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protocols::indel::IndelOptimizationMover Class Reference

#include <IndelOptimizationMover.hh>

Inheritance diagram for protocols::indel::IndelOptimizationMover:
Inheritance graph
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Public Member Functions

 IndelOptimizationMover (core::Size start_res, core::Size end_res, core::Size loop_length, std::string const &remodel, std::string const &intermedrelax, std::string const &refine, std::string const &relax, bool frag_files, core::Size num_to_dock, bool dump_initial_results)
 
 ~IndelOptimizationMover () override=default
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
core::Size start_res ()
 
core::Size end_res ()
 
core::Size loop_length ()
 
std::string remodel ()
 
std::string intermedrelax ()
 
std::string refine ()
 
std::string relax ()
 
bool frag_files ()
 
core::Size num_to_dock ()
 
bool dump_initial_results ()
 
void start_res (core::Size i)
 
void end_res (core::Size i)
 
void loop_length (core::Size i)
 
void remodel (std::string i)
 
void intermedrelax (std::string i)
 
void refine (std::string i)
 
void relax (std::string i)
 
void frag_files (bool i)
 
void num_to_dock (core::Size i)
 
void dump_initial_results (bool i)
 
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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
 
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 Attributes

core::Size start_res_
 
core::Size end_res_
 
core::Size loop_length_
 
std::string remodel_
 
std::string intermedrelax_
 
std::string refine_
 
std::string relax_
 
bool frag_files_
 
core::Size num_to_dock_
 
bool dump_initial_results_
 

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::indel::IndelOptimizationMover::IndelOptimizationMover ( core::Size  start_res,
core::Size  end_res,
core::Size  loop_length,
std::string const &  remodel,
std::string const &  intermedrelax,
std::string const &  refine,
std::string const &  relax,
bool  frag_files,
core::Size  num_to_dock,
bool  dump_initial_results 
)
inline
protocols::indel::IndelOptimizationMover::~IndelOptimizationMover ( )
overridedefault

Member Function Documentation

void protocols::indel::IndelOptimizationMover::apply ( core::pose::Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), protocols::relax::AtomCoordinateCstMover::apply(), core::pose::Pose::conformation(), protocols::jd2::current_nstruct_index(), core::conformation::Conformation::declare_chemical_bond(), core::conformation::Conformation::delete_residue_range_slow(), core::conformation::Conformation::detect_disulfides(), core::kinematics::FoldTree::downstream_jump_residue(), dump_initial_results_, core::pose::Pose::dump_pdb(), end_res_, core::pose::Pose::fold_tree(), frag_files_, protocols::comparative_modeling::LoopRelaxMover::frag_libs(), protocols::comparative_modeling::LoopRelaxMover::get_loops(), core::scoring::get_score_function(), protocols::comparative_modeling::LoopRelaxMover::intermedrelax(), intermedrelax_, loop_length_, protocols::comparative_modeling::LoopRelaxMover::loops(), core::conformation::Conformation::num_chains(), core::kinematics::FoldTree::num_jump(), num_to_dock_, core::pose::Pose::pdb_info(), protocols::loops::read_loop_fragments(), protocols::comparative_modeling::LoopRelaxMover::refine(), refine_, protocols::comparative_modeling::LoopRelaxMover::relax(), relax_, protocols::comparative_modeling::LoopRelaxMover::remodel(), remodel_, protocols::hybridization::score, protocols::relax::AtomCoordinateCstMover::set_refstruct(), core::pose::Pose::size(), start_res_, and core::kinematics::FoldTree::upstream_jump_residue().

bool protocols::indel::IndelOptimizationMover::dump_initial_results ( )
inline

References dump_initial_results_.

void protocols::indel::IndelOptimizationMover::dump_initial_results ( bool  i)
inline

References dump_initial_results_.

core::Size protocols::indel::IndelOptimizationMover::end_res ( )
inline

References end_res_.

void protocols::indel::IndelOptimizationMover::end_res ( core::Size  i)
inline

References end_res_.

bool protocols::indel::IndelOptimizationMover::frag_files ( )
inline

References frag_files_.

void protocols::indel::IndelOptimizationMover::frag_files ( bool  i)
inline

References frag_files_.

std::string protocols::indel::IndelOptimizationMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

std::string protocols::indel::IndelOptimizationMover::intermedrelax ( )
inline

References intermedrelax_.

void protocols::indel::IndelOptimizationMover::intermedrelax ( std::string  i)
inline

References intermedrelax_.

core::Size protocols::indel::IndelOptimizationMover::loop_length ( )
inline

References loop_length_.

void protocols::indel::IndelOptimizationMover::loop_length ( core::Size  i)
inline

References loop_length_.

core::Size protocols::indel::IndelOptimizationMover::num_to_dock ( )
inline

References num_to_dock_.

void protocols::indel::IndelOptimizationMover::num_to_dock ( core::Size  i)
inline

References num_to_dock_.

std::string protocols::indel::IndelOptimizationMover::refine ( )
inline

References refine_.

void protocols::indel::IndelOptimizationMover::refine ( std::string  i)
inline

References refine_.

std::string protocols::indel::IndelOptimizationMover::relax ( )
inline

References relax_.

void protocols::indel::IndelOptimizationMover::relax ( std::string  i)
inline

References relax_.

std::string protocols::indel::IndelOptimizationMover::remodel ( )
inline

References remodel_.

void protocols::indel::IndelOptimizationMover::remodel ( std::string  i)
inline

References remodel_.

core::Size protocols::indel::IndelOptimizationMover::start_res ( )
inline

References start_res_.

void protocols::indel::IndelOptimizationMover::start_res ( core::Size  i)
inline

References start_res_.

Member Data Documentation

bool protocols::indel::IndelOptimizationMover::dump_initial_results_
private

Referenced by apply(), and dump_initial_results().

core::Size protocols::indel::IndelOptimizationMover::end_res_
private

Referenced by apply(), and end_res().

bool protocols::indel::IndelOptimizationMover::frag_files_
private

Referenced by apply(), and frag_files().

std::string protocols::indel::IndelOptimizationMover::intermedrelax_
private

Referenced by apply(), and intermedrelax().

core::Size protocols::indel::IndelOptimizationMover::loop_length_
private

Referenced by apply(), and loop_length().

core::Size protocols::indel::IndelOptimizationMover::num_to_dock_
private

Referenced by apply(), and num_to_dock().

std::string protocols::indel::IndelOptimizationMover::refine_
private

Referenced by apply(), and refine().

std::string protocols::indel::IndelOptimizationMover::relax_
private

Referenced by apply(), and relax().

std::string protocols::indel::IndelOptimizationMover::remodel_
private

Referenced by apply(), and remodel().

core::Size protocols::indel::IndelOptimizationMover::start_res_
private

Referenced by apply(), and start_res().


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