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protocols::pose_creation::MakeJunctionsMover Class Reference

#include <MakeJunctionsMover.hh>

Inheritance diagram for protocols::pose_creation::MakeJunctionsMover:
Inheritance graph


struct  Design

Public Member Functions

std::string get_name () const override
 Each derived class must specify its name. The class name. More...
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...
 MakeJunctionsMover ()
Design line_to_design (std::string line)
std::queue< Designread_in_designs ()
void parse_attach_description (std::string attach_description, std::string &pdb_location, char &chain, core::Size &n_term_trim, core::Size &c_term_trim, core::Size &n_repeats, core::Size &n_term_attach_length, core::Size &c_term_attach_length, std::string &n_term_seq, std::string &c_term_seq)
void generate_start_pose (core::pose::Pose &pose, core::pose::Pose &background_pose, std::string attach_description)
bool attach_next_part (core::pose::Pose &pose, std::string attach_termini, std::string attach_description)
void trim_pose (core::pose::Pose &pose, core::Size n_term_trim, core::Size c_term_trim)
void assign_seq (core::pose::Pose &pose, std::string n_term_seq, std::string c_term_seq)
core::pose::Pose get_and_cache_pdb (std::string pdb_location)
bool check_all_junctions_good (MakeJunctionsMover::Design design)
bool make_pose_from_design (MakeJunctionsMover::Design design, core::pose::PoseOP &return_pose)
void apply (core::pose::Pose &pose) override
 Main Method. More...
core::pose::PoseOP get_additional_output () override
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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...
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...

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

std::map< std::string,
core::scoring::ScoreFunctionOP sfxn_
std::string designs_fn_
std::queue< Designdesign_q_
bool pdb_cache_bool_
core::Size pdb_cache_max_size_
core::Real junction_rmsd_thresh_
std::multiset< std::string > junction_failure_set_
char chain_

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...

Constructor & Destructor Documentation

protocols::pose_creation::MakeJunctionsMover::MakeJunctionsMover ( )

Member Function Documentation

void protocols::pose_creation::MakeJunctionsMover::apply ( core::pose::Pose )

Main Method.

Implements protocols::moves::Mover.

References design_q_, get_additional_output(), and read_in_designs().

void protocols::pose_creation::MakeJunctionsMover::assign_seq ( core::pose::Pose pose,
std::string  n_term_seq,
std::string  c_term_seq 
bool protocols::pose_creation::MakeJunctionsMover::attach_next_part ( core::pose::Pose pose,
std::string  attach_termini,
std::string  attach_description 
bool protocols::pose_creation::MakeJunctionsMover::check_all_junctions_good ( MakeJunctionsMover::Design  design)
moves::MoverOP protocols::pose_creation::MakeJunctionsMover::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.

moves::MoverOP protocols::pose_creation::MakeJunctionsMover::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.

void protocols::pose_creation::MakeJunctionsMover::generate_start_pose ( core::pose::Pose pose,
core::pose::Pose background_pose,
std::string  attach_description 
core::pose::PoseOP protocols::pose_creation::MakeJunctionsMover::get_additional_output ( )

Mechanism by which a mover may return multiple output poses from a single input pose.


Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References design_q_, protocols::moves::FAIL_DO_NOT_RETRY, make_pose_from_design(), protocols::moves::Mover::set_last_move_status(), and sfxn_.

Referenced by apply().

core::pose::Pose protocols::pose_creation::MakeJunctionsMover::get_and_cache_pdb ( std::string  pdb_location)
std::string protocols::pose_creation::MakeJunctionsMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

MakeJunctionsMover::Design protocols::pose_creation::MakeJunctionsMover::line_to_design ( std::string  line)
bool protocols::pose_creation::MakeJunctionsMover::make_pose_from_design ( MakeJunctionsMover::Design  design,
core::pose::PoseOP return_pose 
std::string protocols::pose_creation::MakeJunctionsMover::mover_name ( )

Referenced by get_name(), and provide_xml_schema().

void protocols::pose_creation::MakeJunctionsMover::parse_attach_description ( std::string  attach_description,
std::string &  pdb_location,
char &  chain,
core::Size n_term_trim,
core::Size c_term_trim,
core::Size n_repeats,
core::Size n_term_attach_length,
core::Size c_term_attach_length,
std::string &  n_term_seq,
std::string &  c_term_seq 
void protocols::pose_creation::MakeJunctionsMover::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 designs_fn_, junction_rmsd_thresh_, pdb_cache_bool_, pdb_cache_max_size_, and sfxn_.

void protocols::pose_creation::MakeJunctionsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
std::queue< MakeJunctionsMover::Design > protocols::pose_creation::MakeJunctionsMover::read_in_designs ( )

References designs_fn_, and line_to_design().

Referenced by apply().

void protocols::pose_creation::MakeJunctionsMover::trim_pose ( core::pose::Pose pose,
core::Size  n_term_trim,
core::Size  c_term_trim 

Member Data Documentation

char protocols::pose_creation::MakeJunctionsMover::chain_

Referenced by generate_start_pose().

std::queue<Design> protocols::pose_creation::MakeJunctionsMover::design_q_

Referenced by apply(), and get_additional_output().

std::string protocols::pose_creation::MakeJunctionsMover::designs_fn_

Referenced by parse_my_tag(), and read_in_designs().

std::multiset<std::string> protocols::pose_creation::MakeJunctionsMover::junction_failure_set_
core::Real protocols::pose_creation::MakeJunctionsMover::junction_rmsd_thresh_

Referenced by attach_next_part(), and parse_my_tag().

std::map<std::string,core::pose::Pose> protocols::pose_creation::MakeJunctionsMover::pdb_cache_

Referenced by get_and_cache_pdb().

bool protocols::pose_creation::MakeJunctionsMover::pdb_cache_bool_

Referenced by get_and_cache_pdb(), and parse_my_tag().

core::Size protocols::pose_creation::MakeJunctionsMover::pdb_cache_max_size_

Referenced by get_and_cache_pdb(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::pose_creation::MakeJunctionsMover::sfxn_

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