#include <NonlocalFrags.hh>
Public Member Functions | |
| NonlocalFrags () | |
| Constructs a new mover. More... | |
| void | apply (core::pose::Pose &pose) override |
| Finds interacting non-local fragment pairs. More... | |
| std::string | get_name () const override |
| Returns the name of this mover. More... | |
| protocols::moves::MoverOP | clone () const override |
| Creates a copy of this instance. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Creates a new instance by calling the no-argument constructor. 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... | |
Static Public Member Functions | |
| static void | register_options () |
| Registers applicable options. More... | |
| 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 Member Functions | |
| void | initialize () |
| bool | recover_checkpoint (std::string const &tag, core::pose::Pose &pose) |
| void | write_checkpoint (std::string const &tag, std::string const &data) |
| void | read_checkpoint_file () |
Private Attributes | |
| bool | single_chain_ |
| bool | relax_input_ |
| bool | relax_input_with_coordinate_constraints_ |
| core::Size | relax_frags_repeats_ |
| std::string | checkpointfile_ |
| std::map< std::string, std::string > | checkpoints_map_ |
| utility::vector1< core::Size > | frag_sizes_ |
| core::Size | min_seq_sep_ |
| core::Real | ca_dist_squared_ |
| core::Size | min_contacts_per_res_ |
| core::Real | max_rmsd_after_relax_ |
| core::Real | max_ddg_score_ |
| bool | output_frags_pdbs_ |
| bool | output_idealized_ |
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... | |
Constructor & Destructor Documentation
◆ NonlocalFrags()
| protocols::frag_picker::nonlocal::NonlocalFrags::NonlocalFrags | ( | ) |
Constructs a new mover.
References initialize().
Member Function Documentation
◆ apply()
|
overridevirtual |
Finds interacting non-local fragment pairs.
Implements protocols::moves::Mover.
References core::pose::add_comment(), core::scoring::angle_constraint, protocols::idealize::IdealizeMover::apply(), core::scoring::atom_pair_constraint, ca_dist_squared_, core::scoring::CA_rmsd(), core::conformation::Residue::chain(), protocols::idealize::IdealizeMover::chainbreaks(), core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pose::create_subpose(), protocols::jd2::current_input_tag(), protocols::jd2::JobDistributor::current_job(), protocols::jd2::current_output_name(), core::conformation::Conformation::detect_disulfides(), core::scoring::dihedral_constraint, core::pose::Pose::dump_pdb(), protocols::idealize::IdealizeMover::fast(), frag_sizes_, protocols::relax::generate_relax_from_cmd(), protocols::jd2::JobDistributor::get_instance(), core::scoring::get_score_function(), core::conformation::Residue::has(), core::conformation::Conformation::insert_chain_ending(), core::conformation::Residue::is_protein(), protocols::jd2::JobDistributor::job_outputter(), max_ddg_score_, max_rmsd_after_relax_, min_contacts_per_res_, min_seq_sep_, core::kinematics::FoldTree::new_jump(), output_frags_pdbs_, output_idealized_, core::pose::Pose::pdb_info(), recover_checkpoint(), relax_frags_repeats_, relax_input_, relax_input_with_coordinate_constraints_, core::pose::Pose::replace_residue(), core::scoring::res_type_constraint, core::pose::Pose::residue(), protocols::hybridization::score, core::kinematics::FoldTree::set_jump_atoms(), single_chain_, core::pose::Pose::size(), protocols::frag_picker::nonlocal::TR(), write_checkpoint(), and core::conformation::Residue::xyz().
◆ clone()
|
overridevirtual |
Creates a copy of this instance.
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
Creates a new instance by calling the no-argument constructor.
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Returns the name of this mover.
Implements protocols::moves::Mover.
◆ initialize()
|
private |
References ca_dist_squared_, frag_sizes_, max_ddg_score_, max_rmsd_after_relax_, min_contacts_per_res_, min_seq_sep_, output_frags_pdbs_, output_idealized_, read_checkpoint_file(), relax_frags_repeats_, relax_input_, relax_input_with_coordinate_constraints_, and single_chain_.
Referenced by NonlocalFrags().
◆ read_checkpoint_file()
|
private |
References checkpointfile_, checkpoints_map_, and protocols::frag_picker::nonlocal::TR().
Referenced by initialize().
◆ recover_checkpoint()
|
private |
References core::pose::add_comment(), checkpoints_map_, and protocols::frag_picker::nonlocal::TR().
Referenced by apply().
◆ register_options()
|
static |
Registers applicable options.
◆ write_checkpoint()
|
private |
References checkpointfile_, checkpoints_map_, and protocols::frag_picker::nonlocal::TR().
Referenced by apply().
Member Data Documentation
◆ ca_dist_squared_
|
private |
Referenced by apply(), and initialize().
◆ checkpointfile_
|
private |
Referenced by read_checkpoint_file(), and write_checkpoint().
◆ checkpoints_map_
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private |
Referenced by read_checkpoint_file(), recover_checkpoint(), and write_checkpoint().
◆ frag_sizes_
|
private |
Referenced by apply(), and initialize().
◆ max_ddg_score_
|
private |
Referenced by apply(), and initialize().
◆ max_rmsd_after_relax_
|
private |
Referenced by apply(), and initialize().
◆ min_contacts_per_res_
|
private |
Referenced by apply(), and initialize().
◆ min_seq_sep_
|
private |
Referenced by apply(), and initialize().
◆ output_frags_pdbs_
|
private |
Referenced by apply(), and initialize().
◆ output_idealized_
|
private |
Referenced by apply(), and initialize().
◆ relax_frags_repeats_
|
private |
Referenced by apply(), and initialize().
◆ relax_input_
|
private |
Referenced by apply(), and initialize().
◆ relax_input_with_coordinate_constraints_
|
private |
Referenced by apply(), and initialize().
◆ single_chain_
|
private |
Referenced by apply(), and initialize().
The documentation for this class was generated from the following files:
- src/protocols/frag_picker/nonlocal/NonlocalFrags.hh
- src/protocols/frag_picker/nonlocal/NonlocalFrags.cc
