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protocols::abinitio::DoubleLayerKinematicAbinitio Class Reference

#include <DoubleLayerKinematicAbinitio.hh>

Inheritance diagram for protocols::abinitio::DoubleLayerKinematicAbinitio:
Inheritance graph
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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 () override
 
KinematicControlOP new_kinematics (core::pose::Pose &pose) override
 
std::string get_name () const override
 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 () 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)
 
core::scoring::ScoreFunctionOP fullatom_scorefxn ()
 
core::scoring::ScoreFunctionOP centroid_scorefxn ()
 
- 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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Protected Member Functions

virtual void select_core_loops (loops::Loops &loops_select) const
 heuristic to select subset of loops from loops_ More...
 
bool inner_loop (core::pose::Pose &pose) override
 
- 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 ()
 
- 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...
 

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

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 ( )
overridedefault

Member Function Documentation

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

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

Implements protocols::moves::Mover.

bool protocols::abinitio::DoubleLayerKinematicAbinitio::inner_loop ( core::pose::Pose pose)
overrideprotectedvirtual
KinematicControlOP protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics ( core::pose::Pose pose)
overridevirtual
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(), core::scoring::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: