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

#include <ConstraintFragmentSampler.hh>

Inheritance diagram for protocols::abinitio::ConstraintFragmentSampler:
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List of all members.

Public Member Functions

 ConstraintFragmentSampler (topology_broker::TopologyBrokerOP broker)
 This constructor does not work -- Fix it before using it.
virtual moves::MoverOP clone () const
 ConstraintFragmentSampler has virtual functions... use this to obtain a new instance.
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.

Static Public Member Functions

static void register_options ()

Protected Member Functions

void set_constraint_weight (core::Real setting)
void set_defaults ()
virtual void do_stage1_cycles (core::pose::Pose &pose)
virtual void prepare_stage1 (core::pose::Pose &pose)
virtual void prepare_stage2 (core::pose::Pose &pose)
virtual void prepare_loop_in_stage3 (core::pose::Pose &, Size, Size)
virtual void prepare_loop_in_stage4 (core::pose::Pose &, Size, Size)
void set_show_viol_level (core::Size setting)
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 ()
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)
virtual void replace_scorefxn (core::pose::Pose &pose, StageID stage, core::Real intra_stage_progress)

Detailed Description

@ detail general usage: ConstraintFragmentSampler abinitio; abinitio.init( pose ); ... while(nstruct) { abinitio.apply( pose ); }

call ConstraintFragmentSampler::register_options() before core::init to add relevant options to the applications help

, with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:

The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() ...

Behaviour can be changed in the following ways:

use non-classic FragmentMover --> eg. not uniformly sampled fragments, but using some weighting --> large and small moves doesn't have to be 3mers and 9mers... use other movers... ---> or other fragets for the "convenience constructor" use custom trial classes --> overload update_moves()

change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves ...

change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()


Constructor & Destructor Documentation

protocols::abinitio::ConstraintFragmentSampler::ConstraintFragmentSampler ( topology_broker::TopologyBrokerOP  broker)

This constructor does not work -- Fix it before using it.

large (stage1/stage2) small(stage2/stage3/stage4) smooth_small ( stage3/stage4)

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

Referenced by clone().


Member Function Documentation

void protocols::abinitio::ConstraintFragmentSampler::apply ( core::pose::Pose pose) [virtual]
moves::MoverOP protocols::abinitio::ConstraintFragmentSampler::clone ( ) const [virtual]

ConstraintFragmentSampler has virtual functions... use this to obtain a new instance.

Reimplemented from protocols::abinitio::FragmentSampler.

References ConstraintFragmentSampler().

constraints_additional::MaxSeqSepConstraintSet const& protocols::abinitio::ConstraintFragmentSampler::constraints ( ) [inline, protected]
void protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles ( core::pose::Pose pose) [protected, virtual]
string protocols::abinitio::ConstraintFragmentSampler::get_name ( ) const [virtual]

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

Reimplemented from protocols::abinitio::FragmentSampler.

core::Real protocols::abinitio::ConstraintFragmentSampler::max_seq_sep_fudge ( ) const [inline, protected]
void protocols::abinitio::ConstraintFragmentSampler::max_seq_sep_fudge ( core::Real  setting) [inline, protected]
void protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage3 ( core::pose::Pose pose,
Size  loop_iteration,
Size  total_iterations 
) [protected, virtual]
void protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage4 ( core::pose::Pose pose,
Size  loop_iteration,
Size  total_iterations 
) [protected, virtual]
void protocols::abinitio::ConstraintFragmentSampler::prepare_stage1 ( core::pose::Pose pose) [protected, virtual]
void protocols::abinitio::ConstraintFragmentSampler::prepare_stage2 ( core::pose::Pose pose) [protected, virtual]
void protocols::abinitio::ConstraintFragmentSampler::register_options ( ) [static]

call this: FragmentSampler::register_options() before protocols::init::init(). Derived classes that overload this function should also call Parent::register_options()

Reimplemented from protocols::abinitio::FragmentSampler.

References protocols::evaluation::register_options().

void protocols::abinitio::ConstraintFragmentSampler::replace_scorefxn ( core::pose::Pose pose,
StageID  stage,
core::Real  intra_stage_progress 
) [protected, virtual]
void protocols::abinitio::ConstraintFragmentSampler::set_constraint_weight ( core::Real  setting) [inline, protected]
void protocols::abinitio::ConstraintFragmentSampler::set_defaults ( ) [protected]
void protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep ( core::pose::Pose pose,
core::Size  setting 
) [protected, virtual]
void protocols::abinitio::ConstraintFragmentSampler::set_seq_sep_stage1 ( core::Real  setting) [inline, protected]
void protocols::abinitio::ConstraintFragmentSampler::set_seq_sep_stage3 ( core::Real  setting) [inline, protected]
void protocols::abinitio::ConstraintFragmentSampler::set_show_viol_level ( core::Size  setting) [inline, protected]
Size protocols::abinitio::ConstraintFragmentSampler::total_res ( core::pose::Pose const &  pose) const [protected]

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