Rosetta 3.4
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protocols::abinitio::FoldConstraints Class Reference

extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles() More...

#include <FoldConstraints.hh>

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List of all members.

Public Types

typedef ClassicAbinitio Parent

Public Member Functions

 FoldConstraints (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy)
 c'stor from Movers
 FoldConstraints (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap)
 c'stor from FragSets --- ClassicFragmentMover and SmoothFragmentMover will be created
 FoldConstraints (FoldConstraints const &src)
 Explicit copy constructor to handle OPs.
 ~FoldConstraints ()
 Explicit destructor to handle OPs.
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.
void set_default_scores ()
 sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0
void set_constraint_weight (core::Real setting)
virtual void set_default_options ()
void set_show_viol_level (core::Size setting)

Static Public Member Functions

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

Protected Member Functions

bool prepare_stage1 (core::pose::Pose &pose)
bool prepare_stage2 (core::pose::Pose &pose)
bool prepare_stage4 (core::pose::Pose &pose)
bool prepare_loop_in_stage3 (core::pose::Pose &pose, Size loop_iteration, Size total_iterations)
bool prepare_loop_in_stage4 (core::pose::Pose &pose, Size loop_iteration, Size total_iterations)
bool do_stage1_cycles (core::pose::Pose &pose)
bool do_stage2_cycles (core::pose::Pose &pose)
virtual void setup_default_min_move ()
virtual void set_movemap (core::kinematics::MoveMapCOP mm)
void set_min_move (protocols::simple_moves::MinMoverOP mm)
protocols::simple_moves::MinMovermin_move ()
void min_trial (core::pose::Pose &pose)
virtual void set_max_seq_sep (core::pose::Pose &pose, Size setting)
core::Real max_seq_sep_fudge () const
void max_seq_sep_fudge (core::Real setting)
constraints_additional::MaxSeqSepConstraintSet
const & 
constraints ()
void bIgnoreSequenceSeparation (bool setting)
bool bIgnoreSequenceSeparation ()
Size total_res (core::pose::Pose const &pose) const
void set_seq_sep_stage1 (core::Real setting)
void set_seq_sep_stage3 (core::Real setting)

Detailed Description

extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees ) This is achieved by replacing the pose's ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles()

the other substantial difference to ClassicAbinitio is that minimizations are carried out. method min_trial() is called each time the max_seq_sep is changed. ( inhibit: -no_minimize )


Member Typedef Documentation


Constructor & Destructor Documentation

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

c'stor from Movers

References set_default_options(), and protocols::moves::Mover::type().

Referenced by clone().

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

c'stor from FragSets --- ClassicFragmentMover and SmoothFragmentMover will be created

References set_default_options(), and protocols::moves::Mover::type().

protocols::abinitio::FoldConstraints::FoldConstraints ( FoldConstraints const &  src)

Explicit copy constructor to handle OPs.

SHALLOW copy.

protocols::abinitio::FoldConstraints::~FoldConstraints ( )

Explicit destructor to handle OPs.


Member Function Documentation

void protocols::abinitio::FoldConstraints::apply ( core::pose::Pose pose) [virtual]
void protocols::abinitio::FoldConstraints::bIgnoreSequenceSeparation ( bool  setting) [inline, protected]
bool protocols::abinitio::FoldConstraints::bIgnoreSequenceSeparation ( ) [inline, protected]

Referenced by apply(), and set_max_seq_sep().

moves::MoverOP protocols::abinitio::FoldConstraints::clone ( ) const [virtual]
constraints_additional::MaxSeqSepConstraintSet const& protocols::abinitio::FoldConstraints::constraints ( ) [inline, protected]
bool protocols::abinitio::FoldConstraints::do_stage1_cycles ( core::pose::Pose pose) [protected, virtual]
bool protocols::abinitio::FoldConstraints::do_stage2_cycles ( core::pose::Pose pose) [protected, virtual]
std::string protocols::abinitio::FoldConstraints::get_name ( ) const [virtual]

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

Reimplemented from protocols::abinitio::ClassicAbinitio.

Reimplemented in protocols::abinitio::KinematicAbinitio, and protocols::abinitio::JumpingFoldConstraintsWrapper.

core::Real protocols::abinitio::FoldConstraints::max_seq_sep_fudge ( ) const [inline, protected]
void protocols::abinitio::FoldConstraints::max_seq_sep_fudge ( core::Real  setting) [inline, protected]
protocols::simple_moves::MinMover& protocols::abinitio::FoldConstraints::min_move ( ) [inline, protected]
void protocols::abinitio::FoldConstraints::min_trial ( core::pose::Pose pose) [protected]
bool protocols::abinitio::FoldConstraints::prepare_loop_in_stage3 ( core::pose::Pose pose,
Size  loop_iteration,
Size  total_iterations 
) [protected, virtual]
bool protocols::abinitio::FoldConstraints::prepare_loop_in_stage4 ( core::pose::Pose pose,
Size  loop_iteration,
Size  total_iterations 
) [protected, virtual]
bool protocols::abinitio::FoldConstraints::prepare_stage1 ( core::pose::Pose pose) [protected, virtual]
bool protocols::abinitio::FoldConstraints::prepare_stage2 ( core::pose::Pose pose) [protected, virtual]
bool protocols::abinitio::FoldConstraints::prepare_stage4 ( core::pose::Pose pose) [protected, virtual]
void protocols::abinitio::FoldConstraints::register_options ( ) [static]

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

Reimplemented from protocols::abinitio::ClassicAbinitio.

Reimplemented in protocols::abinitio::JumpingFoldConstraints, and protocols::abinitio::KinematicAbinitio.

void protocols::abinitio::FoldConstraints::set_constraint_weight ( core::Real  setting) [inline]
void protocols::abinitio::FoldConstraints::set_default_options ( ) [virtual]
void protocols::abinitio::FoldConstraints::set_default_scores ( ) [virtual]

sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0

Reimplemented from protocols::abinitio::ClassicAbinitio.

Reimplemented in protocols::abinitio::JumpingFoldConstraints, and protocols::abinitio::KinematicAbinitio.

References core::scoring::atom_pair_constraint, protocols::abinitio::ClassicAbinitio::set_score_weight(), and tr().

Referenced by protocols::abinitio::KinematicAbinitio::set_default_scores().

void protocols::abinitio::FoldConstraints::set_max_seq_sep ( core::pose::Pose pose,
Size  setting 
) [protected, virtual]
void protocols::abinitio::FoldConstraints::set_min_move ( protocols::simple_moves::MinMoverOP  mm) [protected]
void protocols::abinitio::FoldConstraints::set_movemap ( core::kinematics::MoveMapCOP  mm) [protected, virtual]
void protocols::abinitio::FoldConstraints::set_seq_sep_stage1 ( core::Real  setting) [inline, protected]
void protocols::abinitio::FoldConstraints::set_seq_sep_stage3 ( core::Real  setting) [inline, protected]
void protocols::abinitio::FoldConstraints::set_show_viol_level ( core::Size  setting) [inline]
void protocols::abinitio::FoldConstraints::setup_default_min_move ( ) [protected, virtual]
Size protocols::abinitio::FoldConstraints::total_res ( core::pose::Pose const &  pose) const [protected]

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