override
	Create a Clone of this mover. More...

protocols::moves::MoverOP	fresh_instance () const override
	Create a Fresh Instance of this Mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Parse Rosetta Scripts Options for this Mover. More...

bool	get_optimize1 () const
	Get Methods ///. More...

bool	get_optimize2 () const
	get optimize1 More...

utility::vector1< core::pose::PoseOP >	get_poses () const
	get pose vector More...

utility::vector1< std::string >	get_spanfiles () const
	get spanfile vector More...

void	apply (Pose &pose) override
	Mover Methods ///. 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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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	read_poses ()

void	read_spanfiles ()

void	init_from_cmd ()

void	transform_pose_into_membrane (core::pose::Pose &pose, core::Vector center, core::Vector normal, std::string spanfile, core::Size partner)

Private Attributes
utility::vector1< core::pose::PoseOP >	poses_

utility::vector1< std::string >	spanfiles_

bool	optimize1_

bool	optimize2_

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

Setup for MPDocking.

Reads in 2 poses and 2 spanfiles, concatenates the poses and spanfiles and prints them out CURRENTLY ONLY WORKS FOR 2 POSES!!!

Constructor & Destructor Documentation

◆ MPDockingSetupMover() [1/2]

protocols::docking::membrane::MPDockingSetupMover::MPDockingSetupMover ( )

Constructors ///.

Default Constructor

◆ MPDockingSetupMover() [2/2]

protocols::docking::membrane::MPDockingSetupMover::MPDockingSetupMover ( MPDockingSetupMover const & src )

default

Copy Constructor.

◆ ~MPDockingSetupMover()

protocols::docking::membrane::MPDockingSetupMover::~MPDockingSetupMover ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

void protocols::docking::membrane::MPDockingSetupMover::apply ( Pose & pose )

overridevirtual

Mover Methods ///.

Create a new copy of this mover.

Get the name of this Mover (MPDockingSetupMover)

Reads in 2 poses and 2 spanfiles, concatenates the poses and spanfiles and prints them out

Return the Name of this mover (as seen by Rscripts)

Mover name for Rosetta Scripts Mover Methods ///

Get the name of this Mover (MPDockingSetupMover)

Add membrane components to the pose, then dock proteins along the flexible jump

Implements protocols::moves::Mover.

References core::pose::append_pose_to_pose(), protocols::toolbox::CA_superimpose(), core::conformation::membrane::center, core::pose::Pose::dump_pdb(), core::pose::Pose::fold_tree(), init_from_cmd(), protocols::membrane::is_membrane_fixed(), core::conformation::membrane::normal, poses_, read_poses(), read_spanfiles(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::membrane::reorder_membrane_foldtree(), core::kinematics::FoldTree::show(), spanfiles_, protocols::docking::TR(), and transform_pose_into_membrane().

◆ clone()

protocols::moves::MoverOP protocols::docking::membrane::MPDockingSetupMover::clone ( ) const

overridevirtual

Create a Clone of this mover.

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::docking::membrane::MPDockingSetupMover::fresh_instance ( ) const

overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::docking::membrane::MPDockingSetupMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_optimize1()

bool protocols::docking::membrane::MPDockingSetupMover::get_optimize1 ( ) const

Get Methods ///.

get optimize1

References optimize1_.

◆ get_optimize2()

bool protocols::docking::membrane::MPDockingSetupMover::get_optimize2 ( ) const

get optimize1

References optimize2_.

◆ get_poses()

utility::vector1< core::pose::PoseOP > protocols::docking::membrane::MPDockingSetupMover::get_poses ( ) const

get pose vector

References poses_.

◆ get_spanfiles()

utility::vector1< std::string > protocols::docking::membrane::MPDockingSetupMover::get_spanfiles ( ) const

get spanfile vector

References spanfiles_.

◆ init_from_cmd()

void protocols::docking::membrane::MPDockingSetupMover::init_from_cmd ( )

private

References optimize1_, and optimize2_.

Referenced by apply().

◆ mover_name()

std::string protocols::docking::membrane::MPDockingSetupMover::mover_name ( )

static

Referenced by get_name(), protocols::docking::membrane::MPDockingSetupMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::docking::membrane::MPDockingSetupMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References optimize1_, optimize2_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), poses_, and spanfiles_.

◆ provide_xml_schema()

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

static

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

Referenced by protocols::docking::membrane::MPDockingSetupMoverCreator::provide_xml_schema().

◆ read_poses()

void protocols::docking::membrane::MPDockingSetupMover::read_poses ( )

private

References core::import_pose::PDB_file, core::import_pose::pose_from_file(), and poses_.

Referenced by apply().

◆ read_spanfiles()

void protocols::docking::membrane::MPDockingSetupMover::read_spanfiles ( )

private

References core::conformation::membrane::spanfile_names(), and spanfiles_.

Referenced by apply().

◆ transform_pose_into_membrane()

void protocols::docking::membrane::MPDockingSetupMover::transform_pose_into_membrane	(	core::pose::Pose &	pose,
		core::Vector	center,
		core::Vector	normal,
		std::string	spanfile,
		core::Size	partner
	)

private

References core::conformation::membrane::center, core::conformation::membrane::normal, optimize1_, optimize2_, protocols::membrane::reorder_membrane_foldtree(), and protocols::docking::TR().

Referenced by apply().

Member Data Documentation

◆ optimize1_

bool protocols::docking::membrane::MPDockingSetupMover::optimize1_

private

Referenced by get_optimize1(), init_from_cmd(), parse_my_tag(), and transform_pose_into_membrane().

◆ optimize2_

bool protocols::docking::membrane::MPDockingSetupMover::optimize2_

private

Referenced by get_optimize2(), init_from_cmd(), parse_my_tag(), and transform_pose_into_membrane().

◆ poses_

utility::vector1< core::pose::PoseOP > protocols::docking::membrane::MPDockingSetupMover::poses_

private

Referenced by apply(), get_poses(), parse_my_tag(), and read_poses().

◆ spanfiles_

utility::vector1< std::string > protocols::docking::membrane::MPDockingSetupMover::spanfiles_

private

Referenced by apply(), get_spanfiles(), parse_my_tag(), and read_spanfiles().

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

src/protocols/docking/membrane/MPDockingSetupMover.hh
src/protocols/docking/membrane/MPDockingSetupMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MPDockingSetupMover() [1/2]

◆ MPDockingSetupMover() [2/2]

◆ ~MPDockingSetupMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ get_optimize1()

◆ get_optimize2()

◆ get_poses()

◆ get_spanfiles()

◆ init_from_cmd()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ read_poses()

◆ read_spanfiles()

◆ transform_pose_into_membrane()

Member Data Documentation

◆ optimize1_

◆ optimize2_

◆ poses_

◆ spanfiles_