protocols::star Namespace Reference

Classes
class	Extender
class	StarAbinitio

Typedefs
using	Probabilities = utility::vector1< core::Real >
typedef utility::pointer::shared_ptr< StarAbinitio >	StarAbinitioOP
typedef utility::pointer::shared_ptr< StarAbinitio const >	StarAbinitioCOP

Functions
void	generate_extended_pose (Pose *extended_pose, const std::string &sequence)
void	copy_residues (const Pose &src, core::Size start, core::Size stop, Pose *dst)
static basic::Tracer	TR ("protocols.star.StarAbinitio")
void	compute_per_residue_probabilities (core::Size num_residues, core::Size fragment_len, const FoldTree &tree, Probabilities *probs)
void	update_sequence_separation (core::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, core::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

Probabilities

using protocols::star::Probabilities = typedef utility::vector1<core::Real>

StarAbinitioCOP

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

StarAbinitioOP

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

Function Documentation

check_required()

void protocols::star::check_required

(

)

References core::scoring::alignment, and ERROR_PREFIX.

Referenced by StarAbinitio_main().

compute_per_residue_probabilities()

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

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

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

configure_rmc()

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

@detail 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::hybridization::score, 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().

copy_residues()

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

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

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

emit_intermediate()

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 core::pack::interaction_graph::debug, and protocols::kinmatch::str().

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

generate_extended_pose()

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

References core::chemical::CENTROID, 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::size().

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

graphics_main()

void* protocols::star::graphics_main

(

protocols::moves::MoverOP

mover

)

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

Referenced by StarAbinitio_main().

setup_constraints()

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

@detail 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(), core::kinematics::distance(), core::pose::Pose::fold_tree(), core::kinematics::ShortestPathInFoldTree::max_dist(), core::chemical::rings::q, 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().

setup_score()

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

@detail 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, and protocols::hybridization::score.

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

simple_fold_tree()

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::size().

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

StarAbinitio_main()

void * protocols::star::StarAbinitio_main

(

void *

)

Entry point for StarAbinitio protocol.

References check_required(), and graphics_main().

tear_down_constraints()

void protocols::star::tear_down_constraints

(

Pose *

pose

)

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

to_centroid()

void protocols::star::to_centroid

(

core::pose::Pose &

pose

)

Converts pose to centroid residue type set.

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

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

TR()

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().

update_sequence_separation()

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

@detail 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::kinematics::distance(), core::pose::Pose::fold_tree(), and TR().

Referenced by setup_constraints().

Variable Documentation

ERROR_PREFIX

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

Referenced by check_required().

EXT_OMG

const Real protocols::star::EXT_OMG = +180

static

Referenced by generate_extended_pose().

EXT_PHI

const Real protocols::star::EXT_PHI = -150

static

Referenced by generate_extended_pose().

EXT_PSI

const Real protocols::star::EXT_PSI = +150

static

Referenced by generate_extended_pose().