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protocols::anchored_design::AnchoredRefineMover Class Reference

#include <AnchorMovers.hh>

Inheritance diagram for protocols::anchored_design::AnchoredRefineMover:
Inheritance graph
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Public Member Functions

 AnchoredRefineMover (protocols::anchored_design::AnchorMoversDataOP interface_in)
 
 ~AnchoredRefineMover () 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...
 
bool get_debug () const
 debugging mode activates a bunch of extra output More...
 
bool get_refine_CCD_off () const
 do not perform CCD style closure (use KIC only) More...
 
bool get_refine_KIC_off () const
 do not perform KIC style closure (use CCD only) More...
 
bool get_nonpivot_torsion_sampling () const
 use nonpivot torsion sampling for KIC? More...
 
bool get_vicinity_sampling () const
 KIC use vicinity sampling? More...
 
core::Real get_vicinity_degree () const
 KIC vicinity sampling degrees. More...
 
core::Real get_refine_temp () const
 MC temperature. More...
 
core::Size get_refine_cycles () const
 number of MC cycles More...
 
std::string const & get_min_type () const
 what minimizer type to use? More...
 
core::Size get_refine_repack_cycles () const
 how many cycles between repack/design opportunities? More...
 
void set_debug (bool const debug)
 debugging mode activates a bunch of extra output More...
 
void set_refine_CCD_off (bool const refine_CCD_off)
 do not perform CCD style closure (use KIC only) More...
 
void set_refine_KIC_off (bool const refine_KIC_off)
 do not perform KIC style closure (use CCD only) More...
 
void set_nonpivot_torsion_sampling (bool const nonpivot_torsion_sampling)
 use nonpivot torsion sampling for KIC? More...
 
void set_vicinity_sampling (bool const vicinity_sampling)
 KIC use vicinity sampling? More...
 
void set_vicinity_degree (core::Size const vicinity_degree)
 KIC vicinity sampling degrees. More...
 
void set_refine_temp (core::Real const refine_temp)
 MC temperature. More...
 
void set_refine_cycles (core::Size const refine_cycles)
 number of MC cycles More...
 
void set_min_type (std::string const &min_type)
 what minimizer type to use? More...
 
void set_refine_repack_cycles (core::Size const refine_repack_cycles)
 how many cycles between repack/design opportunities? More...
 
void read_options ()
 read in options from the options system 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 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 Attributes

protocols::anchored_design::AnchorMoversDataOP interface_
 
bool debug_
 debugging mode activates a bunch of extra output More...
 
bool refine_CCD_off_
 do not perform CCD style closure (use KIC only) More...
 
bool refine_KIC_off_
 do not perform KIC style closure (use CCD only) More...
 
bool nonpivot_torsion_sampling_
 use nonpivot torsion sampling for KIC? More...
 
bool vicinity_sampling_
 KIC use vicinity sampling? More...
 
core::Real vicinity_degree_
 KIC vicinity sampling degrees. More...
 
core::Real refine_temp_
 MC temperature. More...
 
core::Size refine_cycles_
 number of MC cycles More...
 
std::string min_type_
 what minimizer type to use? More...
 
core::Size refine_repack_cycles_
 how many cycles between repack/design opportunities? More...
 

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::anchored_design::AnchoredRefineMover::AnchoredRefineMover ( protocols::anchored_design::AnchorMoversDataOP  interface_in)
protocols::anchored_design::AnchoredRefineMover::~AnchoredRefineMover ( )
overridedefault

Member Function Documentation

void protocols::anchored_design::AnchoredRefineMover::apply ( core::pose::Pose )
overridevirtual
bool protocols::anchored_design::AnchoredRefineMover::get_debug ( ) const

debugging mode activates a bunch of extra output

References debug_.

std::string const & protocols::anchored_design::AnchoredRefineMover::get_min_type ( ) const

what minimizer type to use?

References min_type_.

std::string protocols::anchored_design::AnchoredRefineMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::anchored_design::AnchoredRefineMover::get_nonpivot_torsion_sampling ( ) const

use nonpivot torsion sampling for KIC?

References nonpivot_torsion_sampling_.

bool protocols::anchored_design::AnchoredRefineMover::get_refine_CCD_off ( ) const

do not perform CCD style closure (use KIC only)

References refine_CCD_off_.

core::Size protocols::anchored_design::AnchoredRefineMover::get_refine_cycles ( ) const

number of MC cycles

References refine_cycles_.

bool protocols::anchored_design::AnchoredRefineMover::get_refine_KIC_off ( ) const

do not perform KIC style closure (use CCD only)

References refine_KIC_off_.

core::Size protocols::anchored_design::AnchoredRefineMover::get_refine_repack_cycles ( ) const

how many cycles between repack/design opportunities?

References refine_repack_cycles_.

core::Real protocols::anchored_design::AnchoredRefineMover::get_refine_temp ( ) const

MC temperature.

References refine_temp_.

core::Real protocols::anchored_design::AnchoredRefineMover::get_vicinity_degree ( ) const

KIC vicinity sampling degrees.

References vicinity_degree_.

bool protocols::anchored_design::AnchoredRefineMover::get_vicinity_sampling ( ) const

KIC use vicinity sampling?

References vicinity_sampling_.

void protocols::anchored_design::AnchoredRefineMover::read_options ( )
void protocols::anchored_design::AnchoredRefineMover::set_debug ( bool const  debug)

debugging mode activates a bunch of extra output

References core::pack::interaction_graph::debug, and debug_.

void protocols::anchored_design::AnchoredRefineMover::set_min_type ( std::string const &  min_type)

what minimizer type to use?

References min_type_.

void protocols::anchored_design::AnchoredRefineMover::set_nonpivot_torsion_sampling ( bool const  nonpivot_torsion_sampling)

use nonpivot torsion sampling for KIC?

References nonpivot_torsion_sampling_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_CCD_off ( bool const  refine_CCD_off)

do not perform CCD style closure (use KIC only)

References refine_CCD_off_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_cycles ( core::Size const  refine_cycles)

number of MC cycles

References refine_cycles_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_KIC_off ( bool const  refine_KIC_off)

do not perform KIC style closure (use CCD only)

References refine_KIC_off_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_repack_cycles ( core::Size const  refine_repack_cycles)

how many cycles between repack/design opportunities?

References refine_repack_cycles_.

void protocols::anchored_design::AnchoredRefineMover::set_refine_temp ( core::Real const  refine_temp)

MC temperature.

References refine_temp_.

void protocols::anchored_design::AnchoredRefineMover::set_vicinity_degree ( core::Size const  vicinity_degree)

KIC vicinity sampling degrees.

References vicinity_degree_.

void protocols::anchored_design::AnchoredRefineMover::set_vicinity_sampling ( bool const  vicinity_sampling)

KIC use vicinity sampling?

References vicinity_sampling_.

Member Data Documentation

bool protocols::anchored_design::AnchoredRefineMover::debug_
private

debugging mode activates a bunch of extra output

Referenced by apply(), get_debug(), read_options(), and set_debug().

protocols::anchored_design::AnchorMoversDataOP protocols::anchored_design::AnchoredRefineMover::interface_
private

Referenced by apply().

std::string protocols::anchored_design::AnchoredRefineMover::min_type_
private

what minimizer type to use?

Referenced by apply(), get_min_type(), read_options(), and set_min_type().

bool protocols::anchored_design::AnchoredRefineMover::nonpivot_torsion_sampling_
private

use nonpivot torsion sampling for KIC?

Referenced by apply(), get_nonpivot_torsion_sampling(), read_options(), and set_nonpivot_torsion_sampling().

bool protocols::anchored_design::AnchoredRefineMover::refine_CCD_off_
private

do not perform CCD style closure (use KIC only)

Referenced by apply(), get_refine_CCD_off(), read_options(), and set_refine_CCD_off().

core::Size protocols::anchored_design::AnchoredRefineMover::refine_cycles_
private

number of MC cycles

Referenced by apply(), get_refine_cycles(), read_options(), and set_refine_cycles().

bool protocols::anchored_design::AnchoredRefineMover::refine_KIC_off_
private

do not perform KIC style closure (use CCD only)

Referenced by apply(), get_refine_KIC_off(), read_options(), and set_refine_KIC_off().

core::Size protocols::anchored_design::AnchoredRefineMover::refine_repack_cycles_
private

how many cycles between repack/design opportunities?

Referenced by apply(), get_refine_repack_cycles(), read_options(), and set_refine_repack_cycles().

core::Real protocols::anchored_design::AnchoredRefineMover::refine_temp_
private

MC temperature.

Referenced by apply(), get_refine_temp(), read_options(), and set_refine_temp().

core::Real protocols::anchored_design::AnchoredRefineMover::vicinity_degree_
private

KIC vicinity sampling degrees.

Referenced by apply(), get_vicinity_degree(), read_options(), and set_vicinity_degree().

bool protocols::anchored_design::AnchoredRefineMover::vicinity_sampling_
private

KIC use vicinity sampling?

Referenced by get_vicinity_sampling(), read_options(), and set_vicinity_sampling().


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