#include <ConstraintFragmentSampler.hh>

Inheritance diagram for protocols::abinitio::ConstraintFragmentSampler:

Collaboration diagram for protocols::abinitio::ConstraintFragmentSampler:

Public Member Functions
	ConstraintFragmentSampler (topology_broker::TopologyBrokerOP broker)
	This constructor does not work – Fix it before using it. More...

virtual moves::MoverOP	clone () const
	ConstraintFragmentSampler has virtual functions... use this to obtain a new instance. More...

virtual void	apply (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::FragmentSampler
virtual	~FragmentSampler ()

	FragmentSampler (topology_broker::TopologyBrokerOP broker)
	This constructor does not work – Fix it before using it. More...

virtual void	set_cycles (core::Real increase_cycles=1.0)

virtual void	set_score_weight (core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES)
	sets a score weight for all stages of abinitio More...

virtual checkpoint::CheckPointer &	get_checkpoints ()

void	topology_broker (topology_broker::TopologyBrokerOP set)

core::scoring::ScoreFunction const &	current_scorefxn () const

bool	just_smooth_cycles () const

core::Size	stage1_cycles () const

core::Size	stage2_cycles () const

core::Size	stage3_cycles () const

void	set_stage4_cycles (core::Size stage4_cycles_new)

core::Size	stage4_cycles () const

bool	bQuickTest () const

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)

Mover &	operator= (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 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 Strings &	info ()
	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

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::abinitio::FragmentSampler
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

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)

Protected Member Functions inherited from protocols::abinitio::FragmentSampler
topology_broker::TopologyBroker const &	topology_broker ()

void	set_mc (moves::MonteCarloOP)

moves::MonteCarlo &	mc ()

moves::MonteCarlo const &	mc () const

void	set_defaults ()

void	current_scorefxn (core::scoring::ScoreFunction const &scorefxn)

void	recover_low (core::pose::Pose &pose, StageID stage)

void	set_current_weight (core::scoring::ScoreType type, core::Real setting)

virtual void	do_stage2_cycles (core::pose::Pose &pose)

virtual void	do_stage3_cycles (core::pose::Pose &pose)

virtual void	do_stage4_cycles (core::pose::Pose &pose)

virtual moves::MoverOP	mover (core::pose::Pose const &pose, StageID stage_id, core::scoring::ScoreFunction const &scorefxn, core::Real progress=1.0)

virtual void	prepare_stage3 (core::pose::Pose &pose)

virtual void	prepare_stage4 (core::pose::Pose &pose)

moves::MonteCarloOP	mc_ptr ()

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 Types
typedef FragmentSampler	Parent

typedef moves::Mover	BaseClass

Private Member Functions
core::Real	evaluate_constraint_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &) const

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Protected Attributes inherited from protocols::abinitio::FragmentSampler
Size	stage1_cycles_

Size	stage2_cycles_

Size	stage3_cycles_

Size	stage4_cycles_

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:

Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on. Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.
Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch and runs for 2000 cycles.
Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.
Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.

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()

Definition at line 100 of file ConstraintFragmentSampler.hh.

Member Typedef Documentation

typedef moves::Mover protocols::abinitio::ConstraintFragmentSampler::BaseClass

private

Definition at line 102 of file ConstraintFragmentSampler.hh.

typedef FragmentSampler protocols::abinitio::ConstraintFragmentSampler::Parent

private

Definition at line 101 of file ConstraintFragmentSampler.hh.

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)

Definition at line 100 of file ConstraintFragmentSampler.cc.

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

Referenced by clone().

Member Function Documentation

void protocols::abinitio::ConstraintFragmentSampler::apply ( core::pose::Pose & pose)

virtual

Reimplemented from protocols::abinitio::FragmentSampler.

Definition at line 353 of file ConstraintFragmentSampler.cc.

References protocols::abinitio::FragmentSampler::apply(), protocols::moves::MonteCarlo::clear_poses(), core::pose::Pose::constraint_set(), constraints_, core::pose::Pose::fold_tree(), protocols::moves::Mover::get_current_tag(), protocols::abinitio::FragmentSampler::mc(), protocols::moves::MonteCarlo::reset(), core::pose::Pose::total_residue(), and tr().

moves::MoverOP protocols::abinitio::ConstraintFragmentSampler::clone ( ) const

virtual

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

Reimplemented from protocols::abinitio::FragmentSampler.

Definition at line 107 of file ConstraintFragmentSampler.cc.

References ConstraintFragmentSampler().

constraints_additional::MaxSeqSepConstraintSet const& protocols::abinitio::ConstraintFragmentSampler::constraints ( )

inlineprotected

Definition at line 166 of file ConstraintFragmentSampler.hh.

References constraints_.

void protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles ( core::pose::Pose & pose)

protectedvirtual

Reimplemented from protocols::abinitio::FragmentSampler.

Definition at line 301 of file ConstraintFragmentSampler.cc.

References bSkipOnNoViolation_, core::pose::Pose::constraint_set(), protocols::abinitio::FragmentSampler::current_scorefxn(), protocols::abinitio::FragmentSampler::do_stage1_cycles(), evaluate_constraint_energy(), protocols::abinitio::FragmentSampler::mc(), protocols::abinitio::FragmentSampler::mc_ptr(), protocols::abinitio::FragmentSampler::mover(), seq_sep_stage(), seq_sep_stage1_, set_max_seq_sep(), show_viol_level_, protocols::abinitio::FragmentSampler::stage1_cycles(), protocols::abinitio::STAGE_1, total_res(), and tr().

Real protocols::abinitio::ConstraintFragmentSampler::evaluate_constraint_energy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	scfxn
	)		const

inlineprivate

Definition at line 384 of file ConstraintFragmentSampler.cc.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::Pose::energies(), and core::scoring::Energies::total_energies().

Referenced by do_stage1_cycles().

string protocols::abinitio::ConstraintFragmentSampler::get_name ( ) const

virtual

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

Reimplemented from protocols::abinitio::FragmentSampler.

Definition at line 380 of file ConstraintFragmentSampler.cc.

core::Real protocols::abinitio::ConstraintFragmentSampler::max_seq_sep_fudge ( ) const

inlineprotected

Definition at line 158 of file ConstraintFragmentSampler.hh.

References max_seq_sep_fudge_.

void protocols::abinitio::ConstraintFragmentSampler::max_seq_sep_fudge ( core::Real setting)

inlineprotected

Definition at line 162 of file ConstraintFragmentSampler.hh.

References max_seq_sep_fudge_.

void protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage3	(	core::pose::Pose &	pose,
		Size	loop_iteration,
		Size	total_iterations
	)

protectedvirtual

Reimplemented from protocols::abinitio::FragmentSampler.

Definition at line 342 of file ConstraintFragmentSampler.cc.

References core::pose::Pose::constraint_set(), protocols::abinitio::FragmentSampler::prepare_loop_in_stage3(), show_viol_level_, and tr().

void protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage4	(	core::pose::Pose &	pose,
		Size	loop_iteration,
		Size	total_iterations
	)

protectedvirtual

Reimplemented from protocols::abinitio::FragmentSampler.

Definition at line 348 of file ConstraintFragmentSampler.cc.

References core::pose::Pose::constraint_set(), protocols::abinitio::FragmentSampler::prepare_loop_in_stage4(), show_viol_level_, and tr().

void protocols::abinitio::ConstraintFragmentSampler::prepare_stage1 ( core::pose::Pose & pose)

protectedvirtual

Reimplemented from protocols::abinitio::FragmentSampler.

Definition at line 329 of file ConstraintFragmentSampler.cc.

References protocols::abinitio::FragmentSampler::prepare_stage1().

void protocols::abinitio::ConstraintFragmentSampler::prepare_stage2 ( core::pose::Pose & pose)

protectedvirtual

Reimplemented from protocols::abinitio::FragmentSampler.

Definition at line 335 of file ConstraintFragmentSampler.cc.

References core::pose::Pose::constraint_set(), protocols::abinitio::FragmentSampler::prepare_stage2(), show_viol_level_, and tr().

void protocols::abinitio::ConstraintFragmentSampler::register_options ( )

static

Definition at line 79 of file ConstraintFragmentSampler.cc.

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

void protocols::abinitio::ConstraintFragmentSampler::replace_scorefxn	(	core::pose::Pose &	pose,
		StageID	stage,
		core::Real	intra_stage_progress
	)

protectedvirtual

void protocols::abinitio::ConstraintFragmentSampler::set_constraint_weight ( core::Real setting)

inlineprotected

Definition at line 122 of file ConstraintFragmentSampler.hh.

References core::scoring::atom_pair_constraint, constraint_weight_, and protocols::abinitio::FragmentSampler::set_score_weight().

Referenced by set_defaults().

void protocols::abinitio::ConstraintFragmentSampler::set_defaults ( )

protected

void protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep	(	core::pose::Pose &	pose,
		core::Size	setting
	)

protectedvirtual

Definition at line 202 of file ConstraintFragmentSampler.cc.

References bNoRecoverLowAtSwitch_, protocols::moves::MonteCarlo::boltzmann(), core::pose::Pose::constraint_set(), constraints_, core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep(), protocols::abinitio::FragmentSampler::current_scorefxn(), core::scoring::ScoreFunction::energy_method_options(), protocols::abinitio::FragmentSampler::mc(), protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), core::scoring::ScoreFunction::set_energy_method_options(), core::scoring::ScoreFunction::show(), protocols::abinitio::FragmentSampler::topology_broker(), and tr().

Referenced by do_stage1_cycles(), and replace_scorefxn().

void protocols::abinitio::ConstraintFragmentSampler::set_seq_sep_stage1 ( core::Real setting)

inlineprotected

Definition at line 172 of file ConstraintFragmentSampler.hh.

References seq_sep_stage1_.

void protocols::abinitio::ConstraintFragmentSampler::set_seq_sep_stage3 ( core::Real setting)

inlineprotected

Definition at line 176 of file ConstraintFragmentSampler.hh.

References seq_sep_stage3_.

void protocols::abinitio::ConstraintFragmentSampler::set_show_viol_level ( core::Size setting)

inlineprotected

Definition at line 152 of file ConstraintFragmentSampler.hh.

References show_viol_level_.

Size protocols::abinitio::ConstraintFragmentSampler::total_res ( core::pose::Pose const & pose) const

protected

Definition at line 196 of file ConstraintFragmentSampler.cc.

References constraints_, max_seq_sep_fudge_, and core::pose::Pose::total_residue().

Referenced by do_stage1_cycles(), and replace_scorefxn().

Member Data Documentation

bool protocols::abinitio::ConstraintFragmentSampler::bMinTrial_

private

Definition at line 189 of file ConstraintFragmentSampler.hh.

bool protocols::abinitio::ConstraintFragmentSampler::bNoRecoverLowAtSwitch_

private

Definition at line 203 of file ConstraintFragmentSampler.hh.

Referenced by set_defaults(), and set_max_seq_sep().

bool protocols::abinitio::ConstraintFragmentSampler::bOverlapChainbreaks_

private

Definition at line 212 of file ConstraintFragmentSampler.hh.

Referenced by replace_scorefxn(), and set_defaults().

bool protocols::abinitio::ConstraintFragmentSampler::bRampChainbreaks_

private

Definition at line 206 of file ConstraintFragmentSampler.hh.

Referenced by replace_scorefxn(), and set_defaults().

bool protocols::abinitio::ConstraintFragmentSampler::bRampCoordConstraints_

private

Definition at line 209 of file ConstraintFragmentSampler.hh.

Referenced by replace_scorefxn(), and set_defaults().

bool protocols::abinitio::ConstraintFragmentSampler::bSkipOnNoViolation_

private

Definition at line 197 of file ConstraintFragmentSampler.hh.

Referenced by do_stage1_cycles(), and set_defaults().

core::Real protocols::abinitio::ConstraintFragmentSampler::constraint_weight_

private

Definition at line 187 of file ConstraintFragmentSampler.hh.

Referenced by set_constraint_weight().

constraints_additional::MaxSeqSepConstraintSetOP protocols::abinitio::ConstraintFragmentSampler::constraints_

private

Definition at line 186 of file ConstraintFragmentSampler.hh.

Referenced by apply(), constraints(), set_max_seq_sep(), and total_res().

core::Real protocols::abinitio::ConstraintFragmentSampler::max_seq_sep_fudge_

private

Definition at line 191 of file ConstraintFragmentSampler.hh.

Referenced by max_seq_sep_fudge(), set_defaults(), and total_res().

core::Real protocols::abinitio::ConstraintFragmentSampler::seq_sep_stage1_

private

Definition at line 192 of file ConstraintFragmentSampler.hh.

Referenced by do_stage1_cycles(), replace_scorefxn(), set_defaults(), and set_seq_sep_stage1().

core::Real protocols::abinitio::ConstraintFragmentSampler::seq_sep_stage3_

private

Definition at line 193 of file ConstraintFragmentSampler.hh.

Referenced by replace_scorefxn(), set_defaults(), and set_seq_sep_stage3().

core::Real protocols::abinitio::ConstraintFragmentSampler::seq_sep_stage4_

private

Definition at line 194 of file ConstraintFragmentSampler.hh.

Referenced by replace_scorefxn(), and set_defaults().

Size protocols::abinitio::ConstraintFragmentSampler::show_viol_level_

private

Definition at line 200 of file ConstraintFragmentSampler.hh.

Referenced by do_stage1_cycles(), prepare_loop_in_stage3(), prepare_loop_in_stage4(), prepare_stage2(), set_defaults(), and set_show_viol_level().

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

src/protocols/abinitio/ConstraintFragmentSampler.hh
src/protocols/abinitio/ConstraintFragmentSampler.cc

Private Attributes
constraints_additional::MaxSeqSepConstraintSetOP	constraints_

core::Real	constraint_weight_

bool	bMinTrial_

core::Real	max_seq_sep_fudge_

core::Real	seq_sep_stage1_

core::Real	seq_sep_stage3_

core::Real	seq_sep_stage4_

bool	bSkipOnNoViolation_

Size	show_viol_level_

bool	bNoRecoverLowAtSwitch_

bool	bRampChainbreaks_

bool	bRampCoordConstraints_

bool	bOverlapChainbreaks_

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation