Rosetta 3.4
Public Member Functions | Static Public Member Functions | Protected Member Functions
protocols::abinitio::KinematicAbinitio Class Reference

#include <KinematicAbinitio.hh>

Inheritance diagram for protocols::abinitio::KinematicAbinitio:
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Collaboration diagram for protocols::abinitio::KinematicAbinitio:
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List of all members.

Public Member Functions

 KinematicAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)
 KinematicAbinitio (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)
 ~KinematicAbinitio ()
virtual moves::MoverOP clone () const
 ...
virtual void apply (core::pose::Pose &pose)
 run the protocol
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
virtual void set_max_seq_sep (core::pose::Pose &pose, Size setting)
virtual bool prepare_stage1 (core::pose::Pose &pose)
virtual bool prepare_stage2 (core::pose::Pose &pose)
virtual bool prepare_stage3 (core::pose::Pose &pose)
virtual bool prepare_loop_in_stage3 (core::pose::Pose &, Size, Size)
virtual bool prepare_loop_in_stage4 (core::pose::Pose &, Size, Size)
virtual moves::TrialMoverOP stage1_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
virtual moves::TrialMoverOP stage2_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in)
virtual moves::TrialMoverOP stage3_mover (core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in)
virtual moves::TrialMoverOP stage4_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in)
void closure_protocol (loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol)
 set the closure_protocol... if not set no closure...

Static Public Member Functions

static void register_options ()
 Why is this not being registered ? Probably not actually needed.

Protected Member Functions

virtual void set_default_scores ()
 sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0
virtual void set_default_options ()
virtual void replace_scorefxn (core::pose::Pose &pose, StageID, core::Real intra_stage_progress)

Constructor & Destructor Documentation

protocols::abinitio::KinematicAbinitio::KinematicAbinitio ( simple_moves::FragmentMoverOP  brute_move_small,
simple_moves::FragmentMoverOP  brute_move_large,
simple_moves::FragmentMoverOP  smooth_move_small,
int  dummy 
)

References protocols::moves::Mover::type().

Referenced by clone().

protocols::abinitio::KinematicAbinitio::KinematicAbinitio ( core::fragment::FragSetCOP  fragset3mer,
core::fragment::FragSetCOP  fragset9mer,
core::kinematics::MoveMapCOP  movemap 
)
protocols::abinitio::KinematicAbinitio::~KinematicAbinitio ( )

Member Function Documentation

void protocols::abinitio::KinematicAbinitio::apply ( core::pose::Pose pose) [virtual]

run the protocol

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

References protocols::idealize::IdealizeMover::apply(), protocols::abinitio::ClassicAbinitio::brute_move_small(), protocols::jumping::close_chainbreaks(), core::pose::Pose::constraint_set(), protocols::abinitio::ClassicAbinitio::current_scorefxn(), core::pack::interaction_graph::debug, protocols::abinitio::Protocol::evaluator(), protocols::moves::FAIL_RETRY, protocols::idealize::IdealizeMover::fast(), core::io::silent::SilentStruct::fill_pose(), core::pose::Pose::fold_tree(), protocols::abinitio::Protocol::get_checkpoints(), protocols::moves::Mover::get_current_job(), protocols::moves::Mover::get_current_tag(), protocols::jumping::StandardPairingLibrary::get_instance(), protocols::moves::Mover::get_last_move_status(), core::io::silent::SilentFileData::get_structure(), core::io::silent::SilentFileData::has_tag(), protocols::abinitio::Protocol::kinematics(), protocols::abinitio::FoldConstraints::max_seq_sep_fudge(), protocols::abinitio::ClassicAbinitio::movemap(), protocols::moves::MS_SUCCESS, protocols::abinitio::ClassicAbinitio::output_debug_structure(), protocols::abinitio::KinematicControl::prepare_pose_for_sampling(), core::io::silent::SilentFileData::read_file(), protocols::abinitio::RG(), protocols::moves::Mover::set_current_tag(), protocols::abinitio::Protocol::set_kinematics(), protocols::moves::Mover::set_last_move_status(), protocols::abinitio::FoldConstraints::set_movemap(), protocols::abinitio::FoldConstraints::set_seq_sep_stage1(), protocols::abinitio::FoldConstraints::set_seq_sep_stage3(), protocols::abinitio::ClassicAbinitio::set_skip_stage1(), protocols::abinitio::ClassicAbinitio::set_skip_stage2(), protocols::jumping::JumpSample::steal_orientation_and_pleating(), tr(), core::scoring::constraints::SkipViolFunc::viols(), and core::fragment::FragmentIO::write_data().

Referenced by protocols::abinitio::JumpingFoldConstraintsWrapper::apply().

virtual moves::MoverOP protocols::abinitio::KinematicAbinitio::clone ( ) const [inline, virtual]
void protocols::abinitio::KinematicAbinitio::closure_protocol ( loops::loop_closure::ccd::SlidingWindowLoopClosureOP  closure_protocol) [inline]

set the closure_protocol... if not set no closure...

std::string protocols::abinitio::KinematicAbinitio::get_name ( ) const [virtual]

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

Reimplemented from protocols::abinitio::FoldConstraints.

Reimplemented in protocols::abinitio::JumpingFoldConstraintsWrapper.

bool protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage3 ( core::pose::Pose pose,
Size  iteration,
Size  total 
) [virtual]
bool protocols::abinitio::KinematicAbinitio::prepare_loop_in_stage4 ( core::pose::Pose pose,
Size  iteration,
Size  total 
) [virtual]
bool protocols::abinitio::KinematicAbinitio::prepare_stage1 ( core::pose::Pose pose) [virtual]
bool protocols::abinitio::KinematicAbinitio::prepare_stage2 ( core::pose::Pose pose) [virtual]
bool protocols::abinitio::KinematicAbinitio::prepare_stage3 ( core::pose::Pose pose) [virtual]
void protocols::abinitio::KinematicAbinitio::register_options ( ) [static]

Why is this not being registered ? Probably not actually needed.

Reimplemented from protocols::abinitio::FoldConstraints.

References core::scoring::overlap_chainbreak, and protocols::evaluation::register_options().

void protocols::abinitio::KinematicAbinitio::replace_scorefxn ( core::pose::Pose pose,
StageID  stage,
core::Real  intra_stage_progress 
) [protected, virtual]
void protocols::abinitio::KinematicAbinitio::set_default_options ( ) [protected, virtual]
void protocols::abinitio::KinematicAbinitio::set_default_scores ( ) [protected, virtual]
void protocols::abinitio::KinematicAbinitio::set_max_seq_sep ( core::pose::Pose pose,
Size  setting 
) [virtual]
moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage1_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
) [virtual]
moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage2_mover ( core::pose::Pose pose,
moves::TrialMoverOP  trials_in 
) [virtual]
moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage3_mover ( core::pose::Pose pose,
int  lct1,
int  lct2,
moves::TrialMoverOP  trials_in 
) [virtual]
moves::TrialMoverOP protocols::abinitio::KinematicAbinitio::stage4_mover ( core::pose::Pose pose,
int  kk,
moves::TrialMoverOP  trials_in 
) [virtual]

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