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protocols::seeded_abinitio::GrowPeptides Class Reference

#include <GrowPeptides.hh>

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

 GrowPeptides ()
 
 ~GrowPeptides () 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...
 
bool ddg ()
 
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

void append_residues_nterminally (core::Size seq_register, core::Size res_pos, core::Size stop, std::string &nat_seq, core::pose::Pose &target_seeds)
 functions More...
 
void append_residues_cterminally (core::Size seq_register, core::Size res_pos, core::Size stop, std::string &nat_seq, core::pose::Pose &target_seeds)
 
void grow_from_seeds (core::pose::Pose curr_pose, std::string sequence, protocols::loops::Loops &seeds, utility::vector1< core::Size > cutpoints)
 
void grow_from_vertices (core::pose::Pose &curr_pose, std::string sequence, protocols::loops::Loops &seeds, std::set< core::Size > vertex_set)
 
void setup_cached_observers (core::pose::Pose &pose)
 

Private Attributes

core::Size extend_nterm
 data More...
 
core::Size extend_cterm
 
std::string nsequence_
 
std::string csequence_
 
std::string seq_
 
bool all_ala_N
 
bool all_ala_C
 
bool ddg_
 
core::pose::PoseOP template_pdb_
 template pose to derrive a sequence from More...
 
bool template_presence
 
bool anchor_specified_
 
utility::vector1< core::Sizeanchors_
 
core::scoring::ScoreFunctionOP scorefxn_
 
bool output_centroid
 
utility::vector1< std::string > sequence_chunks_
 vector of sequence pieces More...
 
utility::vector1
< GrowPeptidesSegmentOP
all_seeds_
 
bool fetch_foldtree
 
core::kinematics::FoldTreeOP seed_foldtree_
 foldtree after growing out peptide pieces More...
 
core::pose::PoseCOP reference_pose_
 pointer for the reference pose for seeds More...
 
std::set< core::Sizevertices_
 

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::GrowPeptides::GrowPeptides ( )
default
protocols::seeded_abinitio::GrowPeptides::~GrowPeptides ( )
overridedefault

Member Function Documentation

void protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally ( core::Size  seq_register,
core::Size  res_pos,
core::Size  stop,
std::string &  nat_seq,
core::pose::Pose target_seeds 
)
private
void protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally ( core::Size  seq_register,
core::Size  res_pos,
core::Size  stop,
std::string &  nat_seq,
core::pose::Pose target_seeds 
)
private
void protocols::seeded_abinitio::GrowPeptides::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::seeded_abinitio::GrowPeptides::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.

bool protocols::seeded_abinitio::GrowPeptides::ddg ( )
protocols::moves::MoverOP protocols::seeded_abinitio::GrowPeptides::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::GrowPeptides::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::seeded_abinitio::GrowPeptides::grow_from_seeds ( core::pose::Pose  curr_pose,
std::string  sequence,
protocols::loops::Loops seeds,
utility::vector1< core::Size cutpoints 
)
private
void protocols::seeded_abinitio::GrowPeptides::grow_from_vertices ( core::pose::Pose curr_pose,
std::string  sequence,
protocols::loops::Loops seeds,
std::set< core::Size vertex_set 
)
private
std::string protocols::seeded_abinitio::GrowPeptides::mover_name ( )
static
void protocols::seeded_abinitio::GrowPeptides::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 core::sequence::end, protocols::rosetta_scripts::legacy_saved_pose_or_input(), core::pose::parse_resnum(), core::scoring::parse_score_function(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and TR().

void protocols::seeded_abinitio::GrowPeptides::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::seeded_abinitio::GrowPeptides::setup_cached_observers ( core::pose::Pose pose)
private

Member Data Documentation

bool protocols::seeded_abinitio::GrowPeptides::all_ala_C
private
bool protocols::seeded_abinitio::GrowPeptides::all_ala_N
private
utility::vector1< GrowPeptidesSegmentOP > protocols::seeded_abinitio::GrowPeptides::all_seeds_
private
bool protocols::seeded_abinitio::GrowPeptides::anchor_specified_
private
utility::vector1< core::Size > protocols::seeded_abinitio::GrowPeptides::anchors_
private
std::string protocols::seeded_abinitio::GrowPeptides::csequence_
private
bool protocols::seeded_abinitio::GrowPeptides::ddg_
private
core::Size protocols::seeded_abinitio::GrowPeptides::extend_cterm
private
core::Size protocols::seeded_abinitio::GrowPeptides::extend_nterm
private

data

bool protocols::seeded_abinitio::GrowPeptides::fetch_foldtree
private
std::string protocols::seeded_abinitio::GrowPeptides::nsequence_
private
bool protocols::seeded_abinitio::GrowPeptides::output_centroid
private
core::pose::PoseCOP protocols::seeded_abinitio::GrowPeptides::reference_pose_
private

pointer for the reference pose for seeds

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::GrowPeptides::scorefxn_
private
core::kinematics::FoldTreeOP protocols::seeded_abinitio::GrowPeptides::seed_foldtree_
private

foldtree after growing out peptide pieces

std::string protocols::seeded_abinitio::GrowPeptides::seq_
private
utility::vector1< std::string > protocols::seeded_abinitio::GrowPeptides::sequence_chunks_
private

vector of sequence pieces

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

template pose to derrive a sequence from

bool protocols::seeded_abinitio::GrowPeptides::template_presence
private
std::set< core::Size > protocols::seeded_abinitio::GrowPeptides::vertices_
private

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