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protocols::denovo_design::components::VLBProtected Class Reference

#include <Picker.hh>

Inheritance diagram for protocols::denovo_design::components::VLBProtected:
Inheritance graph
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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 Stringsinfo ()
 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...
 

Member Function Documentation

FrameList protocols::denovo_design::components::VLBProtected::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 
)
inline

pick fragments of a given length, padding when necessary

Parameters
[in]complete_ssThe complete secondary structure string, typically from a Pose.
[in]complete_aaThe complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]complete_abegoThe complete abego string, typically from a setter, set_abego
[in]intervalThe interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]frag_lengthThe desired length of the fragments
[in]n_fragsThe 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().


The documentation for this class was generated from the following file: