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protocols::stepwise::modeler::StepWiseMinimizer Class Reference

#include <StepWiseMinimizer.hh>

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

 StepWiseMinimizer (utility::vector1< core::pose::PoseOP > const &pose_list, working_parameters::StepWiseWorkingParametersCOP working_parameters, options::StepWiseModelerOptionsCOP options, core::scoring::ScoreFunctionCOP scorefxn)
 
 ~StepWiseMinimizer () override
 
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_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
 
void set_working_pack_res (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Size >
const & 
working_pack_res () const
 
utility::vector1
< core::pose::PoseOP
pose_list () const
 
core::Size const & num_pose_minimize () const
 
utility::vector1< core::Size >
const & 
working_minimize_res () const
 
- 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_parameters ()
 
void let_neighboring_side_chains_minimize (core::kinematics::MoveMap &mm, core::pose::Pose const &pose)
 
void setup_minimizers ()
 
void setup_scorefxns (core::pose::Pose const &pose)
 
void do_minimize (core::pose::Pose &pose, core::kinematics::MoveMap &mm)
 
void do_full_minimizing (core::pose::Pose &pose)
 
void do_clustering (core::pose::Pose &pose)
 
void get_move_map_and_atom_level_domain_map (core::kinematics::MoveMap &mm, core::pose::Pose const &pose)
 
void close_chainbreaks (core::pose::Pose &pose, core::kinematics::MoveMap &mm)
 
void setup_all_moving_res (core::pose::Pose const &pose)
 
void move_side_chain (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, core::Size const j)
 
void output_empty_minimizer_silent_file () const
 
bool check_pose_list (core::pose::Pose const &pose)
 
void output_minimized_pose_list () const
 
void setup_vary_bond_geometry (core::pose::Pose &pose, core::kinematics::MoveMap &mm)
 
utility::vector1< core::Sizefigure_out_working_minimize_res (core::pose::Pose const &pose)
 

Private Attributes

utility::vector1
< core::pose::PoseOP
pose_list_
 
options::StepWiseModelerOptionsCOP options_
 
core::scoring::ScoreFunctionCOP scorefxn_
 
core::scoring::ScoreFunctionOP minimize_scorefxn_
 
core::scoring::ScoreFunctionOP final_scorefxn_
 
core::Size num_pose_minimize_
 
utility::vector1< core::Size >
const 
working_moving_res_
 
utility::vector1< core::Sizeworking_fixed_res_
 
utility::vector1< core::Sizeworking_calc_rms_res_
 
utility::vector1< core::Sizeworking_pack_res_
 
utility::vector1< core::Sizeworking_minimize_res_
 
core::optimization::CartesianMinimizerOP cartesian_minimizer_
 
core::optimization::AtomTreeMinimizerOP atom_tree_minimizer_
 
core::optimization::MinimizerOptionsOP minimizer_options_
 
bool const allow_virtual_o2prime_hydrogens_
 
protein::loop_close::StepWiseProteinCCD_CloserOP protein_ccd_closer_
 
working_parameters::StepWiseWorkingParametersCOP working_parameters_
 
core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map_
 

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::StepWiseMinimizer::StepWiseMinimizer ( utility::vector1< core::pose::PoseOP > const &  pose_list,
working_parameters::StepWiseWorkingParametersCOP  working_parameters,
options::StepWiseModelerOptionsCOP  options,
core::scoring::ScoreFunctionCOP  scorefxn 
)
protocols::stepwise::modeler::StepWiseMinimizer::~StepWiseMinimizer ( )
overridedefault

Member Function Documentation

void protocols::stepwise::modeler::StepWiseMinimizer::apply ( core::pose::Pose )
overridevirtual
bool protocols::stepwise::modeler::StepWiseMinimizer::check_pose_list ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseMinimizer::close_chainbreaks ( core::pose::Pose pose,
core::kinematics::MoveMap mm 
)
private
void protocols::stepwise::modeler::StepWiseMinimizer::do_clustering ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseMinimizer::do_full_minimizing ( core::pose::Pose pose)
private
void protocols::stepwise::modeler::StepWiseMinimizer::do_minimize ( core::pose::Pose pose,
core::kinematics::MoveMap mm 
)
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::figure_out_working_minimize_res ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseMinimizer::get_move_map_and_atom_level_domain_map ( core::kinematics::MoveMap mm,
core::pose::Pose const &  pose 
)
private
std::string protocols::stepwise::modeler::StepWiseMinimizer::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::StepWiseMinimizer::initialize_parameters ( )
private
void protocols::stepwise::modeler::StepWiseMinimizer::let_neighboring_side_chains_minimize ( core::kinematics::MoveMap mm,
core::pose::Pose const &  pose 
)
private
void protocols::stepwise::modeler::StepWiseMinimizer::move_side_chain ( core::kinematics::MoveMap mm,
core::pose::Pose const &  pose,
core::Size const  j 
)
private
core::Size const& protocols::stepwise::modeler::StepWiseMinimizer::num_pose_minimize ( ) const
inline

References num_pose_minimize_.

void protocols::stepwise::modeler::StepWiseMinimizer::output_empty_minimizer_silent_file ( ) const
private

References options_.

Referenced by check_pose_list().

void protocols::stepwise::modeler::StepWiseMinimizer::output_minimized_pose_list ( ) const
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseMinimizer::pose_list ( ) const
inline

References pose_list_.

void protocols::stepwise::modeler::StepWiseMinimizer::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)
inline

References scorefxn_.

void protocols::stepwise::modeler::StepWiseMinimizer::set_working_pack_res ( utility::vector1< core::Size > const &  setting)
inline

References working_pack_res_.

void protocols::stepwise::modeler::StepWiseMinimizer::setup_all_moving_res ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseMinimizer::setup_minimizers ( )
private
void protocols::stepwise::modeler::StepWiseMinimizer::setup_scorefxns ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::StepWiseMinimizer::setup_vary_bond_geometry ( core::pose::Pose pose,
core::kinematics::MoveMap mm 
)
private
utility::vector1< core::Size > const& protocols::stepwise::modeler::StepWiseMinimizer::working_minimize_res ( ) const
inline
utility::vector1< core::Size > const& protocols::stepwise::modeler::StepWiseMinimizer::working_pack_res ( ) const
inline

References working_pack_res_.

Member Data Documentation

bool const protocols::stepwise::modeler::StepWiseMinimizer::allow_virtual_o2prime_hydrogens_
private

Referenced by do_minimize().

core::pose::toolbox::AtomLevelDomainMapOP protocols::stepwise::modeler::StepWiseMinimizer::atom_level_domain_map_
private
core::optimization::AtomTreeMinimizerOP protocols::stepwise::modeler::StepWiseMinimizer::atom_tree_minimizer_
private

Referenced by do_minimize(), and setup_minimizers().

core::optimization::CartesianMinimizerOP protocols::stepwise::modeler::StepWiseMinimizer::cartesian_minimizer_
private

Referenced by do_minimize(), and setup_minimizers().

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::StepWiseMinimizer::final_scorefxn_
private

Referenced by setup_scorefxns().

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::StepWiseMinimizer::minimize_scorefxn_
private
core::optimization::MinimizerOptionsOP protocols::stepwise::modeler::StepWiseMinimizer::minimizer_options_
private

Referenced by do_minimize(), and setup_minimizers().

core::Size protocols::stepwise::modeler::StepWiseMinimizer::num_pose_minimize_
private
options::StepWiseModelerOptionsCOP protocols::stepwise::modeler::StepWiseMinimizer::options_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::StepWiseMinimizer::pose_list_
private
protein::loop_close::StepWiseProteinCCD_CloserOP protocols::stepwise::modeler::StepWiseMinimizer::protein_ccd_closer_
private

Referenced by close_chainbreaks().

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::StepWiseMinimizer::scorefxn_
private

Referenced by set_scorefxn(), and setup_scorefxns().

utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::working_calc_rms_res_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::working_fixed_res_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::working_minimize_res_
private
utility::vector1< core::Size > const protocols::stepwise::modeler::StepWiseMinimizer::working_moving_res_
private
utility::vector1< core::Size > protocols::stepwise::modeler::StepWiseMinimizer::working_pack_res_
private
working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::StepWiseMinimizer::working_parameters_
private

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