Public Member Functions | Private Attributes | List of all members
protocols::indel::IndelOptimizationMover Class Reference

#include <IndelOptimizationMover.hh>

Inheritance diagram for protocols::indel::IndelOptimizationMover:
Inheritance graph

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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

◆ IndelOptimizationMover()

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 

◆ ~IndelOptimizationMover()

protocols::indel::IndelOptimizationMover::~IndelOptimizationMover ( )

Member Function Documentation

◆ apply()

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

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::relax::loop::LoopRelaxMover::frag_libs(), protocols::relax::loop::LoopRelaxMover::get_loops(), core::scoring::get_score_function(), protocols::relax::loop::LoopRelaxMover::intermedrelax(), intermedrelax_, loop_length_, protocols::relax::loop::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::relax::loop::LoopRelaxMover::refine(), refine_, protocols::relax::loop::LoopRelaxMover::relax(), relax_, protocols::relax::loop::LoopRelaxMover::remodel(), remodel_, protocols::hybridization::score, protocols::relax::AtomCoordinateCstMover::set_refstruct(), core::pose::Pose::size(), start_res_, protocols::indel::TR(), and core::kinematics::FoldTree::upstream_jump_residue().

◆ dump_initial_results() [1/2]

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

References dump_initial_results_.

◆ dump_initial_results() [2/2]

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

References dump_initial_results_.

◆ end_res() [1/2]

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

References end_res_.

◆ end_res() [2/2]

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

References end_res_.

◆ frag_files() [1/2]

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

References frag_files_.

◆ frag_files() [2/2]

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

References frag_files_.

◆ get_name()

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

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

Implements protocols::moves::Mover.

◆ intermedrelax() [1/2]

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

References intermedrelax_.

◆ intermedrelax() [2/2]

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

References intermedrelax_.

◆ loop_length() [1/2]

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

References loop_length_.

◆ loop_length() [2/2]

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

References loop_length_.

◆ num_to_dock() [1/2]

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

References num_to_dock_.

◆ num_to_dock() [2/2]

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

References num_to_dock_.

◆ refine() [1/2]

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

References refine_.

◆ refine() [2/2]

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

References refine_.

◆ relax() [1/2]

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

References relax_.

◆ relax() [2/2]

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

References relax_.

◆ remodel() [1/2]

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

References remodel_.

◆ remodel() [2/2]

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

References remodel_.

◆ start_res() [1/2]

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

References start_res_.

◆ start_res() [2/2]

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

References start_res_.

Member Data Documentation

◆ dump_initial_results_

bool protocols::indel::IndelOptimizationMover::dump_initial_results_

Referenced by apply(), and dump_initial_results().

◆ end_res_

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

Referenced by apply(), and end_res().

◆ frag_files_

bool protocols::indel::IndelOptimizationMover::frag_files_

Referenced by apply(), and frag_files().

◆ intermedrelax_

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

Referenced by apply(), and intermedrelax().

◆ loop_length_

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

Referenced by apply(), and loop_length().

◆ num_to_dock_

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

Referenced by apply(), and num_to_dock().

◆ refine_

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

Referenced by apply(), and refine().

◆ relax_

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

Referenced by apply(), and relax().

◆ remodel_

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

Referenced by apply(), and remodel().

◆ start_res_

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

Referenced by apply(), and start_res().

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