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protocols::abinitio::LoopJumpFoldCst Class Reference

#include <LoopJumpFoldCst.hh>

Inheritance diagram for protocols::abinitio::LoopJumpFoldCst:
Inheritance graph

Public Member Functions

 LoopJumpFoldCst (jumping::BaseJumpSetupOP jump_def, loops::Loops loops, ProtocolOP sampler, core::fragment::SecondaryStructureOP ss_def, core::Real coord_cst_weight, bool bCstAllAtom=false)
 ~LoopJumpFoldCst () override
KinematicControlOP new_kinematics (core::pose::Pose &pose) override
void set_coord_cst_weight_array (utility::vector1< core::Real > const &vec)
void set_dump_weights_file (std::string const &str)
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
- Public Member Functions inherited from protocols::abinitio::KinematicTaskControl
 KinematicTaskControl ()
 KinematicTaskControl (ProtocolOP sampler)
 ~KinematicTaskControl () override
void apply (core::pose::Pose &pose) override
 Main Method. More...
void init (core::pose::Pose const &pose) override
KinematicControlOP current_kinematics ()
void set_input_pose_is_fa (bool setting=true)
ProtocolOP sampling_protocol ()
checkpoint::CheckPointerget_checkpoints () override
- Public Member Functions inherited from protocols::abinitio::Protocol
 Protocol ()
 ~Protocol () override=default
void set_evaluation (evaluation::MetaPoseEvaluatorOP ev)
void add_evaluation (evaluation::PoseEvaluatorOP ev)
void evaluate_pose (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const
evaluation::MetaPoseEvaluatorOP evaluator ()
virtual void output_debug_structure (core::pose::Pose &pose, std::string prefix)
void set_kinematics (abinitio::KinematicControlOP kc)
abinitio::KinematicControl const & kinematics ()
virtual bool start_from_centroid () const
virtual bool return_centroid () const
virtual void return_centroid (bool setting)
void apply (core::pose::Pose &) override
 Main Method. More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void set_fullatom_scorefxn (core::scoring::ScoreFunctionOP sfxn)
void set_centroid_scorefxn (core::scoring::ScoreFunctionOP sfxn)
void set_silentout_file_name (std::string str)
void set_use_trRosetta_constraints (bool const setting)
 Set whether we're using trRosetta constraints. More...
core::scoring::ScoreFunctionOP fullatom_scorefxn ()
core::scoring::ScoreFunctionOP centroid_scorefxn ()
virtual bool supports_trRosetta_constraints () const
 Report whether this protocol supports trRosetta constraints. The base class returns false; derived classes can override this and return true. More...
bool use_trRosetta_constraints () const
 Get whether we're using trRosetta constraints. 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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...

Protected Member Functions

virtual void select_loops (loops::Loops &loops_select) const
 heuristic to select subset of loops from loops_ More...
virtual bool add_rigidity_jumps (loops::Loops const &rigid, KinematicControlOP current_kinematics)
virtual bool add_coord_cst (loops::Loops const &loops, core::pose::Pose &pose)
virtual bool parse_jump_def (KinematicControlOP current_kinematics, core::kinematics::MoveMapOP)
- Protected Member Functions inherited from protocols::abinitio::KinematicTaskControl
virtual bool inner_loop (core::pose::Pose &pose)
void set_extended_torsions_and_idealize_loops (core::pose::Pose &pose, loops::Loops loops) const
ResolutionSwitcherres_switch ()
- 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...

Protected Attributes

core::Real coordinate_constraint_weight_
utility::vector1< core::Realcoordinate_constraint_weights_
- Protected Attributes inherited from protocols::abinitio::KinematicTaskControl
KinematicControlOP current_kinematics_

Private Attributes

jumping::BaseJumpSetupOP jump_def_
loops::Loops loops_
core::fragment::SecondaryStructureOP ss_def_
std::string dump_weights_file_
bool bCstAllAtom_

Additional Inherited Members

- Public Types inherited from protocols::abinitio::Protocol
typedef Mover BaseClass
- 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::abinitio::Protocol
static void register_options ()
- 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...

Constructor & Destructor Documentation

protocols::abinitio::LoopJumpFoldCst::LoopJumpFoldCst ( jumping::BaseJumpSetupOP  jump_def,
loops::Loops  loops,
ProtocolOP  sampler,
core::fragment::SecondaryStructureOP  ss_def,
core::Real  coord_cst_weight,
bool  bCstAllAtom = false 

References dump_weights_file_.

protocols::abinitio::LoopJumpFoldCst::~LoopJumpFoldCst ( )

Member Function Documentation

bool protocols::abinitio::LoopJumpFoldCst::add_coord_cst ( loops::Loops const &  loops,
core::pose::Pose pose 
bool protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps ( loops::Loops const &  rigid,
KinematicControlOP  current_kinematics 
std::string protocols::abinitio::LoopJumpFoldCst::get_name ( ) const

Each derived class must specify its name. The class name.

Reimplemented from protocols::abinitio::KinematicTaskControl.

KinematicControlOP protocols::abinitio::LoopJumpFoldCst::new_kinematics ( core::pose::Pose pose)
bool protocols::abinitio::LoopJumpFoldCst::parse_jump_def ( KinematicControlOP  current_kinematics,
core::kinematics::MoveMapOP  movemap 
void protocols::abinitio::LoopJumpFoldCst::select_loops ( loops::Loops loops_select) const

heuristic to select subset of loops from loops_

Select loop set at random using skip rate.

References protocols::loops::Loops::clear(), protocols::loops::Loops::push_back(), core::scoring::rg, and protocols::loops::Loops::size().

void protocols::abinitio::LoopJumpFoldCst::set_coord_cst_weight_array ( utility::vector1< core::Real > const &  vec)
void protocols::abinitio::LoopJumpFoldCst::set_dump_weights_file ( std::string const &  str)

Member Data Documentation

bool protocols::abinitio::LoopJumpFoldCst::bCstAllAtom_
core::Real protocols::abinitio::LoopJumpFoldCst::coordinate_constraint_weight_
utility::vector1< core::Real > protocols::abinitio::LoopJumpFoldCst::coordinate_constraint_weights_
std::string protocols::abinitio::LoopJumpFoldCst::dump_weights_file_
jumping::BaseJumpSetupOP protocols::abinitio::LoopJumpFoldCst::jump_def_
loops::Loops protocols::abinitio::LoopJumpFoldCst::loops_
core::fragment::SecondaryStructureOP protocols::abinitio::LoopJumpFoldCst::ss_def_

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