#include <MPMutateRelaxMover.hh>

Inheritance diagram for protocols::membrane::MPMutateRelaxMover:

[legend]

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

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

MPMutateRelaxMover &	operator= (MPMutateRelaxMover const &src)
	Assignment Operator. More...

	~MPMutateRelaxMover () override
	Destructor. More...

protocols::moves::MoverOP	clone () const override
	Rosetta Scripts Methods ///. 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
	Pase Rosetta Scripts Options for this Mover. More...

std::string	get_name () const override
	Mover Methods ///. More...

void	apply (core::pose::Pose &pose) override
	Mutate residue and then quick relax the membrane protein. 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...

Private Member Functions
void	register_options ()
	Setup Methods ///. More...

void	init_from_cmd ()
	Initialize from commandline. More...

void	get_repack_residues (Pose &pose)
	Get repack residues. More...

void	finalize_setup (Pose &pose)
	Finalize setup. More...

std::string	make_mutations (Pose &pose, core::Size num_construct)
	Make mutations. More...

std::string	output_filename (std::string mutation_tag, core::Size counter)
	Create output filename. More...

Private Attributes
core::scoring::ScoreFunctionOP	sfxn_
	Scorefunction. More...

std::string	mutant_file_
	Input file containing desired mutants to make. More...

utility::vector1< utility::vector1< char > >	wt_res_
	Wildtype residue. More...

utility::vector1< utility::vector1< core::Size > >	resn_
	Pose residue numbers to mutate. More...

utility::vector1< utility::vector1< char > >	mut_res_
	Residue identities to mutate into, three letter code. More...

core::Size	nstruct_
	Number of iterations the mover runs on the inside, i.e. number of output models (Mover doesn't run in JD2!) More...

std::string	protein_
	Protein name for dumping PDBs. More...

bool	repack_mutation_only_
	Repack? More...

core::Real	repack_radius_

utility::vector1< utility::vector1< bool > >	repack_residues_

bool	relax_
	Full relax? 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

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...

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...

Constructor & Destructor Documentation

◆ MPMutateRelaxMover() [1/2]

protocols::membrane::MPMutateRelaxMover::MPMutateRelaxMover ( )

Constructors ///.

Default Constructor for calls from JD2

Mutations will be read in by commandline

Default Constructor

Mutations will be read in by commandline

References init_from_cmd(), and register_options().

Referenced by operator=().

◆ MPMutateRelaxMover() [2/2]

protocols::membrane::MPMutateRelaxMover::MPMutateRelaxMover ( MPMutateRelaxMover const & src )

default

Copy Constructor.

Create a deep copy of this mover

◆ ~MPMutateRelaxMover()

protocols::membrane::MPMutateRelaxMover::~MPMutateRelaxMover ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

void protocols::membrane::MPMutateRelaxMover::apply ( core::pose::Pose & pose )

overridevirtual

Mutate residue and then quick relax the membrane protein.

Mover Methods ///.

Mutate residue and then range relax the membrane protein

Implements protocols::moves::Mover.

References core::pose::motif::a(), core::pose::Pose::dump_scored_pdb(), finalize_setup(), core::pose::Pose::fold_tree(), protocols::membrane::is_membrane_fixed(), make_mutations(), mut_res_, nstruct_, output_filename(), core::pack::pack_rotamers(), protocols::antibody::design::relax, relax_, protocols::antibody::design::repack, repack_mutation_only_, repack_radius_, repack_residues_, resn_, sfxn_, core::kinematics::FoldTree::show(), core::pose::Pose::size(), protocols::TR(), and wt_res_.

◆ clone()

protocols::moves::MoverOP protocols::membrane::MPMutateRelaxMover::clone ( ) const

overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

◆ finalize_setup()

void protocols::membrane::MPMutateRelaxMover::finalize_setup ( Pose & pose )

private

Finalize setup.

References protocols::relax::membrane::add_mutant_to_vectors(), protocols::relax::membrane::check_mutants_ok(), core::pose::Pose::conformation(), core::scoring::ScoreFunctionFactory::create_score_function(), get_repack_residues(), core::conformation::Conformation::is_membrane(), mut_res_, mutant_file_, resn_, sfxn_, protocols::TR(), and wt_res_.

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::membrane::MPMutateRelaxMover::fresh_instance ( ) const

overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::membrane::MPMutateRelaxMover::get_name ( ) const

overridevirtual

Mover Methods ///.

Get the name of this Mover (MPMutateRelaxMover)

Implements protocols::moves::Mover.

◆ get_repack_residues()

void protocols::membrane::MPMutateRelaxMover::get_repack_residues ( Pose & pose )

private

Get repack residues.

References core::pose::nres_protein(), repack_mutation_only_, repack_radius_, repack_residues_, core::pose::Pose::residue(), resn_, core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by finalize_setup().

◆ init_from_cmd()

void protocols::membrane::MPMutateRelaxMover::init_from_cmd ( )

private

Initialize from commandline.

References mutant_file_, nstruct_, protein_, protocols::antibody::design::relax, relax_, repack_mutation_only_, repack_radius_, and protocols::TR().

Referenced by MPMutateRelaxMover().

◆ make_mutations()

std::string protocols::membrane::MPMutateRelaxMover::make_mutations	(	Pose &	pose,
		core::Size	num_construct
	)

private

Make mutations.

Make mutations, returns string of output file.

References core::chemical::aa_from_oneletter_code(), mut_res_, protocols::ligand_docking::ga_ligand_dock::mutate(), core::chemical::name_from_aa(), resn_, core::id::to_string(), protocols::TR(), and wt_res_.

Referenced by apply().

◆ operator=()

MPMutateRelaxMover & protocols::membrane::MPMutateRelaxMover::operator= ( MPMutateRelaxMover const & src )

Assignment Operator.

References MPMutateRelaxMover().

◆ output_filename()

std::string protocols::membrane::MPMutateRelaxMover::output_filename	(	std::string	mutation_tag,
		core::Size	counter
	)

private

Create output filename.

References protocols::hybridization::path, protein_, and core::id::to_string().

Referenced by apply().

◆ parse_my_tag()

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

overridevirtual

Pase Rosetta Scripts Options for this Mover.

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

◆ register_options()

void protocols::membrane::MPMutateRelaxMover::register_options ( )

private

Setup Methods ///.

Register Options from Command Line

References protocols::antibody::design::relax.

Referenced by MPMutateRelaxMover().

Member Data Documentation

◆ mut_res_

utility::vector1< utility::vector1< char > > protocols::membrane::MPMutateRelaxMover::mut_res_

private

Residue identities to mutate into, three letter code.

Outer vector is different constructs, inner vector is multiple residues per construct

Referenced by apply(), finalize_setup(), and make_mutations().

◆ mutant_file_

std::string protocols::membrane::MPMutateRelaxMover::mutant_file_

private

Input file containing desired mutants to make.

Referenced by finalize_setup(), and init_from_cmd().

◆ nstruct_

core::Size protocols::membrane::MPMutateRelaxMover::nstruct_

private

Number of iterations the mover runs on the inside, i.e. number of output models (Mover doesn't run in JD2!)

Referenced by apply(), and init_from_cmd().

◆ protein_

std::string protocols::membrane::MPMutateRelaxMover::protein_

private

Protein name for dumping PDBs.

Referenced by init_from_cmd(), and output_filename().

◆ relax_

bool protocols::membrane::MPMutateRelaxMover::relax_

private

Full relax?

Referenced by apply(), and init_from_cmd().

◆ repack_mutation_only_

bool protocols::membrane::MPMutateRelaxMover::repack_mutation_only_

private

Repack?

Referenced by apply(), get_repack_residues(), and init_from_cmd().

◆ repack_radius_

core::Real protocols::membrane::MPMutateRelaxMover::repack_radius_

private

Referenced by apply(), get_repack_residues(), and init_from_cmd().

◆ repack_residues_

utility::vector1< utility::vector1< bool > > protocols::membrane::MPMutateRelaxMover::repack_residues_

private

Referenced by apply(), and get_repack_residues().

◆ resn_

utility::vector1< utility::vector1< core::Size > > protocols::membrane::MPMutateRelaxMover::resn_

private

Pose residue numbers to mutate.

Outer vector is different constructs, inner vector is multiple residues per construct

Referenced by apply(), finalize_setup(), get_repack_residues(), and make_mutations().

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::membrane::MPMutateRelaxMover::sfxn_

private

Scorefunction.

Referenced by apply(), and finalize_setup().

◆ wt_res_

utility::vector1< utility::vector1< char > > protocols::membrane::MPMutateRelaxMover::wt_res_

private

Wildtype residue.

Outer vector is different constructs, inner vector is multiple residues per construct

Referenced by apply(), finalize_setup(), and make_mutations().

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

src/protocols/relax/membrane/MPMutateRelaxMover.hh
src/protocols/relax/membrane/MPMutateRelaxMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MPMutateRelaxMover() [1/2]

◆ MPMutateRelaxMover() [2/2]

◆ ~MPMutateRelaxMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ finalize_setup()

◆ fresh_instance()

◆ get_name()

◆ get_repack_residues()

◆ init_from_cmd()

◆ make_mutations()

◆ operator=()

◆ output_filename()

◆ parse_my_tag()

◆ register_options()

Member Data Documentation

◆ mut_res_

◆ mutant_file_

◆ nstruct_

◆ protein_

◆ relax_

◆ repack_mutation_only_

◆ repack_radius_

◆ repack_residues_

◆ resn_

◆ sfxn_

◆ wt_res_