Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
protocols::abinitio::LoopJumpFoldCst Class Reference

#include <LoopJumpFoldCst.hh>

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 ()
virtual KinematicControlOP new_kinematics (core::pose::Pose &pose)
void set_coord_cst_weight_array (utility::vector1< core::Real > const &vec)
void set_dump_weights_file (std::string const &str)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
- Public Member Functions inherited from protocols::abinitio::KinematicTaskControl
 KinematicTaskControl ()
 KinematicTaskControl (ProtocolOP sampler)
 ~KinematicTaskControl ()
virtual void apply (core::pose::Pose &pose)
virtual void init (core::pose::Pose const &pose)
KinematicControlOP current_kinematics ()
void set_input_pose_is_fa (bool setting=true)
ProtocolOP sampling_protocol ()
virtual checkpoint::CheckPointerget_checkpoints ()
- Public Member Functions inherited from protocols::abinitio::Protocol
 Protocol ()
 ~Protocol ()
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 set_fullatom_scorefxn (core::scoring::ScoreFunctionOP sfxn)
void set_centroid_scorefxn (core::scoring::ScoreFunctionOP sfxn)
void set_silentout_file_name (std::string str)
core::scoring::ScoreFunctionOP fullatom_scorefxn ()
core::scoring::ScoreFunctionOP centroid_scorefxn ()
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
void set_type (std::string const &setting)
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...
void set_current_tag (std::string const &new_tag)
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 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...
void type (const std::string &type_in)
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_type () const
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...
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 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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::stringStrings
- 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.

Reimplemented in protocols::abinitio::DoubleLayerKinematicAbinitio.

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(), protocols::abinitio::RG, protocols::loops::Loops::size(), and numeric::random::RandomGenerator::uniform().

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: