#include <SplitAndMixPoseMover.hh>
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::Size > | order () 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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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::Size > | order_ |
| bool | merge_chains_ |
| utility::vector1< SubPoseIDPair > | pairs_ |
| 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
◆ SubPoseIDPair
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private |
Constructor & Destructor Documentation
◆ SplitAndMixPoseMover()
| protocols::fold_from_loops::movers::SplitAndMixPoseMover::SplitAndMixPoseMover | ( | ) |
Empty Constructor.
◆ ~SplitAndMixPoseMover()
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inlineoverride |
Destructor.
Member Function Documentation
◆ adapt_order_to_pair()
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private |
References global_i_, increase_global_count(), NC_distance_filter(), pairs_, reset_order(), set_order(), protocols::fold_from_loops::movers::TR(), and try_all_pairs_.
Referenced by apply(), and apply_without_merge().
◆ apply()
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overridevirtual |
Apply Mover.
Implements protocols::moves::Mover.
References adapt_order_to_pair(), core::pose::Pose::annotated_sequence(), count_segments(), fill_pair_list(), core::pose::Pose::fold_tree(), protocols::mean_field::max(), merge_poses(), order_, core::pose::Pose::pdb_info(), selector_, set_order(), split_pose(), protocols::fold_from_loops::movers::TR(), and transfer_conformation().
◆ apply_without_merge()
| utility::vector1< core::pose::PoseOP > protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply_without_merge | ( | core::pose::Pose const & | pose | ) |
References adapt_order_to_pair(), count_segments(), fill_pair_list(), protocols::mean_field::max(), order_, set_order(), split_pose(), and protocols::fold_from_loops::movers::TR().
Referenced by protocols::fold_from_loops::utils::Nub::get_nub_pieces(), and protocols::fold_from_loops::NubInitioMover::get_template_pieces().
◆ clone()
|
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.
◆ count_segments() [1/2]
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inline |
Get Number of Segments.
References ranges_.
Referenced by apply(), apply_without_merge(), count_segments(), and split_pose().
◆ count_segments() [2/2]
| core::Size protocols::fold_from_loops::movers::SplitAndMixPoseMover::count_segments | ( | core::pose::Pose const & | pose | ) |
Calculate Number of Segments.
References count_segments(), fix_ranges(), ranges(), selector_, core::pose::Pose::size(), and protocols::fold_from_loops::movers::TR().
◆ default_exclude_consecutive()
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inlinestatic |
Exclude Consecutive Default.
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_max_distance()
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inlinestatic |
MaxDistance Default.
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_merge_chains()
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inlinestatic |
Merge Chains Default.
Referenced by parse_my_tag(), and provide_xml_schema().
◆ default_try_all_pairs()
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inlinestatic |
Try All Pairs Default.
Referenced by parse_my_tag(), and provide_xml_schema().
◆ exclude_consecutive()
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inline |
Exclude Consecutive Getter.
References exclude_consecutive_.
Referenced by set_exclude_consecutive().
◆ fill_pair_list()
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private |
References exclude_consecutive_, pairs_, protocols::fold_from_loops::movers::TR(), and try_all_pairs_.
Referenced by apply(), and apply_without_merge().
◆ fix_ranges()
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private |
◆ fresh_instance()
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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.
◆ get_global_i()
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inline |
GlobalI Getter.
References global_i_.
◆ get_name()
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inlineoverridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ increase_global_count()
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inlineprivate |
References global_i_, and pairs_.
Referenced by adapt_order_to_pair().
◆ max_distance()
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inline |
◆ merge_chains()
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inline |
Merge Chains Getter.
References merge_chains_.
◆ merge_poses()
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private |
References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), core::pose::append_pose_to_pose(), protocols::loops::chainID, core::pose::get_chain_from_chain_id(), merge_chains_, order_, core::pose::remove_lower_terminus_type_from_pose_residue(), and core::pose::remove_upper_terminus_type_from_pose_residue().
Referenced by apply().
◆ mover_name()
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inlinestatic |
◆ NC_distance_filter()
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private |
◆ order()
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inline |
◆ parse_my_tag()
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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().
◆ provide_xml_schema()
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static |
References core::select::residue_selector::attributes_for_parse_residue_selector_when_required(), default_exclude_consecutive(), default_max_distance(), default_merge_chains(), default_try_all_pairs(), mover_name(), core::id::to_string(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::fold_from_loops::movers::SplitAndMixPoseMoverCreator::provide_xml_schema().
◆ ranges()
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inline |
ResidueRanges Getter.
References ranges_.
Referenced by count_segments(), fix_ranges(), and set_ranges().
◆ reset_order()
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inline |
Re-merge order reSet to empty.
References order_.
Referenced by adapt_order_to_pair(), and set_order().
◆ residue_selector()
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inline |
ResidueSelector Getter.
References selector_.
◆ set_exclude_consecutive()
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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().
◆ set_max_distance()
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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().
◆ set_merge_chains()
|
inline |
Merge Chains Setter If True, this will only work as long as the segments of the same chain are ordered together.
References merge(), and merge_chains_.
Referenced by parse_my_tag().
◆ set_order() [1/3]
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inline |
Re-merge order Setter from 1 to max.
References protocols::mean_field::max(), order_, and reset_order().
◆ set_order() [2/3]
| void protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_order | ( | std::string | order | ) |
Re-merge order Setter.
References order(), order_, and reset_order().
◆ set_order() [3/3]
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inline |
Re-merge order Setter.
References order(), and order_.
Referenced by adapt_order_to_pair(), apply(), apply_without_merge(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), and parse_my_tag().
◆ set_ranges()
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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().
◆ set_residue_selector()
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inline |
ResidueSelector Setter.
References selector_.
Referenced by protocols::fold_from_loops::utils::Nub::get_nub_pieces(), and parse_my_tag().
◆ set_try_all_pairs()
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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().
◆ split_pose()
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private |
References protocols::grafting::simple_movers::DeleteRegionMover::apply(), core::pose::Pose::clone(), count_segments(), core::pose::Pose::fold_tree(), order_, protocols::sic_dock::range(), ranges_, protocols::grafting::simple_movers::DeleteRegionMover::set_residue_selector(), core::pose::Pose::size(), and protocols::fold_from_loops::movers::TR().
Referenced by apply(), and apply_without_merge().
◆ transfer_conformation()
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private |
References core::pose::Pose::clear(), core::pose::Pose::conformation_ptr(), core::pose::Pose::fold_tree(), and core::pose::Pose::set_new_conformation().
Referenced by apply().
◆ try_all_pairs()
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inline |
Member Data Documentation
◆ exclude_consecutive_
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private |
Referenced by exclude_consecutive(), fill_pair_list(), and set_exclude_consecutive().
◆ global_i_
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private |
Referenced by adapt_order_to_pair(), get_global_i(), and increase_global_count().
◆ max_distance_
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private |
Referenced by max_distance(), NC_distance_filter(), and set_max_distance().
◆ merge_chains_
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private |
Referenced by merge_chains(), merge_poses(), and set_merge_chains().
◆ order_
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private |
Referenced by apply(), apply_without_merge(), merge_poses(), order(), reset_order(), set_order(), and split_pose().
◆ pairs_
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private |
Referenced by adapt_order_to_pair(), fill_pair_list(), and increase_global_count().
◆ ranges_
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private |
Referenced by count_segments(), fix_ranges(), ranges(), set_ranges(), and split_pose().
◆ selector_
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private |
Referenced by apply(), count_segments(), residue_selector(), and set_residue_selector().
◆ try_all_pairs_
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private |
Referenced by adapt_order_to_pair(), fill_pair_list(), set_try_all_pairs(), and try_all_pairs().
The documentation for this class was generated from the following files:
- src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.hh
- src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc
