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protocols::simple_moves::RepeatPropagationMover Class Reference

#include <RepeatPropagationMover.hh>

Inheritance diagram for protocols::simple_moves::RepeatPropagationMover:
Inheritance graph
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Public Member Functions

 RepeatPropagationMover ()
 
 RepeatPropagationMover (core::Size numb_repeats)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 initialize_repeat_pose (core::pose::Pose &pose, core::pose::Pose &repeat_pose)
 
void duplicate_residues_by_type (core::pose::Pose &pose, core::pose::Pose &repeat_pose)
 
void copy_phi_psi_omega (core::pose::Pose &pose, core::pose::Pose &repeat_pose)
 
void add_cap_seq_and_structure (core::pose::Pose &pose, core::pose::Pose &repeat_pose)
 
void add_cap_seq (core::pose::Pose &pose, core::pose::Pose &repeat_pose)
 
std::vector< core::Realget_center_of_mass (core::Real *coordinates, int number_of_atoms)
 
void repeat_ligand (core::pose::Pose &pose, core::pose::Pose &repeat_pose)
 
utility::vector1< core::Sizeinitial_constrained_residues (const core::pose::Pose &pose)
 
void fix_ligand_residues (core::pose::Pose &pose, core::pose::Pose &repeat_pose)
 
core::id::SequenceMapping setup_repeat_seqmap (core::Size repeat_number, core::Size ligand_in_pose, core::Size ligand_in_repeat)
 
void repeat_ligand_constraints (core::pose::Pose &pose, core::pose::Pose &repeat_pose)
 
void determine_overlap (const core::pose::Pose &pose, core::pose::Pose &parent_pose, core::Size overlap_max_length, core::Size overlap_range, std::string overlap_location_pose, core::Size &start_overlap_parent, core::Size &end_overlap_parent, core::Size &start_overlap_pose, core::Size &end_overlap_pose)
 
void generate_overlap (core::pose::Pose &pose, core::pose::Pose &parent_pose, std::string overlap_location_pose, core::Size start_overlap_parent, core::Size end_overlap_parent, core::Size start_overlap_pose, core::Size end_overlap_pose)
 
void extract_repeat_info_from_pose (const core::pose::Pose &pose)
 
void trim_back_repeat_to_repair_scar (core::pose::Pose &pose)
 

Private Attributes

core::Size first_res_
 
core::Size last_res_
 
core::Size numb_repeats_
 
bool ideal_repeat_
 
bool repeat_without_replacing_pose_
 
bool maintain_cap_
 
bool maintain_cap_sequence_only_
 
bool maintain_ligand_
 
core::Size nTerm_cap_size_
 
core::Size cTerm_cap_size_
 
bool extract_repeat_info_from_pose_
 
core::Size extract_repeat_template_repeat_
 
core::Size start_pose_numb_repeats_
 
core::Size start_pose_length_
 
core::Size start_pose_duplicate_residues_
 
bool deal_with_length_change_scar_
 

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::simple_moves::RepeatPropagationMover::RepeatPropagationMover ( )
protocols::simple_moves::RepeatPropagationMover::RepeatPropagationMover ( core::Size  numb_repeats)

Member Function Documentation

void protocols::simple_moves::RepeatPropagationMover::add_cap_seq ( core::pose::Pose pose,
core::pose::Pose repeat_pose 
)
private
void protocols::simple_moves::RepeatPropagationMover::add_cap_seq_and_structure ( core::pose::Pose pose,
core::pose::Pose repeat_pose 
)
private
void protocols::simple_moves::RepeatPropagationMover::apply ( core::pose::Pose )
overridevirtual
moves::MoverOP protocols::simple_moves::RepeatPropagationMover::clone ( ) const
inlineoverridevirtual

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::simple_moves::RepeatPropagationMover::copy_phi_psi_omega ( core::pose::Pose pose,
core::pose::Pose repeat_pose 
)
private
void protocols::simple_moves::RepeatPropagationMover::determine_overlap ( const core::pose::Pose pose,
core::pose::Pose parent_pose,
core::Size  overlap_max_length,
core::Size  overlap_range,
std::string  overlap_location_pose,
core::Size start_overlap_parent,
core::Size end_overlap_parent,
core::Size start_overlap_pose,
core::Size end_overlap_pose 
)
private
void protocols::simple_moves::RepeatPropagationMover::duplicate_residues_by_type ( core::pose::Pose pose,
core::pose::Pose repeat_pose 
)
private
void protocols::simple_moves::RepeatPropagationMover::extract_repeat_info_from_pose ( const core::pose::Pose pose)
private
void protocols::simple_moves::RepeatPropagationMover::fix_ligand_residues ( core::pose::Pose pose,
core::pose::Pose repeat_pose 
)
private
void protocols::simple_moves::RepeatPropagationMover::generate_overlap ( core::pose::Pose pose,
core::pose::Pose parent_pose,
std::string  overlap_location_pose,
core::Size  start_overlap_parent,
core::Size  end_overlap_parent,
core::Size  start_overlap_pose,
core::Size  end_overlap_pose 
)
private
vector< Real > protocols::simple_moves::RepeatPropagationMover::get_center_of_mass ( core::Real coordinates,
int  number_of_atoms 
)
private
std::string protocols::simple_moves::RepeatPropagationMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

vector1< core::Size > protocols::simple_moves::RepeatPropagationMover::initial_constrained_residues ( const core::pose::Pose pose)
private
void protocols::simple_moves::RepeatPropagationMover::initialize_repeat_pose ( core::pose::Pose pose,
core::pose::Pose repeat_pose 
)
private

References duplicate_residues_by_type().

Referenced by apply().

std::string protocols::simple_moves::RepeatPropagationMover::mover_name ( )
static
void protocols::simple_moves::RepeatPropagationMover::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 cTerm_cap_size_, deal_with_length_change_scar_, extract_repeat_info_from_pose_, extract_repeat_template_repeat_, first_res_, ideal_repeat_, last_res_, maintain_cap_, maintain_cap_sequence_only_, maintain_ligand_, nTerm_cap_size_, numb_repeats_, repeat_without_replacing_pose_, start_pose_duplicate_residues_, start_pose_length_, and start_pose_numb_repeats_.

void protocols::simple_moves::RepeatPropagationMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_moves::RepeatPropagationMover::repeat_ligand ( core::pose::Pose pose,
core::pose::Pose repeat_pose 
)
private
void protocols::simple_moves::RepeatPropagationMover::repeat_ligand_constraints ( core::pose::Pose pose,
core::pose::Pose repeat_pose 
)
private
core::id::SequenceMapping protocols::simple_moves::RepeatPropagationMover::setup_repeat_seqmap ( core::Size  repeat_number,
core::Size  ligand_in_pose,
core::Size  ligand_in_repeat 
)
private
void protocols::simple_moves::RepeatPropagationMover::trim_back_repeat_to_repair_scar ( core::pose::Pose pose)
private

Member Data Documentation

core::Size protocols::simple_moves::RepeatPropagationMover::cTerm_cap_size_
private
bool protocols::simple_moves::RepeatPropagationMover::deal_with_length_change_scar_
private
bool protocols::simple_moves::RepeatPropagationMover::extract_repeat_info_from_pose_
private
core::Size protocols::simple_moves::RepeatPropagationMover::extract_repeat_template_repeat_
private
core::Size protocols::simple_moves::RepeatPropagationMover::first_res_
private
bool protocols::simple_moves::RepeatPropagationMover::ideal_repeat_
private
core::Size protocols::simple_moves::RepeatPropagationMover::last_res_
private
bool protocols::simple_moves::RepeatPropagationMover::maintain_cap_
private
bool protocols::simple_moves::RepeatPropagationMover::maintain_cap_sequence_only_
private
bool protocols::simple_moves::RepeatPropagationMover::maintain_ligand_
private
core::Size protocols::simple_moves::RepeatPropagationMover::nTerm_cap_size_
private
core::Size protocols::simple_moves::RepeatPropagationMover::numb_repeats_
private
bool protocols::simple_moves::RepeatPropagationMover::repeat_without_replacing_pose_
private
core::Size protocols::simple_moves::RepeatPropagationMover::start_pose_duplicate_residues_
private
core::Size protocols::simple_moves::RepeatPropagationMover::start_pose_length_
private
core::Size protocols::simple_moves::RepeatPropagationMover::start_pose_numb_repeats_
private

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