Takes in multiple poses from the VectorPoseJobDistributor and finds the consensus sequence that optimizes energy of all input poses. Used in conjuction with MSDMover at the end of a protocol to make sure that you end up with one multistate solution. Only accessible through recon application. More...

#include <FindConsensusSequence.hh>

Inheritance diagram for protocols::recon_design::FindConsensusSequence:

[legend]

Public Member Functions
	FindConsensusSequence ()
	empty constructor More...

	~FindConsensusSequence () 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...

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...

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	pick_consensus_AA (core::Size res_link_index, utility::vector1< std::string > candidate_AAs)
	Based on all the input poses, find the optimal AA at position res_link_index. candidate_AAs specifies all of the AAs present in any of poses_ at position res_link_index. Fitness is defined implicitly as the sum of energy of all poses. More...

void	pick_consensus_AA_mpi (core::pose::Pose &pose, utility::vector1< std::string > candidate_AAs, core::Size pose_position)

void	initialize_packer ()
	Set up the packer to be used when substituting different candidate AAs and repacking before evaluating energy. More...

core::Real	test_AA (core::pose::PoseOP pose_copy, std::string trial_AA, core::Size pose_position)
	Place a candidate AA (trial_AA) onto a pose (pose_copy) at position pose_position and repack and measure the energy. Function returns the energy of that pose with the trial_AA. More...

core::scoring::ScoreFunctionOP	score_function () const
	Getters and setters. More...

void	score_function (core::scoring::ScoreFunctionOP)

core::pack::task::TaskFactoryOP	task_factory () const

void	task_factory (core::pack::task::TaskFactoryOP)

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

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 Attributes
core::scoring::ScoreFunctionOP	sfxn_
	Scorefunction to be used. More...

core::pack::task::TaskFactoryOP	task_factory_
	TaskFactory to specify tasks in repacking when substituting AAs. More...

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

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

minimization_packing::PackRotamersMoverOP	packer_
	Packer to be used when substituting AAs. More...

bool	debug_ = false
	Output extra debug messages. More...

core::Size	rank_ = 0
	Variables used in MPI. More...

core::Size	n_procs_ = 1

bool	master_ = false

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

Takes in multiple poses from the VectorPoseJobDistributor and finds the consensus sequence that optimizes energy of all input poses. Used in conjuction with MSDMover at the end of a protocol to make sure that you end up with one multistate solution. Only accessible through recon application.

Constructor & Destructor Documentation

◆ FindConsensusSequence()

protocols::recon_design::FindConsensusSequence::FindConsensusSequence ( )

empty constructor

Referenced by clone().

◆ ~FindConsensusSequence()

protocols::recon_design::FindConsensusSequence::~FindConsensusSequence ( )

override

Member Function Documentation

◆ apply()

void protocols::recon_design::FindConsensusSequence::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 designable_residues_, protocols::recon_design::find_pose_in_vector(), protocols::recon_design::get_candidate_AAs(), protocols::recon_design::get_designable_sequence(), parse_resfiles(), pick_consensus_AA(), and protocols::moves::VectorPoseMover::poses_.

◆ apply_mpi()

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

overridevirtual

Pure virtual method to apply this mover under MPI.

Implements protocols::moves::VectorPoseMover.

References debug_, protocols::recon_design::get_candidate_AAs(), protocols::recon_design::get_designable_residues(), protocols::recon_design::get_designable_sequence(), master_, protocols::wum::mpi_rank(), n_procs_, pick_consensus_AA_mpi(), rank_, resfile_at(), and protocols::recon_design::TR().

◆ clone()

moves::MoverOP protocols::recon_design::FindConsensusSequence::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 FindConsensusSequence().

◆ designable_residues()

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

References designable_residues_.

◆ fresh_instance()

moves::MoverOP protocols::recon_design::FindConsensusSequence::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::FindConsensusSequence::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::moves::VectorPoseMover.

◆ initialize_packer()

void protocols::recon_design::FindConsensusSequence::initialize_packer ( )

Set up the packer to be used when substituting different candidate AAs and repacking before evaluating energy.

Set up the packer to be used when substituting different candidate AAs and repacking before evaluating energy

References packer_, sfxn_, and task_factory_.

Referenced by pick_consensus_AA(), and pick_consensus_AA_mpi().

◆ parse_my_tag()

void protocols::recon_design::FindConsensusSequence::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

Read options from RosettaScripts.

Reimplemented from protocols::moves::Mover.

References debug_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), resfiles_, sfxn_, and task_factory_.

◆ parse_resfiles()

void protocols::recon_design::FindConsensusSequence::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)

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

Referenced by apply().

◆ pick_consensus_AA()

void protocols::recon_design::FindConsensusSequence::pick_consensus_AA	(	core::Size	str_position,
		utility::vector1< std::string >	candidate_AAs
	)

Based on all the input poses, find the optimal AA at position res_link_index. candidate_AAs specifies all of the AAs present in any of poses_ at position res_link_index. Fitness is defined implicitly as the sum of energy of all poses.

References debug_, designable_residues_, initialize_packer(), packer_, protocols::moves::VectorPoseMover::poses_, test_AA(), and protocols::recon_design::TR().

Referenced by apply().

◆ pick_consensus_AA_mpi()

void protocols::recon_design::FindConsensusSequence::pick_consensus_AA_mpi	(	core::pose::Pose &	pose,
		utility::vector1< std::string >	candidate_AAs,
		core::Size	pose_position
	)

Based on all the input poses, find the optimal AA at position res_link_index. candidate_AAs specifies all of the AAs present in any of poses_ at position res_link_index. Fitness is defined implicitly as the sum of energy of all poses.

References core::pose::Pose::clone(), debug_, initialize_packer(), master_, n_procs_, packer_, test_AA(), and protocols::recon_design::TR().

Referenced by apply_mpi().

◆ provide_xml_schema()

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

static

Specify XML schema.

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), protocols::recon_design::FindConsensusSequenceCreator::mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

◆ resfile_at()

std::string protocols::recon_design::FindConsensusSequence::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.

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(), and parse_resfiles().

◆ resfiles()

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

References resfiles_.

◆ score_function() [1/2]

core::scoring::ScoreFunctionOP protocols::recon_design::FindConsensusSequence::score_function ( ) const

Getters and setters.

References sfxn_.

◆ score_function() [2/2]

void protocols::recon_design::FindConsensusSequence::score_function ( core::scoring::ScoreFunctionOP sfxn )

References sfxn_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::recon_design::FindConsensusSequence::task_factory ( ) const

References task_factory_.

Referenced by task_factory().

◆ task_factory() [2/2]

void protocols::recon_design::FindConsensusSequence::task_factory ( core::pack::task::TaskFactoryOP task_factory )

References task_factory(), and task_factory_.

◆ test_AA()

core::Real protocols::recon_design::FindConsensusSequence::test_AA	(	core::pose::PoseOP	pose_copy,
		std::string	trial_AA,
		core::Size	pose_position
	)

Place a candidate AA (trial_AA) onto a pose (pose_copy) at position pose_position and repack and measure the energy. Function returns the energy of that pose with the trial_AA.

Place a candidate AA (trial_AA) onto a pose (pose_copy) at position pose_position and repack and measure the energy. Function returns the energy of that pose with the trial_AA

References debug_, packer_, sfxn_, and protocols::recon_design::TR().

Referenced by pick_consensus_AA(), and pick_consensus_AA_mpi().

Member Data Documentation

◆ debug_

bool protocols::recon_design::FindConsensusSequence::debug_ = false

private

Output extra debug messages.

Referenced by apply_mpi(), parse_my_tag(), pick_consensus_AA(), pick_consensus_AA_mpi(), and test_AA().

◆ designable_residues_

utility::vector1< utility::vector1< core::Size > > protocols::recon_design::FindConsensusSequence::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(), parse_resfiles(), and pick_consensus_AA().

◆ master_

bool protocols::recon_design::FindConsensusSequence::master_ = false

private

Referenced by apply_mpi(), and pick_consensus_AA_mpi().

◆ n_procs_

core::Size protocols::recon_design::FindConsensusSequence::n_procs_ = 1

private

Referenced by apply_mpi(), and pick_consensus_AA_mpi().

◆ packer_

minimization_packing::PackRotamersMoverOP protocols::recon_design::FindConsensusSequence::packer_

private

Packer to be used when substituting AAs.

Referenced by initialize_packer(), pick_consensus_AA(), pick_consensus_AA_mpi(), and test_AA().

◆ rank_

core::Size protocols::recon_design::FindConsensusSequence::rank_ = 0

private

Variables used in MPI.

Referenced by apply_mpi().

◆ resfiles_

utility::vector1< std::string > protocols::recon_design::FindConsensusSequence::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().

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::recon_design::FindConsensusSequence::sfxn_

private

Scorefunction to be used.

Referenced by initialize_packer(), parse_my_tag(), score_function(), and test_AA().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::recon_design::FindConsensusSequence::task_factory_

private

TaskFactory to specify tasks in repacking when substituting AAs.

Referenced by initialize_packer(), parse_my_tag(), and task_factory().

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

src/protocols/recon_design/FindConsensusSequence.hh
src/protocols/recon_design/FindConsensusSequence.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FindConsensusSequence()

◆ ~FindConsensusSequence()

Member Function Documentation

◆ apply()

◆ apply_mpi()

◆ clone()

◆ designable_residues()

◆ fresh_instance()

◆ get_name()

◆ initialize_packer()

◆ parse_my_tag()

◆ parse_resfiles()

◆ pick_consensus_AA()

◆ pick_consensus_AA_mpi()

◆ provide_xml_schema()

◆ resfile_at()

◆ resfiles()

◆ score_function() [1/2]

◆ score_function() [2/2]

◆ task_factory() [1/2]

◆ task_factory() [2/2]

◆ test_AA()

Member Data Documentation

◆ debug_

◆ designable_residues_

◆ master_

◆ n_procs_

◆ packer_

◆ rank_

◆ resfiles_

◆ sfxn_

◆ task_factory_