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protocols::ncbb::oop::OopDockDesignProtocol Class Reference

#include <OopDockDesignProtocol.hh>

Inheritance diagram for protocols::ncbb::oop::OopDockDesignProtocol:
Inheritance graph
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Public Member Functions

 OopDockDesignProtocol ()
 
 OopDockDesignProtocol (core::scoring::ScoreFunctionOP score_function, core::Real const mc_temp, core::Real const pert_mc_temp, core::Real const pert_dock_rot_mag, core::Real const pert_dock_trans_mag, core::Real const pert_pep_small_temp, core::Real const pert_pep_small_H, core::Real const pert_pep_small_L, core::Real const pert_pep_small_E, core::Real const pert_pep_shear_temp, core::Real const pert_pep_shear_H, core::Real const pert_pep_shear_L, core::Real const pert_pep_shear_E, core::Size const pert_pep_num_rep, core::Size const pert_num, core::Size const dock_design_loop_num, bool const no_design, bool const final_design_min, bool const use_soft_rep, bool const mc_initial_pose, bool const oop_design_first, bool const pymol, bool const keep_history)
 
 OopDockDesignProtocol (core::scoring::ScoreFunctionOP score_function, core::Real const mc_temp, core::Real const pert_dock_rot_mag, core::Real const pert_dock_trans_mag, core::Size const dock_design_loop_num, bool const no_design, bool const final_design_min, bool const pymol, bool const keep_history)
 
 ~OopDockDesignProtocol () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void parse_my_tag (utility::tag::TagCOP, 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...
 
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 Attributes

core::scoring::ScoreFunctionOP score_fxn_
 
core::Real mc_temp_
 
core::Real pert_mc_temp_
 
core::Real pert_dock_rot_mag_
 
core::Real pert_dock_trans_mag_
 
core::Real pert_pep_small_temp_
 
core::Real pert_pep_small_H_
 
core::Real pert_pep_small_L_
 
core::Real pert_pep_small_E_
 
core::Real pert_pep_shear_temp_
 
core::Real pert_pep_shear_H_
 
core::Real pert_pep_shear_L_
 
core::Real pert_pep_shear_E_
 
core::Size pert_pep_num_rep_
 
core::Size pert_num_
 
core::Size dock_design_loop_num_
 
bool no_design_
 
bool final_design_min_
 
bool use_soft_rep_
 
bool mc_initial_pose_
 
bool oop_design_first_
 
bool pymol_
 
bool keep_history_
 

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::ncbb::oop::OopDockDesignProtocol::OopDockDesignProtocol ( )
protocols::ncbb::oop::OopDockDesignProtocol::OopDockDesignProtocol ( core::scoring::ScoreFunctionOP  score_function,
core::Real const  mc_temp,
core::Real const  pert_mc_temp,
core::Real const  pert_dock_rot_mag,
core::Real const  pert_dock_trans_mag,
core::Real const  pert_pep_small_temp,
core::Real const  pert_pep_small_H,
core::Real const  pert_pep_small_L,
core::Real const  pert_pep_small_E,
core::Real const  pert_pep_shear_temp,
core::Real const  pert_pep_shear_H,
core::Real const  pert_pep_shear_L,
core::Real const  pert_pep_shear_E,
core::Size const  pert_pep_num_rep,
core::Size const  pert_num,
core::Size const  dock_design_loop_num,
bool const  no_design,
bool const  final_design_min,
bool const  use_soft_rep,
bool const  mc_initial_pose,
bool const  oop_design_first,
bool const  pymol,
bool const  keep_history 
)
protocols::ncbb::oop::OopDockDesignProtocol::OopDockDesignProtocol ( core::scoring::ScoreFunctionOP  score_function,
core::Real const  mc_temp,
core::Real const  pert_dock_rot_mag,
core::Real const  pert_dock_trans_mag,
core::Size const  dock_design_loop_num,
bool const  no_design,
bool const  final_design_min,
bool const  pymol,
bool const  keep_history 
)
protocols::ncbb::oop::OopDockDesignProtocol::~OopDockDesignProtocol ( )
inlineoverride

Member Function Documentation

void protocols::ncbb::oop::OopDockDesignProtocol::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::ncbb::oop::OopDockDesignProtocol::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.

References dock_design_loop_num_, final_design_min_, keep_history_, mc_initial_pose_, mc_temp_, no_design_, oop_design_first_, pert_dock_rot_mag_, pert_dock_trans_mag_, pert_mc_temp_, pert_num_, pert_pep_num_rep_, pert_pep_shear_E_, pert_pep_shear_H_, pert_pep_shear_L_, pert_pep_shear_temp_, pert_pep_small_E_, pert_pep_small_H_, pert_pep_small_L_, pert_pep_small_temp_, pymol_, score_fxn_, and use_soft_rep_.

protocols::moves::MoverOP protocols::ncbb::oop::OopDockDesignProtocol::fresh_instance ( ) const
inlineoverridevirtual

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::ncbb::oop::OopDockDesignProtocol::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::ncbb::oop::OopDockDesignProtocol::mover_name ( )
static
void protocols::ncbb::oop::OopDockDesignProtocol::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 protocols::ncbb::init_common_options().

void protocols::ncbb::oop::OopDockDesignProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Member Data Documentation

core::Size protocols::ncbb::oop::OopDockDesignProtocol::dock_design_loop_num_
private

Referenced by apply(), and clone().

bool protocols::ncbb::oop::OopDockDesignProtocol::final_design_min_
private

Referenced by apply(), and clone().

bool protocols::ncbb::oop::OopDockDesignProtocol::keep_history_
private

Referenced by apply(), and clone().

bool protocols::ncbb::oop::OopDockDesignProtocol::mc_initial_pose_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::mc_temp_
private

Referenced by apply(), and clone().

bool protocols::ncbb::oop::OopDockDesignProtocol::no_design_
private

Referenced by apply(), and clone().

bool protocols::ncbb::oop::OopDockDesignProtocol::oop_design_first_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_dock_rot_mag_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_dock_trans_mag_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_mc_temp_
private

Referenced by apply(), and clone().

core::Size protocols::ncbb::oop::OopDockDesignProtocol::pert_num_
private

Referenced by apply(), and clone().

core::Size protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_num_rep_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_shear_E_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_shear_H_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_shear_L_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_shear_temp_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_small_E_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_small_H_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_small_L_
private

Referenced by apply(), and clone().

core::Real protocols::ncbb::oop::OopDockDesignProtocol::pert_pep_small_temp_
private

Referenced by apply(), and clone().

bool protocols::ncbb::oop::OopDockDesignProtocol::pymol_
private

Referenced by apply(), and clone().

core::scoring::ScoreFunctionOP protocols::ncbb::oop::OopDockDesignProtocol::score_fxn_
private

Referenced by apply(), clone(), and OopDockDesignProtocol().

bool protocols::ncbb::oop::OopDockDesignProtocol::use_soft_rep_
private

Referenced by apply(), and clone().


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