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protocols::stepwise::modeler::StepWiseModeler Class Reference

#include <StepWiseModeler.hh>

Inheritance diagram for protocols::stepwise::modeler::StepWiseModeler:
Inheritance graph
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Public Member Functions

 StepWiseModeler (core::Size const moving_res, core::scoring::ScoreFunctionCOP scorefxn)
 
 StepWiseModeler (core::scoring::ScoreFunctionCOP scorefxn)
 
 ~StepWiseModeler () override
 
 StepWiseModeler (StepWiseModeler const &src)
 
virtual StepWiseModelerOP clone_modeler () const
 
StepWiseModeleroperator= (StepWiseModeler const &src)
 
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...
 
void set_moving_res_and_reset (core::Size const moving_res)
 
void set_working_prepack_res (utility::vector1< core::Size > const &setting)
 
void set_working_minimize_res (utility::vector1< core::Size > const &setting)
 
void set_figure_out_prepack_res (bool const setting)
 
void set_working_parameters (working_parameters::StepWiseWorkingParametersCOP working_parameters)
 
working_parameters::StepWiseWorkingParametersCOP working_parameters ()
 
void set_options (options::StepWiseModelerOptionsCOP options)
 
options::StepWiseModelerOptionsCOP options ()
 
void set_precomputed_library_mover (precomputed::PrecomputedLibraryMoverCOP precomputed_library_mover)
 
precomputed::PrecomputedLibraryMoverCOP precomputed_library_mover ()
 
core::Size get_num_sampled ()
 
void set_input_streams (utility::vector1< protein::InputStreamWithResidueInfoOP > const &input_streams)
 
void set_moving_res_list (utility::vector1< core::Size > const &setting)
 
core::scoring::ScoreFunctionCOP scorefxn ()
 
- 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 Member Functions

void initialize (core::pose::Pose &pose)
 
void reinitialize (core::pose::Pose &pose)
 
void initialize_working_parameters_and_root (core::pose::Pose &pose)
 
void initialize_scorefunctions (core::pose::Pose const &pose)
 
void initialize_constraints (core::pose::Pose &pose)
 
void do_prepacking (core::pose::Pose &pose)
 
void do_sampling (core::pose::Pose &pose)
 
void do_minimizing (core::pose::Pose &pose)
 
void do_stepwise_lores (core::pose::Pose &pose)
 
void figure_out_moving_res_list (core::pose::Pose const &pose)
 
void figure_out_moving_res_list_from_most_distal_res (core::pose::Pose const &pose, core::Size const moving_res)
 
bool sampling_successful ()
 
void look_for_precompute_move (core::pose::Pose &pose)
 

Private Attributes

core::Size moving_res_
 
utility::vector1< core::Sizemoving_res_list_
 
utility::vector1< core::Sizeworking_minimize_res_
 
utility::vector1< core::Sizeworking_prepack_res_
 
working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
options::StepWiseModelerOptionsCOP options_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
core::scoring::ScoreFunctionCOP sample_scorefxn_
 
core::scoring::ScoreFunctionCOP pack_scorefxn_
 
utility::vector1
< protein::InputStreamWithResidueInfoOP
input_streams_
 
utility::vector1
< core::pose::PoseOP
pose_list_
 
bool figure_out_prepack_res_
 
bool prepack_res_was_inputted_
 
packer::StepWiseMasterPackerOP master_packer_
 
core::scoring::constraints::ConstraintSetOP cst_set_
 
precomputed::PrecomputedLibraryMoverCOP precomputed_library_mover_
 

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::stepwise::modeler::StepWiseModeler::StepWiseModeler ( core::Size const  moving_res,
core::scoring::ScoreFunctionCOP  scorefxn 
)
protocols::stepwise::modeler::StepWiseModeler::StepWiseModeler ( core::scoring::ScoreFunctionCOP  scorefxn)
protocols::stepwise::modeler::StepWiseModeler::~StepWiseModeler ( )
overridedefault
protocols::stepwise::modeler::StepWiseModeler::StepWiseModeler ( StepWiseModeler const &  src)

Member Function Documentation

void protocols::stepwise::modeler::StepWiseModeler::apply ( core::pose::Pose )
overridevirtual
StepWiseModelerOP protocols::stepwise::modeler::StepWiseModeler::clone_modeler ( ) const
virtual
void protocols::stepwise::modeler::StepWiseModeler::do_minimizing ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseModeler::do_prepacking ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseModeler::do_sampling ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseModeler::do_stepwise_lores ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseModeler::figure_out_moving_res_list ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseModeler::figure_out_moving_res_list_from_most_distal_res ( core::pose::Pose const &  pose,
core::Size const  moving_res 
)
private
std::string protocols::stepwise::modeler::StepWiseModeler::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

core::Size protocols::stepwise::modeler::StepWiseModeler::get_num_sampled ( )
inline

References pose_list_.

void protocols::stepwise::modeler::StepWiseModeler::initialize ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseModeler::initialize_constraints ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseModeler::initialize_scorefunctions ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseModeler::look_for_precompute_move ( core::pose::Pose pose)
private
StepWiseModeler & protocols::stepwise::modeler::StepWiseModeler::operator= ( StepWiseModeler const &  src)
options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::StepWiseModeler::options ( )
inline

References options_.

Referenced by set_options().

precomputed::PrecomputedLibraryMoverCOP protocols::stepwise::modeler::StepWiseModeler::precomputed_library_mover ( )
inline
void protocols::stepwise::modeler::StepWiseModeler::reinitialize ( core::pose::Pose pose)
private
bool protocols::stepwise::modeler::StepWiseModeler::sampling_successful ( )
private

References options_, pose_list_, and protocols::TR().

Referenced by apply().

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseModeler::scorefxn ( )
inline

References scorefxn_.

void protocols::stepwise::modeler::StepWiseModeler::set_figure_out_prepack_res ( bool const  setting)
inline
void protocols::stepwise::modeler::StepWiseModeler::set_input_streams ( utility::vector1< protein::InputStreamWithResidueInfoOP > const &  input_streams)

References input_streams_.

void protocols::stepwise::modeler::StepWiseModeler::set_moving_res_and_reset ( core::Size const  moving_res)
void protocols::stepwise::modeler::StepWiseModeler::set_moving_res_list ( utility::vector1< core::Size > const &  setting)
inline

References moving_res_list_.

void protocols::stepwise::modeler::StepWiseModeler::set_options ( options::StepWiseModelerOptionsCOP  options)
inline

References options(), and options_.

void protocols::stepwise::modeler::StepWiseModeler::set_precomputed_library_mover ( precomputed::PrecomputedLibraryMoverCOP  precomputed_library_mover)
inline
void protocols::stepwise::modeler::StepWiseModeler::set_working_minimize_res ( utility::vector1< core::Size > const &  setting)
inline
void protocols::stepwise::modeler::StepWiseModeler::set_working_parameters ( working_parameters::StepWiseWorkingParametersCOP  working_parameters)
void protocols::stepwise::modeler::StepWiseModeler::set_working_prepack_res ( utility::vector1< core::Size > const &  setting)
inline
working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::StepWiseModeler::working_parameters ( )

References working_parameters_.

Referenced by set_working_parameters().

Member Data Documentation

core::scoring::constraints::ConstraintSetOP protocols::stepwise::modeler::StepWiseModeler::cst_set_
private
bool protocols::stepwise::modeler::StepWiseModeler::figure_out_prepack_res_
private
utility::vector1< protein::InputStreamWithResidueInfoOP > protocols::stepwise::modeler::StepWiseModeler::input_streams_
private
packer::StepWiseMasterPackerOP protocols::stepwise::modeler::StepWiseModeler::master_packer_
private
core::Size protocols::stepwise::modeler::StepWiseModeler::moving_res_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseModeler::moving_res_list_
private
options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::StepWiseModeler::options_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseModeler::pack_scorefxn_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseModeler::pose_list_
private
precomputed::PrecomputedLibraryMoverCOP protocols::stepwise::modeler::StepWiseModeler::precomputed_library_mover_
private
bool protocols::stepwise::modeler::StepWiseModeler::prepack_res_was_inputted_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseModeler::sample_scorefxn_
private
core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseModeler::scorefxn_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseModeler::working_minimize_res_
private
working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::StepWiseModeler::working_parameters_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseModeler::working_prepack_res_
private

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