Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::hybridization::MRMover Class Reference

#include <MRMover.hh>

Inheritance diagram for protocols::hybridization::MRMover:
Inheritance graph

Public Member Functions

 MRMover ()
void init ()
void apply (Pose &pose) override
 Main Method. 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...
void set_centroid_density_weight (core::Real newval)
void set_fullatom_density_weight (core::Real newval, bool fast)
void set_max_gaplength_to_model (core::Size newval)
void set_symmdef_file (std::string newval)
void set_censcale (core::Real newval)
void set_cen_cst_weight (core::Real newval)
void set_fa_cst_weight (core::Real newval)
void set_disulf (utility::vector1< std::string > newval)
void set_big_fragments (core::fragment::FragSetOP newval)
void set_small_fragments (core::fragment::FragSetOP newval)
- 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 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 Member Functions

void trim_target_pose (Pose &query_pose, protocols::loops::Loops &loops, core::Size max_gaplength)
void pack_missing_sidechains (Pose &pose)

Private Attributes

std::string symm_def_file_
core::fragment::FragSetOP fragments_big_
core::fragment::FragSetOP fragments_small_
core::fragment::FragSetOP fragments_big_trim_
core::fragment::FragSetOP fragments_small_trim_
core::scoring::ScoreFunctionOP cen1_scorefxn_
core::scoring::ScoreFunctionOP cen2_scorefxn_
core::scoring::ScoreFunctionOP fa_scorefxn_
utility::vector1< std::string > disulfs_
core::Size max_gaplength_to_model_
core::Size relax_max_iter_
core::Size relax_cycles_
core::Real censcale_

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

◆ MRMover()

protocols::hybridization::MRMover::MRMover ( )

References init().

Member Function Documentation

◆ apply()

void protocols::hybridization::MRMover::apply ( Pose )

Main Method.

Implements protocols::moves::Mover.

References protocols::hybridization::HybridizeProtocol::add_big_fragments(), core::pose::add_lower_terminus_type_to_pose_residue(), protocols::hybridization::HybridizeProtocol::add_small_fragments(), protocols::hybridization::HybridizeProtocol::add_template(), core::pose::add_upper_terminus_type_to_pose_residue(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, cen1_scorefxn_, cen2_scorefxn_, censcale_, core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), disulfs_, fa_scorefxn_, core::conformation::Conformation::fix_disulfides(), fragments_big_trim_, fragments_small_trim_, protocols::moves::Mover::get_current_tag(), protocols::jd2::JobDistributor::get_instance(), core::conformation::idealize_position(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_upper_terminus(), max_gaplength_to_model_, protocols::hybridization::parse_res(), core::scoring::pro_close, relax_cycles_, relax_max_iter_, core::pose::Pose::residue(), protocols::hybridization::HybridizeProtocol::set_batch_relax(), protocols::hybridization::HybridizeProtocol::set_stage1_increase_cycles(), protocols::hybridization::HybridizeProtocol::set_stage1_scorefxn(), protocols::hybridization::HybridizeProtocol::set_stage2_increase_cycles(), protocols::hybridization::HybridizeProtocol::set_stage2_scorefxn(), core::pose::Pose::size(), symm_def_file_, core::id::THETA, protocols::medal::to_centroid(), and trim_target_pose().

◆ clone()

protocols::moves::MoverOP protocols::hybridization::MRMover::clone ( ) const

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.

◆ fresh_instance()

protocols::moves::MoverOP protocols::hybridization::MRMover::fresh_instance ( ) const

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.

◆ get_name()

std::string protocols::hybridization::MRMover::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ init()

void protocols::hybridization::MRMover::init ( void  )

◆ pack_missing_sidechains()

void protocols::hybridization::MRMover::pack_missing_sidechains ( Pose pose)

◆ set_big_fragments()

void protocols::hybridization::MRMover::set_big_fragments ( core::fragment::FragSetOP  newval)

◆ set_cen_cst_weight()

void protocols::hybridization::MRMover::set_cen_cst_weight ( core::Real  newval)

◆ set_censcale()

void protocols::hybridization::MRMover::set_censcale ( core::Real  newval)

References censcale_.

◆ set_centroid_density_weight()

void protocols::hybridization::MRMover::set_centroid_density_weight ( core::Real  newval)

◆ set_disulf()

void protocols::hybridization::MRMover::set_disulf ( utility::vector1< std::string >  newval)

References disulfs_.

◆ set_fa_cst_weight()

void protocols::hybridization::MRMover::set_fa_cst_weight ( core::Real  newval)

◆ set_fullatom_density_weight()

void protocols::hybridization::MRMover::set_fullatom_density_weight ( core::Real  newval,
bool  fast 

◆ set_max_gaplength_to_model()

void protocols::hybridization::MRMover::set_max_gaplength_to_model ( core::Size  newval)

◆ set_small_fragments()

void protocols::hybridization::MRMover::set_small_fragments ( core::fragment::FragSetOP  newval)

◆ set_symmdef_file()

void protocols::hybridization::MRMover::set_symmdef_file ( std::string  newval)

References symm_def_file_.

◆ trim_target_pose()

void protocols::hybridization::MRMover::trim_target_pose ( Pose query_pose,
protocols::loops::Loops loops,
core::Size  max_gaplength 

Member Data Documentation

◆ cen1_scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::MRMover::cen1_scorefxn_

◆ cen2_scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::MRMover::cen2_scorefxn_

◆ censcale_

core::Real protocols::hybridization::MRMover::censcale_

Referenced by apply(), init(), and set_censcale().

◆ disulfs_

utility::vector1<std::string> protocols::hybridization::MRMover::disulfs_

Referenced by apply(), and set_disulf().

◆ fa_scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::MRMover::fa_scorefxn_

◆ fragments_big_

core::fragment::FragSetOP protocols::hybridization::MRMover::fragments_big_

◆ fragments_big_trim_

core::fragment::FragSetOP protocols::hybridization::MRMover::fragments_big_trim_

◆ fragments_small_

core::fragment::FragSetOP protocols::hybridization::MRMover::fragments_small_

◆ fragments_small_trim_

core::fragment::FragSetOP protocols::hybridization::MRMover::fragments_small_trim_

◆ max_gaplength_to_model_

core::Size protocols::hybridization::MRMover::max_gaplength_to_model_

◆ relax_cycles_

core::Size protocols::hybridization::MRMover::relax_cycles_

Referenced by apply(), and init().

◆ relax_max_iter_

core::Size protocols::hybridization::MRMover::relax_max_iter_

Referenced by apply(), and init().

◆ symm_def_file_

std::string protocols::hybridization::MRMover::symm_def_file_

Referenced by apply(), and set_symmdef_file().

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