protocols::medal Namespace Reference

Classes
class	MedalExchangeMover
class	MedalMover

Typedefs
typedef utility::pointer::shared_ptr < MedalFreeMover >	MedalFreeMoverOP
typedef utility::pointer::shared_ptr < MedalFreeMover const >	MedalFreeMoverCOP
typedef boost::function< void(const core::pose::Pose &)>	Trigger
typedef utility::pointer::shared_ptr < MedalMover >	MedalMoverOP
typedef utility::pointer::shared_ptr < MedalMover const >	MedalMoverCOP
typedef utility::vector1< double >	Probabilities

Functions
static thread_local basic::Tracer	TR ("protocols.medal.MedalExchangeMover")
protocols::loops::LoopsCOP	combine_loops (LoopsCOP aligned, LoopsCOP unaligned)
void	setup_coordinate_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)
void	setup_atom_pair_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)
void	setup_constraints (const Pose &pose, LoopsCOP aligned, ConstraintSetOP constraints)
void	check_required_common ()
void	check_required_cm ()
void *	graphics_main (protocols::moves::MoverOP mover)
void *	Medal_main (void *)
	Entry point for Medal protocol. More...
void *	MedalExchange_main (void *)
	Entry point for MedalExchange protocol. More...
static thread_local basic::Tracer	TR ("protocols.medal.MedalMover")
void	on_pose_accept (const core::pose::Pose &pose)
void	end_bias_probabilities (const unsigned num_residues, Probabilities *p)
	Lower sampling probability near termini. More...
void	alignment_probabilities (const unsigned num_residues, const core::sequence::SequenceAlignment &alignment, Probabilities *p)
	Computes per-residue alignment probabilities. To minimize assumptions about the fold tree, the number of residues in the pose is an explicit input. More...
void	chunk_probabilities (const protocols::loops::Loops &chunks, Probabilities *p)
	Computes per-residue chunk probabilities. A linear voting scheme is used to bias sampling toward larger chunks. More...
void	cutpoint_probabilities (const unsigned num_residues, const core::kinematics::FoldTree &tree, Probabilities *p)
	Computes per-residue cutpoint probabilities. Sampling is biased toward residues proximal to a cutpoint. More...
void	invalidate_residues_spanning_cuts (const core::kinematics::FoldTree &tree, const core::Size fragment_len, Probabilities *probs)
	Zeroes out the probability of residues for which fragment insertion would cross cutpoint boundaries. More...
void	as_set (protocols::loops::LoopsCOP loops, boost::unordered_set< core::Size > *s)
	Populates a hash table with the residues contained in loops. More...
void	to_centroid (core::pose::Pose *pose)

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

Typedef Documentation

typedef utility::pointer::shared_ptr<MedalFreeMover const> protocols::medal::MedalFreeMoverCOP

typedef utility::pointer::shared_ptr<MedalFreeMover> protocols::medal::MedalFreeMoverOP

typedef utility::pointer::shared_ptr<MedalMover const> protocols::medal::MedalMoverCOP

typedef utility::pointer::shared_ptr<MedalMover> protocols::medal::MedalMoverOP

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

typedef boost::function<void(const core::pose::Pose&)> protocols::medal::Trigger

Function Documentation

void protocols::medal::alignment_probabilities	(	const unsigned	num_residues,
		const core::sequence::SequenceAlignment &	alignment,
		Probabilities *	p
	)

Computes per-residue alignment probabilities. To minimize assumptions about the fold tree, the number of residues in the pose is an explicit input.

References numeric::normalize(), and core::sequence::SequenceAlignment::sequence_mapping().

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities().

void protocols::medal::as_set	(	protocols::loops::LoopsCOP	loops,
		boost::unordered_set< core::Size > *	s
	)

Populates a hash table with the residues contained in loops.

Referenced by setup_atom_pair_constraints().

void protocols::medal::check_required_cm

(

)

Comparative modeling options

References ERROR_PREFIX, option, user, and utility_exit_with_message.

Referenced by Medal_main(), and MedalExchange_main().

void protocols::medal::check_required_common

(

)

Standard options

References ERROR_PREFIX, option, user, and utility_exit_with_message.

Referenced by Medal_main(), and MedalExchange_main().

void protocols::medal::chunk_probabilities	(	const protocols::loops::Loops &	chunks,
		Probabilities *	p
	)

Computes per-residue chunk probabilities. A linear voting scheme is used to bias sampling toward larger chunks.

Linear voting based on chunk length Assumes <chunks> are in ascending order

References protocols::loops::Loops::begin(), protocols::loops::Loops::end(), protocols::loops::Loop::length(), numeric::normalize(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities().

protocols::loops::LoopsCOP protocols::medal::combine_loops	(	LoopsCOP	aligned,
		LoopsCOP	unaligned
	)

Combines both sets of loops, sorting the result in increasing order of start position

Referenced by protocols::medal::MedalExchangeMover::apply().

void protocols::medal::cutpoint_probabilities	(	const unsigned	num_residues,
		const core::kinematics::FoldTree &	tree,
		Probabilities *	p
	)

Computes per-residue cutpoint probabilities. Sampling is biased toward residues proximal to a cutpoint.

References core::kinematics::FoldTree::cutpoint(), distance(), utility::find_closest(), numeric::normalize(), and core::kinematics::FoldTree::num_cutpoint().

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities().

void protocols::medal::end_bias_probabilities	(	const unsigned	num_residues,
		Probabilities *	p
	)

Lower sampling probability near termini.

Biases sampling away from termini.

References numeric::normalize().

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities().

void* protocols::medal::graphics_main

(

protocols::moves::MoverOP

mover

)

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

Referenced by Medal_main(), and MedalExchange_main().

void protocols::medal::invalidate_residues_spanning_cuts	(	const core::kinematics::FoldTree &	tree,
		const core::Size	fragment_len,
		Probabilities *	probs
	)

Zeroes out the probability of residues for which fragment insertion would cross cutpoint boundaries.

Given a fold tree and fragment library, zero out residues whose modification would span a cutpoint boundary

References core::kinematics::FoldTree::cutpoint(), and core::kinematics::FoldTree::num_cutpoint().

Referenced by protocols::medal::MedalMover::compute_per_residue_probabilities(), protocols::star::compute_per_residue_probabilities(), and protocols::medal::MedalExchangeMover::setup_sampling_probs().

void * protocols::medal::Medal_main

(

void *

)

Entry point for Medal protocol.

References check_required_cm(), check_required_common(), and graphics_main().

void * protocols::medal::MedalExchange_main

(

void *

)

Entry point for MedalExchange protocol.

References check_required_cm(), check_required_common(), and graphics_main().

void protocols::medal::on_pose_accept

(

const core::pose::Pose &

pose

)

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

Referenced by protocols::medal::MedalMover::create_fragment_and_rigid_mover(), protocols::medal::MedalMover::create_fragment_mover(), and protocols::medal::MedalMover::create_small_mover().

void protocols::medal::setup_atom_pair_constraints	(	const Pose &	pose,
		LoopsCOP	aligned,
		ConstraintSetOP	constraints
	)

Retain user-specified distance restraints that operate on pairs of aligned residues

References as_set(), core::scoring::atom_pair_constraint, c, option, and user.

Referenced by setup_constraints().

void protocols::medal::setup_constraints	(	const Pose &	pose,
		LoopsCOP	aligned,
		ConstraintSetOP	constraints
	)

References setup_atom_pair_constraints(), and setup_coordinate_constraints().

Referenced by protocols::medal::MedalExchangeMover::apply().

void protocols::medal::setup_coordinate_constraints	(	const Pose &	pose,
		LoopsCOP	aligned,
		ConstraintSetOP	constraints
	)

Create coordinate constraints restraining aligned residues to their initial positions

References core::pose::Pose::conformation(), distance(), core::conformation::Conformation::residue(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by setup_constraints().

void protocols::medal::to_centroid

(

core::pose::Pose *

pose

)

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

Referenced by protocols::rbsegment_relax::AutoRBMover::apply(), protocols::medal::MedalExchangeMover::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::hybridization::MRMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::flexpep_docking::FlexPepDockingAbInitio::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::CDRH3Modeler::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::antibody_legacy::CloseOneMover::apply(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::docking::DockingEnsemble::load_ensemble(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), and protocols::symmetric_docking::SymDockProtocol::score_only().

static thread_local basic::Tracer protocols::medal::TR ( "protocols.medal.MedalExchangeMover"  )

static

Referenced by protocols::medal::MedalMover::apply(), and protocols::medal::MedalMover::compute_per_residue_probabilities().

static thread_local basic::Tracer protocols::medal::TR ( "protocols.medal.MedalMover"  )

static

Variable Documentation

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

Referenced by check_required_cm(), and check_required_common().