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protocols::membrane::MPMutateRelaxMover Class Reference

#include <MPMutateRelaxMover.hh>

Inheritance diagram for protocols::membrane::MPMutateRelaxMover:
Inheritance graph

Public Member Functions

 MPMutateRelaxMover ()
 Constructors ///. More...
 MPMutateRelaxMover (MPMutateRelaxMover const &src)
 Copy Constructor. More...
MPMutateRelaxMoveroperator= (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 Stringsinfo ()
 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...

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< char > > 
 Wildtype residue. More...
< utility::vector1< core::Size > > 
 Pose residue numbers to mutate. More...
< utility::vector1< char > > 
 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< bool > > 
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

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=().

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

Copy Constructor.

Create a deep copy of this mover

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


Member Function Documentation

void protocols::membrane::MPMutateRelaxMover::apply ( core::pose::Pose pose)
protocols::moves::MoverOP protocols::membrane::MPMutateRelaxMover::clone ( ) const

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

void protocols::membrane::MPMutateRelaxMover::finalize_setup ( Pose pose)
protocols::moves::MoverOP protocols::membrane::MPMutateRelaxMover::fresh_instance ( ) const

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

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

Mover Methods ///.

Get the name of this Mover (MPMutateRelaxMover)

Implements protocols::moves::Mover.

void protocols::membrane::MPMutateRelaxMover::get_repack_residues ( Pose pose)
void protocols::membrane::MPMutateRelaxMover::init_from_cmd ( )
std::string protocols::membrane::MPMutateRelaxMover::make_mutations ( Pose pose,
core::Size  num_construct 
MPMutateRelaxMover & protocols::membrane::MPMutateRelaxMover::operator= ( MPMutateRelaxMover const &  src)

Assignment Operator.

References MPMutateRelaxMover().

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

Create output filename.

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

Referenced by apply().

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

Pase Rosetta Scripts Options for this Mover.

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

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

Setup Methods ///.

Register Options from Command Line

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

Referenced by MPMutateRelaxMover().

Member Data Documentation

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

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().

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

Input file containing desired mutants to make.

Referenced by finalize_setup(), and init_from_cmd().

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

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().

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

Protein name for dumping PDBs.

Referenced by init_from_cmd(), and output_filename().

bool protocols::membrane::MPMutateRelaxMover::relax_

Full relax?

Referenced by apply(), and init_from_cmd().

bool protocols::membrane::MPMutateRelaxMover::repack_mutation_only_


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

core::Real protocols::membrane::MPMutateRelaxMover::repack_radius_
utility::vector1< utility::vector1< bool > > protocols::membrane::MPMutateRelaxMover::repack_residues_

Referenced by apply(), and get_repack_residues().

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

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().

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


Referenced by apply(), and finalize_setup().

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

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: