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)

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

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

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

Typedef Documentation

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

Definition at line 84 of file StarAbinitio.cc.

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

Definition at line 23 of file StarAbinitio.fwd.hh.

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

Definition at line 21 of file StarAbinitio.fwd.hh.

Function Documentation

void protocols::star::check_required ( )

Definition at line 40 of file StarAbinitioMain.cc.

References ERROR_PREFIX.

Referenced by StarAbinitio_main().

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

Definition at line 99 of file StarAbinitio.cc.

References protocols::medal::invalidate_residues_spanning_cuts(), 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.

Definition at line 187 of file StarAbinitio.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
	)

Definition at line 63 of file Extender.cc.

References core::pose::Pose::conformation(), core::conformation::Residue::natoms(), 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.

Definition at line 37 of file util.cc.

References core::pack::interaction_graph::debug, core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct_out(), protocols::kinmatch::str(), and core::io::silent::SilentFileData::write_silent_struct().

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

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

Definition at line 53 of file Extender.cc.

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)

Definition at line 63 of file StarAbinitioMain.cc.

References protocols::jd2::JobDistributor::go().

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.

Definition at line 122 of file StarAbinitio.cc.

References core::pose::Pose::add_constraint(), core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::conformation::Residue::atom_index(), core::pose::Pose::conformation(), core::kinematics::distance(), core::pose::Pose::fold_tree(), core::conformation::Conformation::residue(), protocols::loops::Loops::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), TR(), update_sequence_separation(), 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)

Definition at line 174 of file StarAbinitio.cc.

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

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

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

Restores simple kinematics to pose.

Definition at line 58 of file util.cc.

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

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

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

Entry point for StarAbinitio protocol.

Definition at line 75 of file StarAbinitioMain.cc.

References check_required(), and graphics_main().

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

Definition at line 168 of file StarAbinitio.cc.

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

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

Converts pose to centroid residue type set.

Definition at line 63 of file util.cc.

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

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

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

static

Referenced by protocols::star::StarAbinitio::apply(), compute_per_residue_probabilities(), setup_constraints(), protocols::star::StarAbinitio::setup_kinematics(), and update_sequence_separation().

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.

Definition at line 109 of file StarAbinitio.cc.

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

Referenced by setup_constraints().