#include <SeedFoldTree.hh>

Inheritance diagram for protocols::seeded_abinitio::SeedFoldTree:

Collaboration diagram for protocols::seeded_abinitio::SeedFoldTree:

Public Member Functions
	SeedFoldTree ()

	SeedFoldTree (core::kinematics::FoldTreeOP ft)

virtual	~SeedFoldTree ()

void	fold_tree (core::kinematics::FoldTreeOP ft)

core::kinematics::FoldTreeOP	fold_tree () const

void	apply (core::pose::Pose &pose)

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual protocols::moves::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...

core::scoring::ScoreFunctionOP	scorefxn () const

void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)

utility::vector1< core::Size >	get_cutpoints ()

core::Size	best_by_ala_scan (core::Size start, core::Size end, core::pose::PoseOP &ts_pose)

std::set< core::Size >	get_folding_verteces ()

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

core::kinematics::FoldTreeOP	set_foldtree (core::pose::PoseOP &seed_target_chain, std::string secstr, protocols::loops::Loops &loops, bool protein_not_folded_yet)

bool	ddg_based ()

void	ddg_based (bool ddgb)

void	set_anchor_res (utility::vector1< core::Size > anchor)

void	anchor_specified (bool anchor_specified)

bool	anchor_specified ()

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)

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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Attributes
core::kinematics::FoldTreeOP	fold_tree_
	newly generated foldtree OP More...

bool	add_target_
	is there a second target chain to add More...

bool	pdb_contains_target_
	check whether there is a second target chain loaded More...

bool	twochains_
	is the input pose submitted with the target More...

utility::vector1< Size >	cut_points_
	vector containing all cutpoints More...

protocols::loops::Loops	all_seeds_
	seed info More...

bool	set_jumps_manually
	for manual set up More...

utility::vector1< core::Size >	anchors_
	anchor residues More...

bool	anchor_specified_

bool	ddg_based_
	should the jump atoms be computed based on ddG More...

core::scoring::ScoreFunctionOP	scorefxn_
	scorefunction for ala scan More...

utility::vector1< std::pair < Size, Size > >	manual_jump_pairs_

core::pose::PoseOP	template_pdb_

core::pose::PoseOP	target_chain_

core::pose::PoseOP	seeds_only_

core::pose::PoseOP	only_seeds_chain_

std::set< core::Size >	folding_verteces_

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

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 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...

Constructor & Destructor Documentation

protocols::seeded_abinitio::SeedFoldTree::SeedFoldTree ( )

Referenced by clone().

protocols::seeded_abinitio::SeedFoldTree::SeedFoldTree ( core::kinematics::FoldTreeOP ft)

References all_seeds_, anchor_specified_, anchors_, protocols::loops::Loops::clear(), cut_points_, ddg_based_, fold_tree_, folding_verteces_, pdb_contains_target_, set_jumps_manually, and twochains_.

protocols::seeded_abinitio::SeedFoldTree::~SeedFoldTree ( )

virtual

Member Function Documentation

void protocols::seeded_abinitio::SeedFoldTree::anchor_specified ( bool anchor_specified)

References anchor_specified(), and anchor_specified_.

bool protocols::seeded_abinitio::SeedFoldTree::anchor_specified ( )

References anchor_specified_.

Referenced by anchor_specified().

void protocols::seeded_abinitio::SeedFoldTree::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

References protocols::loops::add_cutpoint_variants(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::num_chains(), core::pose::Pose::split_by_chain(), and protocols::seeded_abinitio::TR().

core::Size protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan	(	core::Size	start,
		core::Size	end,
		core::pose::PoseOP &	ts_pose
	)

References protocols::simple_filters::DdgFilter::compute(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), core::sequence::end, protocols::simple_filters::AlaScan::jump(), core::conformation::Residue::name3(), protocols::simple_filters::AlaScan::repack(), protocols::simple_filters::AlaScan::repeats(), core::pose::Pose::residue(), protocols::simple_filters::AlaScan::scorefxn(), and protocols::seeded_abinitio::TR().

protocols::moves::MoverOP protocols::seeded_abinitio::SeedFoldTree::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References SeedFoldTree().

bool protocols::seeded_abinitio::SeedFoldTree::ddg_based ( )

References ddg_based_.

void protocols::seeded_abinitio::SeedFoldTree::ddg_based ( bool ddgb)

References ddg_based_.

void protocols::seeded_abinitio::SeedFoldTree::fold_tree ( core::kinematics::FoldTreeOP ft)

References fold_tree_.

core::kinematics::FoldTreeOP protocols::seeded_abinitio::SeedFoldTree::fold_tree ( ) const

References fold_tree_.

protocols::moves::MoverOP protocols::seeded_abinitio::SeedFoldTree::fresh_instance ( ) const

virtual

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).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

utility::vector1< core::Size > protocols::seeded_abinitio::SeedFoldTree::get_cutpoints ( )

std::set< core::Size > protocols::seeded_abinitio::SeedFoldTree::get_folding_verteces ( )

std::string protocols::seeded_abinitio::SeedFoldTree::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

References protocols::seeded_abinitio::SeedFoldTreeCreator::mover_name().

void protocols::seeded_abinitio::SeedFoldTree::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References core::sequence::end, protocols::moves::DataMap::get(), core::import_pose::pose_from_pdb(), and protocols::seeded_abinitio::TR().

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::SeedFoldTree::scorefxn ( ) const

References scorefxn_.

Referenced by scorefxn().

void protocols::seeded_abinitio::SeedFoldTree::scorefxn ( core::scoring::ScoreFunctionOP scorefxn)

References scorefxn(), and scorefxn_.

void protocols::seeded_abinitio::SeedFoldTree::set_anchor_res ( utility::vector1< core::Size > anchor)

References anchors_.

core::kinematics::FoldTreeOP protocols::seeded_abinitio::SeedFoldTree::set_foldtree	(	core::pose::PoseOP &	seed_target_chain,
		std::string	secstr,
		protocols::loops::Loops &	loops,
		bool	protein_not_folded_yet
	)

References core::pose::add_variant_type_to_pose_residue(), core::kinematics::FoldTree::clear(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::seeded_abinitio::define_cut_point_stochasticly(), protocols::seeded_abinitio::find_nearest_residue(), protocols::seeded_abinitio::get_closest_residue_pair(), protocols::loops::Loops::size(), core::pose::Pose::total_residue(), and protocols::seeded_abinitio::TR().

Member Data Documentation

bool protocols::seeded_abinitio::SeedFoldTree::add_target_

private

is there a second target chain to add

protocols::loops::Loops protocols::seeded_abinitio::SeedFoldTree::all_seeds_

private

seed info

Referenced by SeedFoldTree().

bool protocols::seeded_abinitio::SeedFoldTree::anchor_specified_

private

Referenced by anchor_specified(), and SeedFoldTree().

utility::vector1< core::Size > protocols::seeded_abinitio::SeedFoldTree::anchors_

private

anchor residues

Referenced by SeedFoldTree(), and set_anchor_res().

utility::vector1<Size> protocols::seeded_abinitio::SeedFoldTree::cut_points_

private

vector containing all cutpoints

Referenced by SeedFoldTree().

bool protocols::seeded_abinitio::SeedFoldTree::ddg_based_

private

should the jump atoms be computed based on ddG

Referenced by ddg_based(), and SeedFoldTree().

core::kinematics::FoldTreeOP protocols::seeded_abinitio::SeedFoldTree::fold_tree_

private

newly generated foldtree OP

Referenced by fold_tree(), and SeedFoldTree().

std::set< core::Size > protocols::seeded_abinitio::SeedFoldTree::folding_verteces_

private

Referenced by SeedFoldTree().

utility::vector1< std::pair< Size, Size > > protocols::seeded_abinitio::SeedFoldTree::manual_jump_pairs_

private

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::only_seeds_chain_

private

bool protocols::seeded_abinitio::SeedFoldTree::pdb_contains_target_

private

check whether there is a second target chain loaded

Referenced by SeedFoldTree().

core::scoring::ScoreFunctionOP protocols::seeded_abinitio::SeedFoldTree::scorefxn_

private

scorefunction for ala scan

Referenced by scorefxn().

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::seeds_only_

private

bool protocols::seeded_abinitio::SeedFoldTree::set_jumps_manually

private

for manual set up

Referenced by SeedFoldTree().

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::target_chain_

private

core::pose::PoseOP protocols::seeded_abinitio::SeedFoldTree::template_pdb_

private

bool protocols::seeded_abinitio::SeedFoldTree::twochains_

private

is the input pose submitted with the target

Referenced by SeedFoldTree().

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

src/protocols/seeded_abinitio/SeedFoldTree.hh
src/protocols/seeded_abinitio/SeedFoldTree.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation