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protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer Class Reference

#include <StepWiseProteinMinimizer.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer:
Inheritance graph
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Public Member Functions

 StepWiseProteinMinimizer (utility::vector1< core::pose::PoseOP > const &pose_list, utility::vector1< core::Size > const &moving_residues)
 
 ~StepWiseProteinMinimizer () override
 
void apply (core::pose::Pose &pose_to_visualize) override
 Apply the minimizer to one pose. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void set_min_tolerance (core::Real const &setting)
 
void set_min_type (std::string const &setting)
 
void set_fixed_res (utility::vector1< core::Size > const &fixed_res)
 
void set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
 
core::Size const & num_pose_minimize () const
 
void set_num_pose_minimize (core::Size const &setting)
 
void set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)
 
void set_move_takeoff_torsions (bool const value)
 
void set_rescore_only (bool const &setting)
 
void set_move_jumps_between_chains (bool const &setting)
 
void set_cartesian (bool const setting)
 
void set_use_coordinate_constraints (bool const &setting)
 
bool use_coordinate_constraints () const
 
utility::vector1
< core::pose::PoseOP
pose_list () 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_chis_minimize (core::kinematics::MoveMap &mm, core::pose::Pose &pose)
 
bool pose_has_chainbreak (core::pose::Pose const &pose)
 

Private Attributes

utility::vector1< core::Size >
const & 
moving_residues_
 
utility::vector1< core::Sizefixed_res_
 
utility::vector1< core::Sizecalc_rms_res_
 
bool move_takeoff_torsions_
 
bool rescore_only_
 
bool move_jumps_between_chains_
 
bool cartesian_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
utility::vector1
< core::pose::PoseOP
pose_list_
 
std::string min_type_
 
core::Real min_tolerance_
 
bool use_coordinate_constraints_
 
core::Size num_pose_minimize_
 

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::legacy::modeler::protein::StepWiseProteinMinimizer::StepWiseProteinMinimizer ( utility::vector1< core::pose::PoseOP > const &  pose_list,
utility::vector1< core::Size > const &  moving_residues 
)
protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::~StepWiseProteinMinimizer ( )
overridedefault

Member Function Documentation

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply ( core::pose::Pose pose_to_visualize)
overridevirtual
std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::initialize_parameters ( )
private
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize ( core::kinematics::MoveMap mm,
core::pose::Pose pose 
)
private
core::Size const& protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::num_pose_minimize ( ) const
inline

References num_pose_minimize_.

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::pose_has_chainbreak ( core::pose::Pose const &  pose)
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::pose_list ( ) const
inline

References pose_list_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_calc_rms_res ( utility::vector1< core::Size > const &  calc_rms_res)

References calc_rms_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_cartesian ( bool const  setting)

References cartesian_, and min_type_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_fixed_res ( utility::vector1< core::Size > const &  fixed_res)

References fixed_res_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_min_tolerance ( core::Real const &  setting)

References min_tolerance_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_min_type ( std::string const &  setting)

References min_type_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_move_jumps_between_chains ( bool const &  setting)
inline
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_move_takeoff_torsions ( bool const  value)
inline
void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_num_pose_minimize ( core::Size const &  setting)
inline

References num_pose_minimize_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_rescore_only ( bool const &  setting)
inline

References rescore_only_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_scorefxn ( core::scoring::ScoreFunctionOP const &  scorefxn)

References fa_scorefxn_.

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::set_use_coordinate_constraints ( bool const &  setting)
inline
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::use_coordinate_constraints ( ) const
inline

Member Data Documentation

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::calc_rms_res_
private

Referenced by set_calc_rms_res().

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::cartesian_
private
core::scoring::ScoreFunctionOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::fa_scorefxn_
private

Referenced by apply(), and set_scorefxn().

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::fixed_res_
private

Referenced by apply(), and set_fixed_res().

core::Real protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::min_tolerance_
private
std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::min_type_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::move_jumps_between_chains_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::move_takeoff_torsions_
private
utility::vector1< core::Size > const& protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::moving_residues_
private
core::Size protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::num_pose_minimize_
private
utility::vector1< core::pose::PoseOP > protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::pose_list_
private

Referenced by apply(), and pose_list().

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::rescore_only_
private
bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::use_coordinate_constraints_
private

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