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protocols::fold_from_loops::movers::SplitAndMixPoseMover Class Reference

#include <SplitAndMixPoseMover.hh>

Inheritance diagram for protocols::fold_from_loops::movers::SplitAndMixPoseMover:
Inheritance graph
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Public Member Functions

 SplitAndMixPoseMover ()
 Empty Constructor. More...
 
 ~SplitAndMixPoseMover () override
 Destructor. More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 ResidueSelector Setter. More...
 
core::select::residue_selector::ResidueSelectorCOP residue_selector () const
 ResidueSelector Getter. More...
 
core::select::residue_selector::ResidueRangesOP ranges () const
 ResidueRanges Getter. More...
 
void set_ranges (core::select::residue_selector::ResidueRangesOP const &ranges)
 ResidueRanges Setter (by doing this, it avoids applying the ResidueSelector) More...
 
void reset_order ()
 Re-merge order reSet to empty. More...
 
void set_order (utility::vector1< core::Size > order)
 Re-merge order Setter. More...
 
void set_order (std::string order)
 Re-merge order Setter. More...
 
void set_order (core::Size max)
 Re-merge order Setter from 1 to max. More...
 
utility::vector1< core::Sizeorder () const
 Re-merge order Getter. More...
 
void set_merge_chains (bool merge)
 Merge Chains Setter If True, this will only work as long as the segments of the same chain are ordered together. More...
 
bool merge_chains () const
 Merge Chains Getter. More...
 
void set_try_all_pairs (bool try_all_pairs)
 If True, at each loop of -nstruct it will generate a new pose combining two different subposes. More...
 
bool try_all_pairs () const
 Try All Pairs Getter. More...
 
void set_exclude_consecutive (bool exclude_consecutive)
 If True, and try_all_pairs_ True, consecutive pairs are excluded from the list. More...
 
bool exclude_consecutive () const
 Exclude Consecutive Getter. More...
 
void set_max_distance (core::Real max_distance)
 If Set to a positive value, that is the max distance between SubPose1-Cterm and SubPose2-Nterm allowed to concatenate them. More...
 
core::Real max_distance () const
 MaxDistance Getter. More...
 
core::Size get_global_i () const
 GlobalI Getter. More...
 
core::Size count_segments () const
 Get Number of Segments. More...
 
core::Size count_segments (core::pose::Pose const &pose)
 Calculate Number of Segments. More...
 
void apply (core::pose::Pose &pose) override
 Apply Mover. More...
 
utility::vector1
< core::pose::PoseOP
apply_without_merge (core::pose::Pose const &pose)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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 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 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...
 

Static Public Member Functions

static bool default_merge_chains ()
 Merge Chains Default. More...
 
static bool default_try_all_pairs ()
 Try All Pairs Default. More...
 
static bool default_exclude_consecutive ()
 Exclude Consecutive Default. More...
 
static core::Real default_max_distance ()
 MaxDistance Default. More...
 
static std::string mover_name ()
 
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 Types

typedef boost::tuple
< core::Size, core::Size
SubPoseIDPair
 

Private Member Functions

void fix_ranges (core::pose::Pose const &pose, core::select::residue_selector::ResidueRanges const &ranges)
 
utility::vector1
< core::pose::PoseOP
split_pose (core::pose::Pose const &pose)
 
core::pose::PoseOP merge_poses (utility::vector1< core::pose::PoseOP > const &pose_list)
 
void transfer_conformation (core::pose::Pose &pose, core::pose::Pose const &merged)
 
void increase_global_count ()
 
void fill_pair_list (core::Size total_subposes)
 
void adapt_order_to_pair (utility::vector1< core::pose::PoseOP > const &pose_list)
 
bool NC_distance_filter (core::pose::Pose const &npose, core::pose::Pose const &cpose)
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector_
 
core::select::residue_selector::ResidueRangesOP ranges_
 
utility::vector1< core::Sizeorder_
 
bool merge_chains_
 
utility::vector1< SubPoseIDPairpairs_
 
bool try_all_pairs_
 
bool exclude_consecutive_
 
core::Real max_distance_
 
core::Size global_i_
 

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
 
- 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

Constructor & Destructor Documentation

protocols::fold_from_loops::movers::SplitAndMixPoseMover::SplitAndMixPoseMover ( )

Empty Constructor.

protocols::fold_from_loops::movers::SplitAndMixPoseMover::~SplitAndMixPoseMover ( )
inlineoverride

Destructor.

Member Function Documentation

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::adapt_order_to_pair ( utility::vector1< core::pose::PoseOP > const &  pose_list)
private
void protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply ( core::pose::Pose pose)
overridevirtual
utility::vector1< core::pose::PoseOP > protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply_without_merge ( core::pose::Pose const &  pose)
moves::MoverOP protocols::fold_from_loops::movers::SplitAndMixPoseMover::clone ( ) const
inlineoverridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

core::Size protocols::fold_from_loops::movers::SplitAndMixPoseMover::count_segments ( ) const
inline

Get Number of Segments.

References ranges_.

Referenced by apply(), apply_without_merge(), count_segments(), and split_pose().

core::Size protocols::fold_from_loops::movers::SplitAndMixPoseMover::count_segments ( core::pose::Pose const &  pose)
static bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::default_exclude_consecutive ( )
inlinestatic

Exclude Consecutive Default.

Referenced by parse_my_tag(), and provide_xml_schema().

static core::Real protocols::fold_from_loops::movers::SplitAndMixPoseMover::default_max_distance ( )
inlinestatic

MaxDistance Default.

Referenced by parse_my_tag(), and provide_xml_schema().

static bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::default_merge_chains ( )
inlinestatic

Merge Chains Default.

Referenced by parse_my_tag(), and provide_xml_schema().

static bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::default_try_all_pairs ( )
inlinestatic

Try All Pairs Default.

Referenced by parse_my_tag(), and provide_xml_schema().

bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::exclude_consecutive ( ) const
inline

Exclude Consecutive Getter.

References exclude_consecutive_.

Referenced by set_exclude_consecutive().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::fill_pair_list ( core::Size  total_subposes)
private
void protocols::fold_from_loops::movers::SplitAndMixPoseMover::fix_ranges ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueRanges const &  ranges 
)
private
moves::MoverOP protocols::fold_from_loops::movers::SplitAndMixPoseMover::fresh_instance ( ) const
inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

core::Size protocols::fold_from_loops::movers::SplitAndMixPoseMover::get_global_i ( ) const
inline

GlobalI Getter.

References global_i_.

std::string protocols::fold_from_loops::movers::SplitAndMixPoseMover::get_name ( ) const
inlineoverridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::increase_global_count ( )
inlineprivate

References global_i_, and pairs_.

Referenced by adapt_order_to_pair().

core::Real protocols::fold_from_loops::movers::SplitAndMixPoseMover::max_distance ( ) const
inline

MaxDistance Getter.

References max_distance_.

Referenced by set_max_distance().

bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_chains ( ) const
inline

Merge Chains Getter.

References merge_chains_.

core::pose::PoseOP protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_poses ( utility::vector1< core::pose::PoseOP > const &  pose_list)
private
static std::string protocols::fold_from_loops::movers::SplitAndMixPoseMover::mover_name ( )
inlinestatic
bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::NC_distance_filter ( core::pose::Pose const &  npose,
core::pose::Pose const &  cpose 
)
private
utility::vector1< core::Size > protocols::fold_from_loops::movers::SplitAndMixPoseMover::order ( ) const
inline

Re-merge order Getter.

References order_.

Referenced by set_order().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References default_exclude_consecutive(), default_max_distance(), default_merge_chains(), default_try_all_pairs(), core::select::residue_selector::parse_residue_selector(), set_exclude_consecutive(), set_max_distance(), set_merge_chains(), set_order(), set_residue_selector(), and set_try_all_pairs().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
core::select::residue_selector::ResidueRangesOP protocols::fold_from_loops::movers::SplitAndMixPoseMover::ranges ( ) const
inline

ResidueRanges Getter.

References ranges_.

Referenced by count_segments(), and set_ranges().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::reset_order ( )
inline

Re-merge order reSet to empty.

References order_.

Referenced by adapt_order_to_pair(), and set_order().

core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::movers::SplitAndMixPoseMover::residue_selector ( ) const
inline

ResidueSelector Getter.

References selector_.

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_exclude_consecutive ( bool  exclude_consecutive)
inline

If True, and try_all_pairs_ True, consecutive pairs are excluded from the list.

References exclude_consecutive(), and exclude_consecutive_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_max_distance ( core::Real  max_distance)
inline

If Set to a positive value, that is the max distance between SubPose1-Cterm and SubPose2-Nterm allowed to concatenate them.

References max_distance(), and max_distance_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_merge_chains ( bool  merge)
inline

Merge Chains Setter If True, this will only work as long as the segments of the same chain are ordered together.

References protocols::forge::methods::merge(), and merge_chains_.

Referenced by parse_my_tag().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_order ( utility::vector1< core::Size order)
inline

Re-merge order Setter.

References order(), and order_.

Referenced by adapt_order_to_pair(), apply(), apply_without_merge(), and parse_my_tag().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_order ( std::string  order)

Re-merge order Setter.

References order_, and reset_order().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_order ( core::Size  max)
inline

Re-merge order Setter from 1 to max.

References protocols::mean_field::max(), order_, and reset_order().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_ranges ( core::select::residue_selector::ResidueRangesOP const &  ranges)
inline

ResidueRanges Setter (by doing this, it avoids applying the ResidueSelector)

References ranges(), and ranges_.

Referenced by protocols::fold_from_loops::NubInitioMover::get_template_pieces().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)
inline

ResidueSelector Setter.

References selector_.

Referenced by protocols::fold_from_loops::utils::Nub::get_nub_pieces(), and parse_my_tag().

void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_try_all_pairs ( bool  try_all_pairs)
inline

If True, at each loop of -nstruct it will generate a new pose combining two different subposes.

References try_all_pairs(), and try_all_pairs_.

Referenced by parse_my_tag().

utility::vector1< core::pose::PoseOP > protocols::fold_from_loops::movers::SplitAndMixPoseMover::split_pose ( core::pose::Pose const &  pose)
private
void protocols::fold_from_loops::movers::SplitAndMixPoseMover::transfer_conformation ( core::pose::Pose pose,
core::pose::Pose const &  merged 
)
private
bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::try_all_pairs ( ) const
inline

Try All Pairs Getter.

References try_all_pairs_.

Referenced by set_try_all_pairs().

Member Data Documentation

bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::exclude_consecutive_
private
core::Size protocols::fold_from_loops::movers::SplitAndMixPoseMover::global_i_
private
core::Real protocols::fold_from_loops::movers::SplitAndMixPoseMover::max_distance_
private
bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::merge_chains_
private
utility::vector1< core::Size > protocols::fold_from_loops::movers::SplitAndMixPoseMover::order_
private
utility::vector1< SubPoseIDPair > protocols::fold_from_loops::movers::SplitAndMixPoseMover::pairs_
private
core::select::residue_selector::ResidueRangesOP protocols::fold_from_loops::movers::SplitAndMixPoseMover::ranges_
private
core::select::residue_selector::ResidueSelectorCOP protocols::fold_from_loops::movers::SplitAndMixPoseMover::selector_
private
bool protocols::fold_from_loops::movers::SplitAndMixPoseMover::try_all_pairs_
private

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