#include <SheetTranslate.hh>
Public Member Functions | |
| SheetTranslate () | |
| SheetTranslate (const protocols::loops::Loop &sheet, core::Real distance_ang) | |
| void | apply (core::pose::Pose &pose) override |
| Translates the sheet by the specified distance (in Angstroms) More... | |
| std::string | get_name () const override |
| Returns the protocol's name. More... | |
| moves::MoverOP | clone () const override |
| Creates a new instance with the copy constructor. More... | |
| moves::MoverOP | fresh_instance () const override |
| Creates a new instance with the default constructor. More... | |
| const protocols::loops::Loop & | get_sheet () const |
| Returns the sheet to be modified. More... | |
| core::Real | get_distance () const |
| Returns the distance (in Angstroms) to translate the sheet. More... | |
| void | set_sheet (const protocols::loops::Loop &sheet) |
| Updates the sheet to be modified. More... | |
| void | set_distance (core::Real distance_ang) |
| Updates the distance (in Angstroms) to translate the sheet. 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 |
| 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 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... | |
Private Member Functions | |
| void | initialize (const protocols::loops::Loop &sheet, core::Real distance) |
| Shared initialization routine. More... | |
| bool | is_valid () const |
| Returns true if this instance is valid and fully configured. More... | |
| void | decompose_structure (unsigned num_residues, protocols::loops::Loops *chunks) const |
| Partitions the structure such that the sheet to be translated belongs to its own chunk, which will be subsequently connected to the star fold tree by its own jump. More... | |
| unsigned | jump_containing_sheet (const protocols::loops::Loops &chunks) const |
| Searches chunks for the member representing the sheet, returning its index. More... | |
Private Attributes | |
| protocols::loops::Loop | sheet_ |
| Stretch of contiguous residues representing the sheet to be rotated. More... | |
| core::Real | distance_ |
| Distance to translate the sheet in Angstroms. 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
◆ SheetTranslate() [1/2]
| protocols::nonlocal::SheetTranslate::SheetTranslate | ( | ) |
References initialize().
◆ SheetTranslate() [2/2]
| protocols::nonlocal::SheetTranslate::SheetTranslate | ( | const protocols::loops::Loop & | sheet, |
| core::Real | distance_ang | ||
| ) |
References initialize(), and core::scoring::sheet.
Member Function Documentation
◆ apply()
|
overridevirtual |
Translates the sheet by the specified distance (in Angstroms)
Implements protocols::moves::Mover.
References core::pose::Pose::conformation(), decompose_structure(), core::pose::Pose::fold_tree(), get_distance(), get_sheet(), is_valid(), core::pose::Pose::jump(), jump_containing_sheet(), core::pose::Pose::set_jump(), protocols::nonlocal::StarTreeBuilder::set_up(), sheet_, core::pose::Pose::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::nonlocal::StarTreeBuilder::tear_down(), protocols::nonlocal::TR(), core::kinematics::Jump::translation_along_axis(), core::conformation::Conformation::upstream_jump_stub(), and core::pose::Pose::xyz().
◆ clone()
|
overridevirtual |
Creates a new instance with the copy constructor.
Reimplemented from protocols::moves::Mover.
◆ decompose_structure()
|
private |
Partitions the structure such that the sheet to be translated belongs to its own chunk, which will be subsequently connected to the star fold tree by its own jump.
References protocols::loops::Loops::add_loop(), get_sheet(), protocols::loops::Loops::sequential_order(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), and protocols::loops::stop.
Referenced by apply().
◆ fresh_instance()
|
overridevirtual |
Creates a new instance with the default constructor.
Reimplemented from protocols::moves::Mover.
◆ get_distance()
| core::Real protocols::nonlocal::SheetTranslate::get_distance | ( | ) | const |
◆ get_name()
|
overridevirtual |
Returns the protocol's name.
Implements protocols::moves::Mover.
◆ get_sheet()
| const protocols::loops::Loop & protocols::nonlocal::SheetTranslate::get_sheet | ( | ) | const |
Returns the sheet to be modified.
References sheet_.
Referenced by apply(), and decompose_structure().
◆ initialize()
|
private |
Shared initialization routine.
References core::kinematics::distance(), distance_, core::scoring::sheet, and sheet_.
Referenced by SheetTranslate().
◆ is_valid()
|
private |
Returns true if this instance is valid and fully configured.
References sheet_, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().
Referenced by apply().
◆ jump_containing_sheet()
|
private |
Searches chunks for the member representing the sheet, returning its index.
References protocols::loops::Loops::num_loop(), sheet_, protocols::loops::Loop::start(), and protocols::loops::start.
Referenced by apply().
◆ set_distance()
| void protocols::nonlocal::SheetTranslate::set_distance | ( | core::Real | distance_ang | ) |
Updates the distance (in Angstroms) to translate the sheet.
References distance_.
◆ set_sheet()
| void protocols::nonlocal::SheetTranslate::set_sheet | ( | const protocols::loops::Loop & | sheet | ) |
Updates the sheet to be modified.
References core::scoring::sheet, and sheet_.
Member Data Documentation
◆ distance_
|
private |
Distance to translate the sheet in Angstroms.
Referenced by get_distance(), initialize(), and set_distance().
◆ sheet_
|
private |
Stretch of contiguous residues representing the sheet to be rotated.
Referenced by apply(), get_sheet(), initialize(), is_valid(), jump_containing_sheet(), and set_sheet().
The documentation for this class was generated from the following files:
- src/protocols/nonlocal/SheetTranslate.hh
- src/protocols/nonlocal/SheetTranslate.cc
