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protocols::abinitio::DoubleLayerKinematicAbinitio Class Reference

#include <DoubleLayerKinematicAbinitio.hh>

Inheritance diagram for protocols::abinitio::DoubleLayerKinematicAbinitio:
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Collaboration diagram for protocols::abinitio::DoubleLayerKinematicAbinitio:
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Public Member Functions

 DoubleLayerKinematicAbinitio (jumping::BaseJumpSetupOP jump_def, loops::Loops extended_loops, loops::Loops rigid_core, ProtocolOP sampler, ProtocolOP extended_chain_sampler, core::fragment::SecondaryStructureOP ss_def, core::Real coord_cst_weight, bool bCstAllAtom=false)
 
 ~DoubleLayerKinematicAbinitio ()
 
virtual KinematicControlOP new_kinematics (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from 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)
 
 ~LoopJumpFoldCst ()
 
void set_coord_cst_weight_array (utility::vector1< core::Real > const &vec)
 
void set_dump_weights_file (std::string const &str)
 
- 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
 
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
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, 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
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Protected Member Functions

virtual void select_core_loops (loops::Loops &loops_select) const
 heuristic to select subset of loops from loops_ More...
 
virtual bool inner_loop (core::pose::Pose &pose)
 
- Protected Member Functions inherited from protocols::abinitio::LoopJumpFoldCst
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
void set_extended_torsions_and_idealize_loops (core::pose::Pose &pose, loops::Loops loops) const
 
ResolutionSwitcherres_switch ()
 

Private Attributes

loops::Loops rigid_loops_
 
loops::Loops extended_loops_
 
ProtocolOP stage1_sampler_
 

Additional Inherited Members

- Public Types inherited from protocols::abinitio::Protocol
typedef Mover BaseClass
 
- Static Public Member Functions inherited from protocols::abinitio::Protocol
static void register_options ()
 
- Protected Attributes inherited from protocols::abinitio::LoopJumpFoldCst
core::Real coordinate_constraint_weight_
 
utility::vector1< core::Realcoordinate_constraint_weights_
 

Constructor & Destructor Documentation

protocols::abinitio::DoubleLayerKinematicAbinitio::DoubleLayerKinematicAbinitio ( jumping::BaseJumpSetupOP  jump_def,
loops::Loops  extended_loops,
loops::Loops  rigid_core,
ProtocolOP  sampler,
ProtocolOP  extended_chain_sampler,
core::fragment::SecondaryStructureOP  ss_def,
core::Real  coord_cst_weight,
bool  bCstAllAtom = false 
)
inline
protocols::abinitio::DoubleLayerKinematicAbinitio::~DoubleLayerKinematicAbinitio ( )

Member Function Documentation

std::string protocols::abinitio::DoubleLayerKinematicAbinitio::get_name ( ) const
virtual

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

Reimplemented from protocols::abinitio::LoopJumpFoldCst.

bool protocols::abinitio::DoubleLayerKinematicAbinitio::inner_loop ( core::pose::Pose pose)
protectedvirtual
KinematicControlOP protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics ( core::pose::Pose pose)
virtual
void protocols::abinitio::DoubleLayerKinematicAbinitio::select_core_loops ( loops::Loops loops_select) const
protectedvirtual

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(), and protocols::loops::Loops::size().

Member Data Documentation

loops::Loops protocols::abinitio::DoubleLayerKinematicAbinitio::extended_loops_
private
loops::Loops protocols::abinitio::DoubleLayerKinematicAbinitio::rigid_loops_
private
ProtocolOP protocols::abinitio::DoubleLayerKinematicAbinitio::stage1_sampler_
private

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