Settings for SewAnything. This is stored for each SS. More...
#include <SewAnythingAddMover.hh>
Public Member Functions | |
| SewAnythingAddMover () | |
| Constructors ///. More... | |
| SewAnythingAddMover (SewAnythingAddMover const &src) | |
| Copy constructor (not needed unless you need deep copies) More... | |
| ~SewAnythingAddMover () override | |
| Destructor (important for properly forward-declaring smart-pointer members) More... | |
| void | apply (core::pose::Pose &pose) override |
| Mover Methods ///. More... | |
| std::pair< core::Size, core::Size > | find_sewable_region (core::pose::Pose &pose) |
| char | find_mod_terminus (core::pose::Pose &pose, std::pair< core::Size, core::Size >) |
| bool | align (core::pose::Pose const &stationary_pose, core::Size stationary_residue, core::pose::Pose &mobile_pose, core::Size mobile_residue, core::Size window_width, core::Real tolerance, bool check_alignment=true) const |
| bool | clashes (core::pose::Pose const &nterm_pose, core::Size first_nterm_res, core::Size last_nterm_res, core::pose::Pose const &cterm_pose, core::Size first_cterm_res, core::Size last_cterm_res, core::Real clash_radius, bool check_all_backbone) const |
| data_storage::TerminalDSSPSortedPoseVectorOP | get_pose_vector () const |
| core::Real | get_clash_radius () const |
| utility::vector1< std::string > | get_segment_file_paths () const |
| bool | get_trim_terminal_loops () const |
| std::string | get_permissible_segment_ends () const |
| void | set_permissible_segment_ends (std::string) |
| std::string | get_permissible_termini () const |
| core::Size | get_max_attempts () const |
| void | show (std::ostream &output=std::cout) const override |
| Show the contents of the Mover. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| Rosetta Scripts Support ///. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| required in the context of the parser/scripting scheme More... | |
| protocols::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... | |
| std::pair< std::string, std::string > | segment_vector_dssp (char mod_terminus, char mod_terminus_dssp, std::string const &permissible_segment_ends) const |
| Mover Methods ///. More... | |
| void | set_segment_file_paths (utility::vector1< std::string > segment_file_paths) |
 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 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 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... | |
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... | |
Detailed Description
Settings for SewAnything. This is stored for each SS.
perform SEWING-like chimerization-based addition of supersecondary structural segments into previously virtual residues
Constructor & Destructor Documentation
◆ SewAnythingAddMover() [1/2]
| protocols::pose_sewing::movers::SewAnythingAddMover::SewAnythingAddMover | ( | ) |
◆ SewAnythingAddMover() [2/2]
|
default |
Copy constructor (not needed unless you need deep copies)
Copy constructor.
◆ ~SewAnythingAddMover()
|
override |
Destructor (important for properly forward-declaring smart-pointer members)
Member Function Documentation
◆ align()
| bool protocols::pose_sewing::movers::SewAnythingAddMover::align | ( | core::pose::Pose const & | stationary_pose, |
| core::Size | stationary_residue, | ||
| core::pose::Pose & | mobile_pose, | ||
| core::Size | mobile_residue, | ||
| core::Size | window_width, | ||
| core::Real | tolerance, | ||
| bool | check_alignment = true |
||
| ) | const |
◆ apply()
|
overridevirtual |
Mover Methods ///.
Apply the mover.
Apply the mover
Implements protocols::moves::Mover.
References align(), alignment_max_distance_, all_post_filters_, all_seg_filters_, allow_DSSP_insertion_, core::pose::Pose::chain(), check_all_backbone_atoms_, protocols::denovo_design::components::check_residue(), core::pose::Pose::chi(), clash_radius_, clashes(), protocols::simple_filters::dssp(), even_sampling_, fail_on_no_match_, find_mod_terminus(), find_sewable_region(), hashable_element_max_size_, hashable_element_min_size_, hashable_element_relative_max_size_, hashable_element_relative_min_size_, core::conformation::Residue::is_virtual_residue(), max_attempts_, max_cter_len_, max_filter_attempts_, max_nter_len_, protocols::moves::MS_FAIL, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), permissible_segment_ends_, pose_vector_, positive_scores_are_better_, core::pose::Pose::real_to_virtual(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::rg, protocols::hybridization::score, core::pose::Pose::secstruct(), seg_filters_, segment_file_paths_, segment_vector_dssp(), protocols::moves::Mover::set_last_move_status(), core::pose::set_reasonable_fold_tree(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), sort_metric_, core::id::to_string(), protocols::TR(), trim_terminal_loops_, use_absolute_sizes_, use_relative_sizes_, and window_width_.
◆ clashes()
| bool protocols::pose_sewing::movers::SewAnythingAddMover::clashes | ( | core::pose::Pose const & | nterm_pose, |
| core::Size | first_nterm_res, | ||
| core::Size | last_nterm_res, | ||
| core::pose::Pose const & | cterm_pose, | ||
| core::Size | first_cterm_res, | ||
| core::Size | last_cterm_res, | ||
| core::Real | clash_radius, | ||
| bool | check_all_backbone | ||
| ) | const |
◆ clone()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
References SewAnythingAddMover().
◆ find_mod_terminus()
| char protocols::pose_sewing::movers::SewAnythingAddMover::find_mod_terminus | ( | core::pose::Pose & | pose, |
| std::pair< core::Size, core::Size > | current_residue_pair | ||
| ) |
References core::conformation::Residue::is_virtual_residue(), permissible_termini_, and core::pose::Pose::residue().
Referenced by apply().
◆ find_sewable_region()
| std::pair< core::Size, core::Size > protocols::pose_sewing::movers::SewAnythingAddMover::find_sewable_region | ( | core::pose::Pose & | pose | ) |
References core::pose::Pose::pdb_info(), and core::pose::Pose::size().
Referenced by apply().
◆ fresh_instance()
|
overridevirtual |
required in the context of the parser/scripting scheme
Reimplemented from protocols::moves::Mover.
◆ get_clash_radius()
| core::Real protocols::pose_sewing::movers::SewAnythingAddMover::get_clash_radius | ( | ) | const |
References clash_radius_.
◆ get_max_attempts()
| core::Size protocols::pose_sewing::movers::SewAnythingAddMover::get_max_attempts | ( | ) | const |
References max_attempts_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ get_permissible_segment_ends()
| std::string protocols::pose_sewing::movers::SewAnythingAddMover::get_permissible_segment_ends | ( | ) | const |
References permissible_segment_ends_.
◆ get_permissible_termini()
| std::string protocols::pose_sewing::movers::SewAnythingAddMover::get_permissible_termini | ( | ) | const |
References permissible_termini_.
◆ get_pose_vector()
| data_storage::TerminalDSSPSortedPoseVectorOP protocols::pose_sewing::movers::SewAnythingAddMover::get_pose_vector | ( | ) | const |
References pose_vector_.
◆ get_segment_file_paths()
| utility::vector1< std::string > protocols::pose_sewing::movers::SewAnythingAddMover::get_segment_file_paths | ( | ) | const |
References segment_file_paths_.
◆ get_trim_terminal_loops()
| bool protocols::pose_sewing::movers::SewAnythingAddMover::get_trim_terminal_loops | ( | ) | const |
References trim_terminal_loops_.
◆ mover_name()
|
static |
◆ parse_my_tag()
|
overridevirtual |
Rosetta Scripts Support ///.
parse XML tag (to use this Mover in Rosetta Scripts)
Reimplemented from protocols::moves::Mover.
References alignment_max_distance_, all_post_filters_, all_seg_filters_, allow_DSSP_insertion_, check_all_backbone_atoms_, clash_radius_, enable_clash_check_v2_, even_sampling_, fail_on_no_match_, hashable_element_max_size_, hashable_element_min_size_, hashable_element_relative_max_size_, hashable_element_relative_min_size_, max_attempts_, max_filter_attempts_, protocols::rosetta_scripts::parse_filter(), permissible_segment_ends_, permissible_termini_, pose_vector_, positive_scores_are_better_, seg_filters_, segment_file_paths_, sort_metric_, protocols::TR(), trim_terminal_loops_, use_absolute_sizes_, use_relative_sizes_, and window_width_.
◆ provide_xml_schema()
|
static |
◆ segment_vector_dssp()
| std::pair< std::string, std::string > protocols::pose_sewing::movers::SewAnythingAddMover::segment_vector_dssp | ( | char | mod_terminus, |
| char | mod_terminus_dssp, | ||
| std::string const & | permissible_segment_ends | ||
| ) | const |
Mover Methods ///.
Referenced by apply().
◆ set_permissible_segment_ends()
| void protocols::pose_sewing::movers::SewAnythingAddMover::set_permissible_segment_ends | ( | std::string | in | ) |
References core::conformation::membrane::in, and permissible_segment_ends_.
◆ set_segment_file_paths()
| void protocols::pose_sewing::movers::SewAnythingAddMover::set_segment_file_paths | ( | utility::vector1< std::string > | segment_file_paths | ) |
References segment_file_paths_.
◆ show()
|
overridevirtual |
Show the contents of the Mover.
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::show().
Referenced by protocols::pose_sewing::movers::operator<<().
Member Data Documentation
◆ alignment_max_distance_
|
private |
Referenced by apply(), and parse_my_tag().
◆ all_post_filters_
|
private |
Referenced by apply(), and parse_my_tag().
◆ all_seg_filters_
|
private |
Referenced by apply(), and parse_my_tag().
◆ allow_DSSP_insertion_
|
private |
Referenced by apply(), and parse_my_tag().
◆ check_all_backbone_atoms_
|
private |
Referenced by apply(), and parse_my_tag().
◆ clash_radius_
|
private |
Referenced by apply(), get_clash_radius(), and parse_my_tag().
◆ enable_clash_check_v2_
|
private |
Referenced by clashes(), and parse_my_tag().
◆ even_sampling_
|
private |
Referenced by apply(), and parse_my_tag().
◆ fail_on_no_match_
|
private |
Referenced by apply(), and parse_my_tag().
◆ hashable_element_max_size_
|
private |
Referenced by apply(), and parse_my_tag().
◆ hashable_element_min_size_
|
private |
Referenced by apply(), and parse_my_tag().
◆ hashable_element_relative_max_size_
|
private |
Referenced by apply(), and parse_my_tag().
◆ hashable_element_relative_min_size_
|
private |
Referenced by apply(), and parse_my_tag().
◆ ht_ref_pose_
|
private |
◆ max_attempts_
|
private |
Referenced by apply(), get_max_attempts(), and parse_my_tag().
◆ max_cter_len_
|
private |
Referenced by apply().
◆ max_filter_attempts_
|
private |
Referenced by apply(), and parse_my_tag().
◆ max_nter_len_
|
private |
Referenced by apply().
◆ permissible_segment_ends_
|
private |
Referenced by apply(), get_permissible_segment_ends(), parse_my_tag(), and set_permissible_segment_ends().
◆ permissible_termini_
|
private |
Referenced by find_mod_terminus(), get_permissible_termini(), and parse_my_tag().
◆ pose_vector_
|
private |
Referenced by apply(), get_pose_vector(), parse_my_tag(), and SewAnythingAddMover().
◆ positive_scores_are_better_
|
private |
Referenced by apply(), and parse_my_tag().
◆ seg_filters_
|
private |
Referenced by apply(), and parse_my_tag().
◆ segment_file_paths_
|
private |
Referenced by apply(), get_segment_file_paths(), parse_my_tag(), and set_segment_file_paths().
◆ sort_metric_
|
private |
Referenced by apply(), and parse_my_tag().
◆ trim_terminal_loops_
|
private |
Referenced by apply(), get_trim_terminal_loops(), and parse_my_tag().
◆ use_absolute_sizes_
|
private |
Referenced by apply(), and parse_my_tag().
◆ use_relative_sizes_
|
private |
Referenced by apply(), and parse_my_tag().
◆ window_width_
|
private |
Referenced by apply(), and parse_my_tag().
The documentation for this class was generated from the following files:
- src/protocols/pose_sewing/movers/SewAnythingAddMover.hh
- src/protocols/pose_sewing/movers/SewAnythingAddMover.cc
