Multistate design mover used for RECON multistate design Takes in multiple poses, applies residue linking constraints based on sequence of all input poses and runs a design submover that has been specified in the tag Only accessible through recon application. More...

#include <MSDMover.hh>

Inheritance diagram for protocols::recon_design::MSDMover:

[legend]

Public Member Functions
	MSDMover ()
	empty constructor fills values with the values read in from the commandline More...

	MSDMover (protocols::moves::MoverOP mover, utility::vector1< std::string > const &resfiles)
	Constructor takes in the design mover and a list of resfiles that specifies the residues to constrain to one another. More...

	~MSDMover () override

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...

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

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	Read options from RosettaScripts. More...

void	apply (Pose &pose) override
	Movers derived from VectorPoseMover must define two apply methods: apply and apply_mpi, depending on whether the protocol is run in MPI or not Running in MPI will distribute each pose to a separate node, so the mover will operate on one pose. More...

void	apply_mpi (Pose &pose) override
	Pure virtual method to apply this mover under MPI. More...

utility::vector1< core::scoring::constraints::ConstraintCOP >	apply_linked_constraints (Pose &pose, utility::vector1< std::string > other_pose_sequences, utility::vector1< core::Size > my_designable_residues)
	Based on the sequence of the other poses, apply a residue type constraint to encourage poses to adopt same sequence. Returns a COP of the constraints that were applied so they can be removed later. More...

void	setup_mover (Pose &pose)
	Initialize mover by checking that input poses were passed correctly, a design mover was specified, and finding the pose given to apply() in the poses_ vector. More...

moves::MoverOP	design_mover ()
	Getters and setters. More...

void	design_mover (moves::MoverOP design_mover)

utility::vector1< std::string >	resfiles ()

void	resfiles (utility::vector1< std::string > resfiles)

void	weight (core::Real weight)

core::Real	weight ()

utility::vector1< utility::vector1< core::Size > >	designable_residues ()

Public Member Functions inherited from protocols::moves::VectorPoseMover
	VectorPoseMover ()
	Constructor. More...

	~VectorPoseMover () override

	VectorPoseMover (std::string const &name)

	VectorPoseMover (VectorPoseMover const &other)

void	set_poses (utility::vector1< core::pose::PoseOP > const &poses)
	Set the vector of poses for the mover to act upon. 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 void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Specify XML schema. More...

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	parse_resfiles ()
	Populates designable_residues_ with a list of designable residues corresponding to the poses in poses_, corresponding element-wise (designables_residues[0] matches to poses_[0], etc) More...

void	update_packer_task ()
	The design mover can't be given its task operations on a global level in the RosettaScript, bc each of the input poses can have different designable residues. This function assigns the design mover its tasks based on the designable residues of the current pose. More...

void	set_current_pose (core::Size current_pose)
	Assign the index of the pose that will be operated on by the current mover. More...

std::string	resfile_at (core::Size index)
	Get the resfile corresponding to the pose at index. If only one resfile is present then it will be returned regardless of the value of index. More...

void	run_post_design_mover (core::pose::Pose &pose)
	Runs the post design mover, if present. More...

Private Attributes
protocols::moves::MoverOP	design_mover_
	Private class members. More...

protocols::moves::MoverOP	post_mover_
	Mover applied after design. More...

utility::vector1< std::string >	resfiles_
	List of resfile file names, must be either 1 resfile, or same length as poses_. More...

core::Real	weight_
	Weight to give the residue linking constraints. More...

core::Size	current_pose_
	Index of the pose to be designed. More...

utility::vector1< utility::vector1< core::Size > >	designable_residues_

bool	debug_
	Output extra debug messages. More...

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...

Protected Attributes inherited from protocols::moves::VectorPoseMover
utility::vector1< core::pose::PoseOP >	poses_
	Vector of all the input poses. More...

Detailed Description

Multistate design mover used for RECON multistate design Takes in multiple poses, applies residue linking constraints based on sequence of all input poses and runs a design submover that has been specified in the tag Only accessible through recon application.

Constructor & Destructor Documentation

◆ MSDMover() [1/2]

protocols::recon_design::MSDMover::MSDMover ( )

empty constructor fills values with the values read in from the commandline

Referenced by clone().

◆ MSDMover() [2/2]

protocols::recon_design::MSDMover::MSDMover	(	protocols::moves::MoverOP	mover,
		utility::vector1< std::string > const &	resfiles
	)

Constructor takes in the design mover and a list of resfiles that specifies the residues to constrain to one another.

◆ ~MSDMover()

protocols::recon_design::MSDMover::~MSDMover ( )

override

Member Function Documentation

◆ apply()

void protocols::recon_design::MSDMover::apply ( Pose & pose )

overridevirtual

Movers derived from VectorPoseMover must define two apply methods: apply and apply_mpi, depending on whether the protocol is run in MPI or not Running in MPI will distribute each pose to a separate node, so the mover will operate on one pose.

Implements protocols::moves::VectorPoseMover.

References apply_linked_constraints(), core::pose::Pose::constraint_set(), current_pose_, debug_, design_mover_, designable_residues_, core::pose::Pose::energies(), protocols::recon_design::get_designable_sequence(), protocols::moves::VectorPoseMover::poses_, core::pose::Pose::remove_constraints(), core::scoring::res_type_constraint, run_post_design_mover(), setup_mover(), core::scoring::Energies::total_energy(), protocols::recon_design::TR(), and core::scoring::Energies::weights().

◆ apply_linked_constraints()

utility::vector1< core::scoring::constraints::ConstraintCOP > protocols::recon_design::MSDMover::apply_linked_constraints	(	Pose &	pose,
		utility::vector1< std::string >	other_pose_sequences,
		utility::vector1< core::Size >	my_designable_residues
	)

Based on the sequence of the other poses, apply a residue type constraint to encourage poses to adopt same sequence. Returns a COP of the constraints that were applied so they can be removed later.

Based on the sequence of the other poses, apply a residue type constraint to encourage poses to adopt same sequence. Returns a COP of the constraints that were applied so they can be removed later

References core::pose::Pose::add_constraint(), debug_, protocols::recon_design::get_candidate_AAs(), protocols::recon_design::TR(), and weight_.

Referenced by apply(), and apply_mpi().

◆ apply_mpi()

void protocols::recon_design::MSDMover::apply_mpi ( Pose & pose )

overridevirtual

Pure virtual method to apply this mover under MPI.

Implements protocols::moves::VectorPoseMover.

References apply_linked_constraints(), current_pose_, debug_, design_mover_, core::pose::Pose::energies(), protocols::recon_design::get_designable_residues(), protocols::recon_design::get_designable_sequence(), protocols::wum::mpi_rank(), core::pose::Pose::remove_constraints(), core::scoring::res_type_constraint, resfile_at(), run_post_design_mover(), core::scoring::Energies::total_energy(), protocols::recon_design::TR(), update_packer_task(), and core::scoring::Energies::weights().

◆ clone()

moves::MoverOP protocols::recon_design::MSDMover::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.

References MSDMover().

◆ design_mover() [1/2]

moves::MoverOP protocols::recon_design::MSDMover::design_mover ( )

Getters and setters.

References design_mover_.

Referenced by design_mover().

◆ design_mover() [2/2]

void protocols::recon_design::MSDMover::design_mover ( moves::MoverOP design_mover )

References design_mover(), and design_mover_.

◆ designable_residues()

utility::vector1< utility::vector1< core::Size > > protocols::recon_design::MSDMover::designable_residues ( )

References designable_residues_.

◆ fresh_instance()

moves::MoverOP protocols::recon_design::MSDMover::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.

◆ get_name()

std::string protocols::recon_design::MSDMover::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::moves::VectorPoseMover.

References protocols::recon_design::MSDMoverCreator::mover_name().

◆ parse_my_tag()

void protocols::recon_design::MSDMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Read options from RosettaScripts.

Reimplemented from protocols::moves::Mover.

References debug_, design_mover_, protocols::rosetta_scripts::parse_mover(), post_mover_, resfiles_, and weight_.

◆ parse_resfiles()

void protocols::recon_design::MSDMover::parse_resfiles ( )

private

Populates designable_residues_ with a list of designable residues corresponding to the poses in poses_, corresponding element-wise (designables_residues[0] matches to poses_[0], etc)

References designable_residues_, protocols::recon_design::get_designable_residues(), protocols::moves::VectorPoseMover::poses_, and resfile_at().

Referenced by setup_mover().

◆ provide_xml_schema()

void protocols::recon_design::MSDMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Specify XML schema.

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

Referenced by protocols::recon_design::MSDMoverCreator::provide_xml_schema().

◆ resfile_at()

std::string protocols::recon_design::MSDMover::resfile_at ( core::Size index )

private

Get the resfile corresponding to the pose at index. If only one resfile is present then it will be returned regardless of the value of index.

References resfiles_.

Referenced by apply_mpi(), parse_resfiles(), and update_packer_task().

◆ resfiles() [1/2]

utility::vector1< std::string > protocols::recon_design::MSDMover::resfiles ( )

References resfiles_.

Referenced by resfiles().

◆ resfiles() [2/2]

void protocols::recon_design::MSDMover::resfiles ( utility::vector1< std::string > resfiles )

References resfiles(), and resfiles_.

◆ run_post_design_mover()

void protocols::recon_design::MSDMover::run_post_design_mover ( core::pose::Pose & pose )

private

Runs the post design mover, if present.

References post_mover_, and protocols::recon_design::TR().

Referenced by apply(), and apply_mpi().

◆ set_current_pose()

void protocols::recon_design::MSDMover::set_current_pose ( core::Size current_pose )

private

Assign the index of the pose that will be operated on by the current mover.

References current_pose_.

◆ setup_mover()

void protocols::recon_design::MSDMover::setup_mover ( Pose & pose )

Initialize mover by checking that input poses were passed correctly, a design mover was specified, and finding the pose given to apply() in the poses_ vector.

Helper functions.

Initialize mover by checking that input poses were passed correctly, a design mover was specified, and finding the pose given to apply() in the poses_ vector

References current_pose_, design_mover_, protocols::recon_design::find_pose_in_vector(), parse_resfiles(), protocols::moves::VectorPoseMover::poses_, and update_packer_task().

Referenced by apply().

◆ update_packer_task()

void protocols::recon_design::MSDMover::update_packer_task ( )

private

The design mover can't be given its task operations on a global level in the RosettaScript, bc each of the input poses can have different designable residues. This function assigns the design mover its tasks based on the designable residues of the current pose.

The design mover can't be given its task operations on a global level in the RosettaScript, bc each of the input poses can have different designable residues. This function assigns the design mover its tasks based on the designable residues of the current pose

References current_pose_, design_mover_, and resfile_at().

Referenced by apply_mpi(), and setup_mover().

◆ weight() [1/2]

core::Real protocols::recon_design::MSDMover::weight ( )

References weight_.

Referenced by weight().

◆ weight() [2/2]

void protocols::recon_design::MSDMover::weight ( core::Real weight )

References weight(), and weight_.

Member Data Documentation

◆ current_pose_

core::Size protocols::recon_design::MSDMover::current_pose_

private

Index of the pose to be designed.

Referenced by apply(), apply_mpi(), set_current_pose(), setup_mover(), and update_packer_task().

◆ debug_

bool protocols::recon_design::MSDMover::debug_

private

Output extra debug messages.

Referenced by apply(), apply_linked_constraints(), apply_mpi(), and parse_my_tag().

◆ design_mover_

protocols::moves::MoverOP protocols::recon_design::MSDMover::design_mover_

private

Private class members.

Mover used for design. Typically a PackRotamersMover but not necessar

Referenced by apply(), apply_mpi(), design_mover(), parse_my_tag(), setup_mover(), and update_packer_task().

◆ designable_residues_

utility::vector1< utility::vector1< core::Size > > protocols::recon_design::MSDMover::designable_residues_

private

Vector of designable residues for each pose in poses_. Must be same length as poses_. Also each pose must have same number of designable residues (i.e. designable_residues[1].size() == designable_residues[2].size())

Referenced by apply(), designable_residues(), and parse_resfiles().

◆ post_mover_

protocols::moves::MoverOP protocols::recon_design::MSDMover::post_mover_

private

Mover applied after design.

Referenced by parse_my_tag(), and run_post_design_mover().

◆ resfiles_

utility::vector1< std::string > protocols::recon_design::MSDMover::resfiles_

private

List of resfile file names, must be either 1 resfile, or same length as poses_.

Referenced by parse_my_tag(), resfile_at(), and resfiles().

◆ weight_

core::Real protocols::recon_design::MSDMover::weight_

private

Weight to give the residue linking constraints.

Referenced by apply_linked_constraints(), parse_my_tag(), and weight().

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

src/protocols/recon_design/MSDMover.hh
src/protocols/recon_design/MSDMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MSDMover() [1/2]

◆ MSDMover() [2/2]

◆ ~MSDMover()

Member Function Documentation

◆ apply()

◆ apply_linked_constraints()

◆ apply_mpi()

◆ clone()

◆ design_mover() [1/2]

◆ design_mover() [2/2]

◆ designable_residues()

◆ fresh_instance()

◆ get_name()

◆ parse_my_tag()

◆ parse_resfiles()

◆ provide_xml_schema()

◆ resfile_at()

◆ resfiles() [1/2]

◆ resfiles() [2/2]

◆ run_post_design_mover()

◆ set_current_pose()

◆ setup_mover()

◆ update_packer_task()

◆ weight() [1/2]

◆ weight() [2/2]

Member Data Documentation

◆ current_pose_

◆ debug_

◆ design_mover_

◆ designable_residues_

◆ post_mover_

◆ resfiles_

◆ weight_