Classes
class	Extender

class	StarAbinitio

Typedefs
typedef utility::vector1< double >	Probabilities

typedef utility::pointer::owning_ptr < StarAbinitio >	StarAbinitioOP

typedef utility::pointer::owning_ptr < StarAbinitio const >	StarAbinitioCOP

Functions
void	generate_extended_pose (Pose *extended_pose, const std::string &sequence)

void	copy_residues (const Pose &src, Size start, Size stop, Pose *dst)

void	compute_per_residue_probabilities (Size num_residues, Size fragment_len, const FoldTree &tree, Probabilities *probs)

void	update_sequence_separation (Size distance, Pose *pose)

void	setup_constraints (const Loops &aligned, Pose *pose)

void	tear_down_constraints (Pose *pose)

ScoreFunctionOP	setup_score (const std::string &weights, Real cb)

void	configure_rmc (MoverOP mover, ScoreFunctionOP score, Size num_cycles, Real temperature, bool recover_low, RationalMonteCarlo *rmc)

void	check_required ()

void *	graphics_main (protocols::moves::MoverOP mover)

void *	StarAbinitio_main (void *)
	Entry point for StarAbinitio protocol. More...

void	emit_intermediate (const core::pose::Pose &pose, const std::string &silent_filename)
	Writes pose to disk with the specified filename if -abinitio:debug is enabled. More...

void	simple_fold_tree (core::pose::Pose &pose)
	Restores simple kinematics to pose. More...

void	to_centroid (core::pose::Pose &pose)
	Converts pose to centroid residue type set. More...

Variables
static const Real	EXT_PHI = -150

static const Real	EXT_PSI = +150

static const Real	EXT_OMG = +180

static basic::Tracer	TR ("protocols.star.StarAbinitio")

const std::string	ERROR_PREFIX = "Failed to specify required option "

Typedef Documentation

typedef utility::vector1<double> protocols::star::Probabilities

typedef utility::pointer::owning_ptr<StarAbinitio const> protocols::star::StarAbinitioCOP

typedef utility::pointer::owning_ptr<StarAbinitio> protocols::star::StarAbinitioOP

Function Documentation

void protocols::star::check_required ( )

References in::file::alignment, cm::aln_format, ERROR_PREFIX, in::file::fasta, in::file::frag3, in::file::frag9, option, in::file::template_pdb, user, and utility_exit_with_message.

Referenced by StarAbinitio_main().

void protocols::star::compute_per_residue_probabilities	(	Size	num_residues,
		Size	fragment_len,
		const FoldTree &	tree,
		Probabilities *	probs
	)

References protocols::medal::invalidate_residues_spanning_cuts(), numeric::normalize(), numeric::print_probabilities(), and TR.

Referenced by protocols::star::StarAbinitio::apply().

void protocols::star::configure_rmc	(	MoverOP	mover,
		ScoreFunctionOP	score,
		Size	num_cycles,
		Real	temperature,
		bool	recover_low,
		RationalMonteCarlo *	rmc
	)

Updates RationalMonteCarlo instance. Calling this method twice without scoring a pose in between will trigger a runtime assertion in core/pose/Pose.cc.

References protocols::simple_moves::rational_mc::RationalMonteCarlo::set_mover(), protocols::simple_moves::rational_mc::RationalMonteCarlo::set_num_trials(), protocols::simple_moves::rational_mc::RationalMonteCarlo::set_recover_low(), protocols::simple_moves::rational_mc::RationalMonteCarlo::set_score_function(), and protocols::simple_moves::rational_mc::RationalMonteCarlo::set_temperature().

Referenced by protocols::star::StarAbinitio::apply().

void protocols::star::copy_residues	(	const Pose &	src,
		Size	start,
		Size	stop,
		Pose *	dst
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::residue(), core::pose::Pose::set_xyz(), protocols::loops::stop, and core::pose::Pose::xyz().

Referenced by protocols::star::Extender::extend_unaligned().

void protocols::star::emit_intermediate	(	const core::pose::Pose &	pose,
		const std::string &	silent_filename
	)

Writes pose to disk with the specified filename if -abinitio:debug is enabled.

References option, silent, and protocols::kinmatch::str().

Referenced by protocols::star::StarAbinitio::apply().

void protocols::star::generate_extended_pose	(	Pose *	extended_pose,
		const std::string &	sequence
	)

References EXT_OMG, EXT_PHI, EXT_PSI, core::pose::make_pose_from_sequence(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

Referenced by protocols::star::Extender::extend_unaligned().

void* protocols::star::graphics_main ( protocols::moves::MoverOP mover )

References protocols::jd2::JobDistributor::go(), and utility::excn::EXCN_Base::show().

Referenced by StarAbinitio_main().

void protocols::star::setup_constraints	(	const Loops &	aligned,
		Pose *	pose
	)

Adds constraints between contacting residues in different aligned chunks, as well as those specified on the command line via -constraints:cst_file. Call this after kinematics are in place.

References core::pose::Pose::add_constraint(), core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::conformation::Residue::atom_index(), core::pose::Pose::conformation(), distance(), core::pose::Pose::fold_tree(), l, option, q, core::conformation::Conformation::residue(), protocols::loops::Loops::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), TR, update_sequence_separation(), utility_exit, and core::pose::Pose::xyz().

Referenced by protocols::star::StarAbinitio::apply().

ScoreFunctionOP protocols::star::setup_score	(	const std::string &	weights,
		Real	cb
	)

Instantiates a score function by name and sets constraint terms to the value specified by the options system (-constraints:cst_weight)

References core::scoring::atom_pair_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::linear_chainbreak, option, and score.

Referenced by protocols::star::StarAbinitio::apply().

void protocols::star::simple_fold_tree ( core::pose::Pose & pose )

Restores simple kinematics to pose.

References core::pose::Pose::fold_tree(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::legacy::modeler::rna::setup_simple_fold_tree(), and protocols::star::StarAbinitio::tear_down_kinematics().

void * protocols::star::StarAbinitio_main ( void * )

Entry point for StarAbinitio protocol.

References check_required(), and graphics_main().

void protocols::star::tear_down_constraints ( Pose * pose )

References core::pose::Pose::remove_constraints().

void protocols::star::to_centroid ( core::pose::Pose & pose )

Converts pose to centroid residue type set.

References core::chemical::CENTROID, core::pose::Pose::is_centroid(), and core::util::switch_to_residue_type_set().

Referenced by protocols::star::StarAbinitio::apply().

void protocols::star::update_sequence_separation	(	Size	distance,
		Pose *	pose
	)

Regulates the application of constraints during folding based on distance between residues in the fold tree. The MonteCarlo object should be reset after calling this function.

References core::pose::Pose::constraint_set(), core::pose::Pose::fold_tree(), and TR.

Referenced by setup_constraints().