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protocols::comparative_modeling::ThreadingMover Class Reference

#include <ThreadingMover.hh>

Inheritance diagram for protocols::comparative_modeling::ThreadingMover:
Inheritance graph
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Public Member Functions

 ThreadingMover ()
 Empty constructor. More...
 
 ThreadingMover (ThreadingMover const &object_to_copy)
 Copy constructor. More...
 
 ThreadingMover (core::sequence::SequenceAlignment const &align, core::pose::Pose const &template_pose)
 align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model. More...
 
 ~ThreadingMover () override=default
 
core::Size query_index () const
 Returns the index of the query sequence in SequenceAlignment object. More...
 
core::Size template_index () const
 Returns the index of the template sequence in SequenceAlignment object. More...
 
core::sequence::SequenceAlignment alignment ()
 Returns the SequenceAlignment object used in threading. More...
 
void query_index (core::Size new_index)
 Sets the index of the query sequence in SequenceAlignment object. More...
 
void template_index (core::Size new_index)
 Sets the index of the template sequence in SequenceAlignment object. More...
 
void alignment (core::sequence::SequenceAlignment new_align)
 Sets the SequenceAlignment associated with this object. More...
 
void template_pose (core::pose::Pose template_pose)
 
void build_loops (bool setting)
 
void randomize_loop_coords (bool setting)
 
void repack_query (bool setting)
 
bool build_loops () const
 
bool repack_query () const
 
bool randomize_loop_coords ()
 
void min_loop_size (core::Size const new_size)
 
core::Size min_loop_size () const
 
utility::vector1
< core::fragment::FragSetOP
frag_libs () const
 
void frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs)
 
core::id::SequenceMapping get_qt_mapping (core::pose::Pose const &query_pose) const
 Returns the SequenceMapping between query and template. More...
 
void apply (core::pose::Pose &query_pose) override
 Threads the given Pose onto the template_pose with the SequenceAlignment provided. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
- 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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

bool atoms_are_equiv (std::string const &a1, std::string const &a2)
 
void add_equiv_atoms (std::string const &a1, std::string const &a2)
 add pair of equivalent atoms to atom_equiv_ table. More...
 
void init_atom_equiv ()
 initialize table of equivalent atoms between all residues. More...
 

Private Attributes

core::Size query_index_
 
core::Size template_index_
 
core::pose::Pose template_pose_
 
core::sequence::SequenceAlignment align_
 
bool build_query_loops_
 
bool repack_query_
 
bool randomize_loop_coords_
 
core::Size min_loop_size_
 
std::map< std::string,
std::set< std::string > > 
atom_equiv_
 
utility::vector1
< core::fragment::FragSetOP
frag_libs_
 

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::comparative_modeling::ThreadingMover::ThreadingMover ( )

Empty constructor.

protocols::comparative_modeling::ThreadingMover::ThreadingMover ( ThreadingMover const &  object_to_copy)

Copy constructor.

protocols::comparative_modeling::ThreadingMover::ThreadingMover ( core::sequence::SequenceAlignment const &  align,
core::pose::Pose const &  template_pose 
)

align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model.

protocols::comparative_modeling::ThreadingMover::~ThreadingMover ( )
overridedefault

Member Function Documentation

void protocols::comparative_modeling::ThreadingMover::add_equiv_atoms ( std::string const &  a1,
std::string const &  a2 
)
private

add pair of equivalent atoms to atom_equiv_ table.

core::sequence::SequenceAlignment protocols::comparative_modeling::ThreadingMover::alignment ( )

Returns the SequenceAlignment object used in threading.

References align_.

void protocols::comparative_modeling::ThreadingMover::alignment ( core::sequence::SequenceAlignment  new_align)

Sets the SequenceAlignment associated with this object.

References align_.

void protocols::comparative_modeling::ThreadingMover::apply ( core::pose::Pose query_pose)
overridevirtual

Threads the given Pose onto the template_pose with the SequenceAlignment provided.

Implements protocols::moves::Mover.

References core::pose::add_score_line_string(), align_, core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), build_loops(), core::chemical::CENTROID_t, core::conformation::Residue::clone(), core::pose::Pose::conformation(), frag_libs(), get_qt_mapping(), core::scoring::get_score_function(), core::chemical::ResidueType::has(), core::conformation::idealize_hydrogens(), core::pose::initialize_atomid_map(), protocols::comparative_modeling::loops_from_alignment(), min_loop_size(), core::conformation::Residue::name1(), core::conformation::Residue::natoms(), core::pack::optimize_H_and_notify(), core::pack::pack_missing_sidechains(), core::pose::Pose::pdb_info(), core::scoring::peptide_bond, query_index_, randomize_loop_coords(), protocols::comparative_modeling::randomize_selected_atoms(), repack_query(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Conformation::residue_typeset_mode(), core::sequence::SequenceAlignment::sequence(), core::pose::Pose::sequence(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), template_index_, template_pose_, protocols::comparative_modeling::tr(), and core::pose::Pose::xyz().

Referenced by protocols::domain_assembly::CombineChainsMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), and protocols::comparative_modeling::ThreadingJobInputter::pose_from_job().

bool protocols::comparative_modeling::ThreadingMover::atoms_are_equiv ( std::string const &  a1,
std::string const &  a2 
)
private
void protocols::comparative_modeling::ThreadingMover::build_loops ( bool  setting)
bool protocols::comparative_modeling::ThreadingMover::build_loops ( ) const

References build_query_loops_.

Referenced by apply().

protocols::moves::MoverOP protocols::comparative_modeling::ThreadingMover::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.

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::ThreadingMover::frag_libs ( ) const

References frag_libs_.

Referenced by apply().

void protocols::comparative_modeling::ThreadingMover::frag_libs ( utility::vector1< core::fragment::FragSetOP new_libs)

References frag_libs_.

protocols::moves::MoverOP protocols::comparative_modeling::ThreadingMover::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::comparative_modeling::ThreadingMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

core::id::SequenceMapping protocols::comparative_modeling::ThreadingMover::get_qt_mapping ( core::pose::Pose const &  query_pose) const

Returns the SequenceMapping between query and template.

References align_, protocols::comparative_modeling::get_qt_mapping_general(), query_index_, template_index_, and template_pose_.

Referenced by apply().

void protocols::comparative_modeling::ThreadingMover::init_atom_equiv ( )
private

initialize table of equivalent atoms between all residues.

void protocols::comparative_modeling::ThreadingMover::min_loop_size ( core::Size const  new_size)

References min_loop_size_.

core::Size protocols::comparative_modeling::ThreadingMover::min_loop_size ( ) const

References min_loop_size_.

Referenced by apply().

core::Size protocols::comparative_modeling::ThreadingMover::query_index ( ) const

Returns the index of the query sequence in SequenceAlignment object.

References query_index_.

void protocols::comparative_modeling::ThreadingMover::query_index ( core::Size  new_index)

Sets the index of the query sequence in SequenceAlignment object.

References query_index_.

void protocols::comparative_modeling::ThreadingMover::randomize_loop_coords ( bool  setting)
bool protocols::comparative_modeling::ThreadingMover::randomize_loop_coords ( )

References randomize_loop_coords_.

Referenced by apply().

void protocols::comparative_modeling::ThreadingMover::repack_query ( bool  setting)
bool protocols::comparative_modeling::ThreadingMover::repack_query ( ) const

References repack_query_.

Referenced by apply().

core::Size protocols::comparative_modeling::ThreadingMover::template_index ( ) const

Returns the index of the template sequence in SequenceAlignment object.

References template_index_.

void protocols::comparative_modeling::ThreadingMover::template_index ( core::Size  new_index)

Sets the index of the template sequence in SequenceAlignment object.

References template_index_.

void protocols::comparative_modeling::ThreadingMover::template_pose ( core::pose::Pose  template_pose)

References template_pose_.

Member Data Documentation

core::sequence::SequenceAlignment protocols::comparative_modeling::ThreadingMover::align_
private

Referenced by alignment(), apply(), and get_qt_mapping().

std::map< std::string, std::set< std::string > > protocols::comparative_modeling::ThreadingMover::atom_equiv_
private
bool protocols::comparative_modeling::ThreadingMover::build_query_loops_
private

Referenced by build_loops().

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::ThreadingMover::frag_libs_
private

Referenced by frag_libs().

core::Size protocols::comparative_modeling::ThreadingMover::min_loop_size_
private

Referenced by min_loop_size().

core::Size protocols::comparative_modeling::ThreadingMover::query_index_
private

Referenced by apply(), get_qt_mapping(), and query_index().

bool protocols::comparative_modeling::ThreadingMover::randomize_loop_coords_
private

Referenced by randomize_loop_coords().

bool protocols::comparative_modeling::ThreadingMover::repack_query_
private

Referenced by repack_query().

core::Size protocols::comparative_modeling::ThreadingMover::template_index_
private
core::pose::Pose protocols::comparative_modeling::ThreadingMover::template_pose_
private

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