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protocols::seeded_abinitio::CloseFold Class Reference

#include <CloseFold.hh>

Inheritance diagram for protocols::seeded_abinitio::CloseFold:
Inheritance graph
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Public Member Functions

 CloseFold ()
 
 ~CloseFold () override
 
void apply (core::pose::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...
 
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 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 Member Functions

protocols::loops::LoopsOP find_loops (core::pose::Pose &pose, std::string secstr, core::Size offset, protocols::loops::Loops seeds)
 functions More...
 
bool is_cut (utility::vector1< core::Size > &cut_points, core::Size residue)
 
bool chainbreakweights ()
 
void add_chainbreakweights (bool acbw)
 
bool use_cutpoints ()
 
void use_cutpoints (bool uc)
 
core::Size trials ()
 
void set_trials (core::Size trials_quick_ccd)
 
void initialize_fragments ()
 
void fast_loopclose (core::pose::Pose &pose, protocols::loops::LoopsOP const loops, bool kic)
 
void quick_closure (core::pose::Pose &pose, protocols::loops::LoopsOP const loops)
 

Private Attributes

core::fragment::FragSetOP fragments_
 data More...
 
boost::unordered_map
< core::Size,
core::fragment::Frame
library_
 index-based access to the data contained in the FragSet More...
 
core::pose::PoseOP template_pdb_
 
std::string secstructure_
 
utility::vector1< core::Sizechains_
 
bool use_cutpoints_
 
utility::vector1< std::pair
< std::string, std::string > > 
seed_vector_
 residues specifying the seeds More...
 
protocols::loops::LoopsOP loops_
 
bool chainbreakweights_
 add cutpoint variants for closure More...
 
core::Size trials_
 option for quick ccd protocol, how many attempts More...
 
bool idealize_
 options for fast_ccd protocol More...
 
bool kic_
 should kinematic loop mover be used after the fast ccd More...
 
bool ccd_
 
core::scoring::ScoreFunctionOP cen_scorefxn_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 

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::seeded_abinitio::CloseFold::CloseFold ( )
protocols::seeded_abinitio::CloseFold::~CloseFold ( )
overridedefault

Member Function Documentation

void protocols::seeded_abinitio::CloseFold::add_chainbreakweights ( bool  acbw)
private

References chainbreakweights_.

void protocols::seeded_abinitio::CloseFold::apply ( core::pose::Pose )
overridevirtual
bool protocols::seeded_abinitio::CloseFold::chainbreakweights ( )
private

References chainbreakweights_.

Referenced by find_loops().

protocols::moves::MoverOP protocols::seeded_abinitio::CloseFold::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.

void protocols::seeded_abinitio::CloseFold::fast_loopclose ( core::pose::Pose pose,
protocols::loops::LoopsOP const  loops,
bool  kic 
)
private
protocols::loops::LoopsOP protocols::seeded_abinitio::CloseFold::find_loops ( core::pose::Pose pose,
std::string  secstr,
core::Size  offset,
protocols::loops::Loops  seeds 
)
private
protocols::moves::MoverOP protocols::seeded_abinitio::CloseFold::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.

std::string protocols::seeded_abinitio::CloseFold::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::seeded_abinitio::CloseFold::initialize_fragments ( )
private

References fragments_, and library_.

bool protocols::seeded_abinitio::CloseFold::is_cut ( utility::vector1< core::Size > &  cut_points,
core::Size  residue 
)
private

References protocols::loops::cut_point.

Referenced by find_loops().

std::string protocols::seeded_abinitio::CloseFold::mover_name ( )
static
void protocols::seeded_abinitio::CloseFold::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 ccd_, cen_scorefxn_, chainbreakweights_, chains_, protocols::simple_filters::dssp(), fa_scorefxn_, fragments_, idealize_, core::scoring::dssp::Dssp::insert_ss_into_pose(), kic_, loops_, core::scoring::parse_score_function(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), secstructure_, seed_vector_, template_pdb_, protocols::seeded_abinitio::TR(), trials_, and use_cutpoints_.

void protocols::seeded_abinitio::CloseFold::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::seeded_abinitio::CloseFold::quick_closure ( core::pose::Pose pose,
protocols::loops::LoopsOP const  loops 
)
private
void protocols::seeded_abinitio::CloseFold::set_trials ( core::Size  trials_quick_ccd)
private

References trials_.

core::Size protocols::seeded_abinitio::CloseFold::trials ( )
private

References trials_.

Referenced by fast_loopclose(), and quick_closure().

bool protocols::seeded_abinitio::CloseFold::use_cutpoints ( )
private

References use_cutpoints_.

Referenced by find_loops().

void protocols::seeded_abinitio::CloseFold::use_cutpoints ( bool  uc)
private

References use_cutpoints_.

Member Data Documentation

bool protocols::seeded_abinitio::CloseFold::ccd_
private

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::CloseFold::cen_scorefxn_
private
bool protocols::seeded_abinitio::CloseFold::chainbreakweights_
private

add cutpoint variants for closure

Referenced by add_chainbreakweights(), chainbreakweights(), CloseFold(), and parse_my_tag().

utility::vector1< core::Size > protocols::seeded_abinitio::CloseFold::chains_
private

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

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::CloseFold::fa_scorefxn_
private
core::fragment::FragSetOP protocols::seeded_abinitio::CloseFold::fragments_
private

data

fragment set used for ccd

Referenced by initialize_fragments(), parse_my_tag(), and quick_closure().

bool protocols::seeded_abinitio::CloseFold::idealize_
private

options for fast_ccd protocol

Referenced by CloseFold(), and parse_my_tag().

bool protocols::seeded_abinitio::CloseFold::kic_
private

should kinematic loop mover be used after the fast ccd

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

boost::unordered_map<core::Size, core::fragment::Frame> protocols::seeded_abinitio::CloseFold::library_
private

index-based access to the data contained in the FragSet

position-indexable list of Frames, populating library void initialize_library();

Referenced by initialize_fragments().

protocols::loops::LoopsOP protocols::seeded_abinitio::CloseFold::loops_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::seeded_abinitio::CloseFold::secstructure_
private

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

utility::vector1< std::pair < std::string,std::string > > protocols::seeded_abinitio::CloseFold::seed_vector_
private

residues specifying the seeds

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

core::pose::PoseOP protocols::seeded_abinitio::CloseFold::template_pdb_
private

Referenced by parse_my_tag().

core::Size protocols::seeded_abinitio::CloseFold::trials_
private

option for quick ccd protocol, how many attempts

Referenced by CloseFold(), parse_my_tag(), set_trials(), and trials().

bool protocols::seeded_abinitio::CloseFold::use_cutpoints_
private

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