Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::evolution::NucleotideMutation Class Reference

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...

#include <NucleotideMutation.hh>

Inheritance diagram for protocols::evolution::NucleotideMutation:
Inheritance graph

Public Types

typedef core::pose::Pose Pose
- 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

Public Member Functions

 NucleotideMutation ()
void add_nt_seq_to_pose (core::pose::Pose &pose)
void find_neighbors (utility::vector1< bool > const &is_mutated, core::pose::Pose const &pose, utility::vector1< bool > &is_flexible, core::Real const heavyatom_distance_threshold)
void compute_folding_energies (core::scoring::ScoreFunctionOP fa_scorefxn, core::pose::Pose &pose, utility::vector1< bool > const &is_flexible, utility::vector1< bool > const &is_mutpos, core::Size bbnbrs, bool flexbb)
void apply (Pose &pose) override
 Main Method. More...
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 ~NucleotideMutation () override
core::pack::task::TaskFactoryOP task_factory () const
void task_factory (core::pack::task::TaskFactoryOP tf)
core::scoring::ScoreFunctionOP scorefxn () const
void scorefxn (core::scoring::ScoreFunctionOP sfxn)
std::string init_sequence () const
void init_sequence (std::string const &s)
bool continue_if_silent () const
void continue_if_silent (bool const c)
bool flexbb () const
void flexbb (bool const f)
core::Size bbnbrs () const
void bbnbrs (core::Size const n)
bool cache_task () const
void cache_task (bool cache)
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 Stringsinfo ()
 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 Attributes

core::pack::task::TaskFactoryOP task_factory_
core::scoring::ScoreFunctionOP scorefxn_
std::string init_sequence_
bool continue_if_silent_
bool flexbb_
core::Size bbnbrs_
core::pose::PoseOP reference_pose_
bool cache_task_
core::pack::task::PackerTaskCOP task_

Additional Inherited Members

- 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

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines.

Member Typedef Documentation

◆ Pose

Constructor & Destructor Documentation

◆ NucleotideMutation()

protocols::evolution::NucleotideMutation::NucleotideMutation ( )

◆ ~NucleotideMutation()

protocols::evolution::NucleotideMutation::~NucleotideMutation ( )

Member Function Documentation

◆ add_nt_seq_to_pose()

void protocols::evolution::NucleotideMutation::add_nt_seq_to_pose ( core::pose::Pose pose)

◆ apply()

void protocols::evolution::NucleotideMutation::apply ( Pose )

◆ bbnbrs() [1/2]

core::Size protocols::evolution::NucleotideMutation::bbnbrs ( ) const

References bbnbrs_.

Referenced by apply(), compute_folding_energies(), and parse_my_tag().

◆ bbnbrs() [2/2]

void protocols::evolution::NucleotideMutation::bbnbrs ( core::Size const  n)

References bbnbrs_.

◆ cache_task() [1/2]

bool protocols::evolution::NucleotideMutation::cache_task ( ) const

References cache_task_.

◆ cache_task() [2/2]

void protocols::evolution::NucleotideMutation::cache_task ( bool  cache)

References cache_task_.

◆ clone()

protocols::moves::MoverOP protocols::evolution::NucleotideMutation::clone ( ) const

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.

◆ compute_folding_energies()

void protocols::evolution::NucleotideMutation::compute_folding_energies ( core::scoring::ScoreFunctionOP  fa_scorefxn,
core::pose::Pose pose,
utility::vector1< bool > const &  is_flexible,
utility::vector1< bool > const &  is_mutpos,
core::Size  bbnbrs = 1,
bool  flexbb = true 

◆ continue_if_silent() [1/2]

bool protocols::evolution::NucleotideMutation::continue_if_silent ( ) const

References continue_if_silent_.

Referenced by apply(), and parse_my_tag().

◆ continue_if_silent() [2/2]

void protocols::evolution::NucleotideMutation::continue_if_silent ( bool const  c)

References continue_if_silent_.

◆ find_neighbors()

void protocols::evolution::NucleotideMutation::find_neighbors ( utility::vector1< bool > const &  is_mutated,
core::pose::Pose const &  pose,
utility::vector1< bool > &  is_flexible,
core::Real const  heavyatom_distance_threshold = 6.0 

◆ flexbb() [1/2]

bool protocols::evolution::NucleotideMutation::flexbb ( ) const

References flexbb_.

Referenced by apply(), compute_folding_energies(), and parse_my_tag().

◆ flexbb() [2/2]

void protocols::evolution::NucleotideMutation::flexbb ( bool const  f)

References flexbb_.

◆ fresh_instance()

protocols::moves::MoverOP protocols::evolution::NucleotideMutation::fresh_instance ( ) const

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::evolution::NucleotideMutation::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

◆ init_sequence() [1/2]

std::string protocols::evolution::NucleotideMutation::init_sequence ( ) const

References init_sequence_.

Referenced by add_nt_seq_to_pose(), and parse_my_tag().

◆ init_sequence() [2/2]

void protocols::evolution::NucleotideMutation::init_sequence ( std::string const &  s)

References init_sequence_.

◆ mover_name()

std::string protocols::evolution::NucleotideMutation::mover_name ( )

◆ parse_my_tag()

void protocols::evolution::NucleotideMutation::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References bbnbrs(), cache_task_, continue_if_silent(), flexbb(), init_sequence(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), scorefxn_, and task_factory().

◆ provide_xml_schema()

void protocols::evolution::NucleotideMutation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::evolution::NucleotideMutation::scorefxn ( ) const

References scorefxn_.

Referenced by apply(), and scorefxn().

◆ scorefxn() [2/2]

void protocols::evolution::NucleotideMutation::scorefxn ( core::scoring::ScoreFunctionOP  sfxn)

References scorefxn(), and scorefxn_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::evolution::NucleotideMutation::task_factory ( ) const

References task_factory_.

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

◆ task_factory() [2/2]

void protocols::evolution::NucleotideMutation::task_factory ( core::pack::task::TaskFactoryOP  tf)

References task_factory(), and task_factory_.

Member Data Documentation

◆ bbnbrs_

core::Size protocols::evolution::NucleotideMutation::bbnbrs_

Referenced by bbnbrs().

◆ cache_task_

bool protocols::evolution::NucleotideMutation::cache_task_

Referenced by apply(), cache_task(), and parse_my_tag().

◆ continue_if_silent_

bool protocols::evolution::NucleotideMutation::continue_if_silent_

Referenced by continue_if_silent().

◆ flexbb_

bool protocols::evolution::NucleotideMutation::flexbb_

Referenced by flexbb().

◆ init_sequence_

std::string protocols::evolution::NucleotideMutation::init_sequence_

Referenced by init_sequence().

◆ reference_pose_

core::pose::PoseOP protocols::evolution::NucleotideMutation::reference_pose_

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::evolution::NucleotideMutation::scorefxn_

Referenced by parse_my_tag(), and scorefxn().

◆ task_

core::pack::task::PackerTaskCOP protocols::evolution::NucleotideMutation::task_

Referenced by apply().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::evolution::NucleotideMutation::task_factory_

Referenced by task_factory().

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