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protocols::dna::DnaInterfaceMinMover Class Reference

#include <DnaInterfaceMinMover.hh>

Inheritance diagram for protocols::dna::DnaInterfaceMinMover:
Inheritance graph
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Public Types

typedef utility::tag::TagCOP TagCOP
 
- Public Types inherited from protocols::minimization_packing::MinMover
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef
core::optimization::MinimizerOptionsOP 
MinimizerOptionsOP
 
typedef
core::optimization::MinimizerOptionsCOP 
MinimizerOptionsCOP
 
typedef core::Real Real
 
- 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
 

Public Member Functions

 DnaInterfaceMinMover ()
 
 DnaInterfaceMinMover (DnaInterfaceMinMover const &)
 
DnaInterfaceMinMoveroperator= (DnaInterfaceMinMover const &)
 
 ~DnaInterfaceMinMover () override
 
 DnaInterfaceMinMover (DnaInterfaceFinderOP)
 
void apply (core::pose::Pose &) override
 Main Method. More...
 
void use_interface (DnaInterfaceFinderOP)
 
void chi (bool value)
 
void bb (bool value)
 
void reset_from_interface ()
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::minimization_packing::MinMover
 MinMover ()
 Constructs a MinMover minmover = protocols::minimization_packing::MinMover() More...
 
 MinMover (std::string const &)
 
 ~MinMover () override
 
 MinMover (core::kinematics::MoveMapOP movemap_in, ScoreFunctionCOP scorefxn_in, std::string const &min_type_in, Real tolerance_in, bool use_nb_list_in, bool deriv_check_in=false, bool deriv_check_verbose_in=false)
 constructor with arguments More...
 
void apply (core::pose::Pose &pose) override
 Minimizes the DOFs of <pose_> specified in the MoveMap using the ScoreFunction. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
void cartesian (bool newval)
 
bool cartesian () const
 
void abs_score_convergence_threshold (Real newval)
 
Real abs_score_convergence_threshold () const
 
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 parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover's parsing. More...
 
void parse_opts (TagCOP, basic::datacache::DataMap &data_map)
 
void parse_movemap_factory (TagCOP, basic::datacache::DataMap &)
 
void parse_dof_tasks (TagCOP tag, basic::datacache::DataMap &data)
 
void parse_dof_task_type (std::string const &tag_name, core::id::DOF_Type dof_type, core::id::TorsionType torsion_type, TagCOP tag, basic::datacache::DataMap &data)
 helper function for parse_of_tasks More...
 
virtual MinimizerOptionsOP min_options ()
 allow non-const access to the internal minimizer options object More...
 
virtual MinimizerOptionsCOP min_options () const
 allow const access to the internal minimizer options object More...
 
virtual void min_options (MinimizerOptionsOP min_options)
 directly set the internal minimizer options object More...
 
virtual void movemap (core::kinematics::MoveMapCOP movemap_in)
 Sets the MoveMap to <movemap_in> determines which DOF to minimize. More...
 
void set_movemap (core::kinematics::MoveMapCOP movemap_in) override
 
virtual void movemap_factory (core::select::movemap::MoveMapFactoryCOP mmf)
 Sets the MoveMapFactory The MoveMapFactory will be used to construct a MoveMap if an explicit one isn't set. More...
 
core::kinematics::MoveMapCOP movemap (core::pose::Pose const &pose) const override
 Get the movemap for the pose. More...
 
core::kinematics::MoveMapCOP explicitly_set_movemap () const
 Get the explicitly set movemap object, if present, nullptr if not Will not create a default or look at the MoveMapFactory. More...
 
virtual void score_function (ScoreFunctionCOP scorefxn_in)
 Sets the ScoreFunction to <scorefxn_in> determines which function to minimize. More...
 
virtual ScoreFunctionCOP score_function () const
 
virtual void min_type (std::string min_type_in)
 
virtual void tolerance (Real tolerance_in)
 
virtual void nb_list (bool nb_list_in)
 Indicate whether or not a handful of optimizations regarding the neighbor list should be enabled. More...
 
virtual void deriv_check (bool deriv_check_in)
 
virtual void max_iter (core::Size max_iter_in)
 
Real tolerance () const
 
std::string min_type () const
 
bool nb_list () const
 Indicate whether or not a handful of optimizations regarding the neighbor list have been enabled. More...
 
bool deriv_check () const
 
bool omega () const
 
void omega (bool const b)
 
Real score_diff_after_minimization () const
 
Real abs_score_diff_after_minimization () const
 
- Public Member Functions inherited from protocols::moves::MoveMapMover
 MoveMapMover ()
 
 MoveMapMover (std::string const &name)
 
 MoveMapMover (MoveMapMover const &)=default
 
 ~MoveMapMover () override=default
 
virtual void initialize (core::pose::Pose &)
 
- 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 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::minimization_packing::MinMover
static std::string mover_name ()
 
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
complex_type_generator_for_min_mover (utility::tag::XMLSchemaDefinition &xsd)
 
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

DnaInterfaceFinderOP interface_
 
bool chi_
 
bool bb_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::minimization_packing::MinMover
void apply_dof_tasks_to_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap) const
 for use with RosettaScripts current method of using TaskOperations to specify residue sets. More...
 
void minimize (core::pose::Pose &pose, core::kinematics::MoveMap const &active_movemap)
 run the minimizer (cartesian or torsion) based on set options, with the final movemap setup. Will call inner_run_minimizer multiple times if abs_score_convergence_threshold is set 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...
 

Member Typedef Documentation

typedef utility::tag::TagCOP protocols::dna::DnaInterfaceMinMover::TagCOP

Constructor & Destructor Documentation

protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( )
protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( DnaInterfaceMinMover const &  src)
protocols::dna::DnaInterfaceMinMover::~DnaInterfaceMinMover ( )
overridedefault
protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( DnaInterfaceFinderOP  interface)

Member Function Documentation

void protocols::dna::DnaInterfaceMinMover::apply ( core::pose::Pose )
overridevirtual
void protocols::dna::DnaInterfaceMinMover::bb ( bool  value)
inline

References bb_.

void protocols::dna::DnaInterfaceMinMover::chi ( bool  value)
inline

References chi_.

MoverOP protocols::dna::DnaInterfaceMinMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

MoverOP protocols::dna::DnaInterfaceMinMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::dna::DnaInterfaceMinMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::dna::DnaInterfaceMinMover::mover_name ( )
static
DnaInterfaceMinMover & protocols::dna::DnaInterfaceMinMover::operator= ( DnaInterfaceMinMover const &  src)
void protocols::dna::DnaInterfaceMinMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

parse XML (in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References protocols::minimization_packing::MinMover::min_type(), protocols::minimization_packing::MinMover::score_function(), protocols::minimization_packing::MinMover::tolerance(), and use_interface().

void protocols::dna::DnaInterfaceMinMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::dna::DnaInterfaceMinMover::reset_from_interface ( )
void protocols::dna::DnaInterfaceMinMover::use_interface ( DnaInterfaceFinderOP  interface)

References interface_, and reset_from_interface().

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::dna::DnaInterfaceMinMover::bb_
private

Referenced by bb(), operator=(), and reset_from_interface().

bool protocols::dna::DnaInterfaceMinMover::chi_
private
DnaInterfaceFinderOP protocols::dna::DnaInterfaceMinMover::interface_
private

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