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Rosetta
2021.16
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Rosetta
2021.16
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#include <Picker.hh>
Public Member Functions | |
| FrameList | pick_fragments_public (String const &complete_ss, String const &complete_aa, utility::vector1< String > const &complete_abego, Interval const &interval, core::Size const frag_length, core::Size const n_frags) |
| pick fragments of a given length, padding when necessary More... | |
 Public Member Functions inherited from protocols::forge::components::VarLengthBuild | |
| VarLengthBuild () | |
| default constructor More... | |
| VarLengthBuild (BuildManager const &manager) | |
| BuildManager constructor. More... | |
| VarLengthBuild (BuildManager const &manager, RemodelData const &remodel_data) | |
| BuildManager + RemodelData constructor. More... | |
| VarLengthBuild (VarLengthBuild const &rval) | |
| copy constructor More... | |
| ~VarLengthBuild () override | |
| default destructor More... | |
| MoverOP | clone () const override |
| clone this object More... | |
| MoverOP | fresh_instance () const override |
| create a new instance of this type of object More... | |
| BuildManager const & | manager () const |
| build manager More... | |
| bool | recover_original_on_failure () const |
| at the end of apply(), reset the Pose to the original Pose if mover was not successful? (default true) More... | |
| String const & | loop_mover_str () const |
| the string id of the loop mover to use (default "RemodelLoopMover") More... | |
| bool | cache_fragments () const |
| cache fragments after picking? (default true) More... | |
| VLB_VallMemoryUsage::Enum | vall_memory_usage () const |
| option dictating whether to keep VallLibrary in memory or clear it under certain circumstances after picking fragments. (default KEEP_IN_MEMORY) More... | |
| core::Size | num_fragpick () const |
| the number of fragments to pick at each position (default 200) More... | |
| bool | use_fullmer () const |
| also use fragments spanning the entire length of a loop? (default false) More... | |
| String const & | original_sequence () |
| full sequence string corresponding to original input pose used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments More... | |
| String const & | new_secondary_structure_override () const |
| full sequence string with length corresponding to the new modified pose used to pick secondary structure biased fragments. More... | |
| String const & | new_sequence_override () const |
| full amino acid string with length corresponding to the new modified pose used to pick sequence biased fragments. More... | |
| Real | max_linear_chainbreak () const |
| return the highest linear chainbreak score a chainbreak can have and still be considered closed More... | |
| bool | restart_mode () const |
| Flag to turn on restart mode, in which VLB assumes that the Pose fed to it during apply() has already been modified by the manager. (default False) More... | |
| void | scorefunction (ScoreFunction const &sfx) |
| set ScoreFunction used during build More... | |
| void | scorefunction (ScoreFunctionOP const &sfx) |
| set ScoreFunction used during build More... | |
| void | manager (BuildManager const &manager) |
| set build manager; also clears any cached fragments More... | |
| void | recover_original_on_failure (bool const flag) |
| at the end of apply(), reset the Pose to the original Pose if mover was not successful? More... | |
| void | loop_mover_str (String const &str) |
| set the loop mover to use via string More... | |
| void | cache_fragments (bool const flag) |
| cache fragments after picking? More... | |
| void | vall_memory_usage (VLB_VallMemoryUsage::Enum const level) |
| option dictating whether to keep VallLibrary in memory or clear it under certain circumstances after picking fragments. More... | |
| void | num_fragpick (core::Size const num) |
| the number of fragments to pick at each position (default 200) More... | |
| void | use_fullmer (bool const flag) |
| also use fragments spanning the entire length of a loop? More... | |
| void | original_sequence (String const &seq) |
| full sequence string corresponding to original input pose used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments More... | |
| void | new_secondary_structure_override (String const &str) |
| full sequence string with length corresponding to the new modified pose used to pick secondary structure biased fragments. More... | |
| void | new_sequence_override (String const &str) |
| full amino acid string with length corresponding to the new modified pose used to pick sequence biased fragments. More... | |
| void | max_linear_chainbreak (Real const tol) |
| set the highest linear chainbreak score a chainbreak can have and still be considered closed More... | |
| void | loop_mover_fold_tree_constant (bool const flag) |
| void | restart_mode (bool const flag) |
| Flag to turn on restart mode, in which VLB assumes that the Pose fed to it during apply() has already been modified by the manager. (default False) More... | |
| void | ignore_cmdline_enzdes_cstfile (bool const flag) |
| void | clear_rcgs () |
| get rid of all rcgs More... | |
| void | add_rcg (RemodelConstraintGeneratorOP rcg) |
| adding an rcg. this will set the rcg internal vlb backpointer More... | |
| void | clear_setup_movers () |
| void | add_setup_mover (moves::MoverOP mover_in) |
| void | clear_user_provided_movers () |
| void | add_user_provided_mover (moves::MoverOP mover_in) |
| void | clear_fragments () |
| clear any currently cached fragments More... | |
| void | set_abego (utility::vector1< String > const &abego) |
| set abego definition for fragments More... | |
| void | apply (Pose &pose) override |
| run protocol on given Pose More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. 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... | |
Additional Inherited Members | |
| Public Types inherited from protocols::forge::components::VarLengthBuild | |
| typedef std::string | String |
| typedef core::Real | Real |
| typedef core::Size | Size |
| typedef core::fragment::ConstantLengthFragSetOP | ConstantLengthFragSetOP |
| typedef core::fragment::FrameList | FrameList |
| typedef core::fragment::OrderedFragSetOP | OrderedFragSetOP |
| typedef core::kinematics::MoveMap | MoveMap |
| typedef core::pose::Pose | Pose |
| typedef core::scoring::ScoreFunction | ScoreFunction |
| typedef core::scoring::ScoreFunctionOP | ScoreFunctionOP |
| typedef protocols::loops::Loops | Loops |
| typedef protocols::forge::remodel::RemodelData | RemodelData |
| typedef protocols::moves::MoverOP | MoverOP |
| typedef protocols::forge::build::BuildManager | BuildManager |
| typedef protocols::forge::build::Interval | Interval |
| typedef protocols::forge::remodel::RemodelConstraintGeneratorOP | RemodelConstraintGeneratorOP |
| typedef BuildManager::BIOPConstIterator | BIOPConstIterator |
| typedef BuildManager::Original2Modified | Original2Modified |
| typedef BuildManager::Positions | Positions |
| 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::forge::components::VarLengthBuild | |
| virtual bool | centroid_build (Pose &pose) |
| run centroid level protocol on given Pose More... | |
| virtual MoverOP | loop_mover_instance (loops::LoopsOP const loops, MoveMap const &false_mm) |
| return the appropriate loop mover More... | |
| void | pick_all_fragments (String const &complete_ss, String const &complete_aa, utility::vector1< String > const &complete_abego, Interval const &interval, core::Size const n_frags) |
| pick fragments of size full, 9, 3, 1 More... | |
| FrameList | pick_fragments (String const &complete_ss, String const &complete_aa, utility::vector1< String > const &complete_abego, Interval const &interval, core::Size const frag_length, core::Size const n_frags) |
| pick fragments of a given length, padding when necessary More... | |
| void | set_starting_non_canonical (Pose &pose) |
| void | setup_remodel_constraints (Pose &pose) |
| telling all rcgs to setup and insert constraints into the pose More... | |
| void | remove_remodel_constraints (Pose &pose) |
| telling all rcgs to remove their constraints from the pose 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... | |
|
inline |
pick fragments of a given length, padding when necessary
| [in] | complete_ss | The complete secondary structure string, typically from a Pose. |
| [in] | complete_aa | The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments. |
| [in] | complete_abego | The complete abego string, typically from a setter, set_abego |
| [in] | interval | The interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing). |
| [in] | frag_length | The desired length of the fragments |
| [in] | n_frags | The number of fragments to pick per position. |
References protocols::forge::components::VarLengthBuild::pick_fragments().
Referenced by protocols::denovo_design::components::Picker::pick_fragments_for_resid().
1.8.7