core::util Namespace Reference

Classes
struct	Line
	struct More...
class	ABEGO
	abego elments More...
class	ABEGOManager
	manager for abego More...
class	ChainbreakUtil

Typedefs
typedef utility::pointer::owning_ptr < ABEGOManager >	ABEGOManagerOP
typedef utility::pointer::owning_ptr < ABEGOManager const >	ABEGOManagerCOP

Functions
utility::vector1< std::string >	get_abego (core::pose::Pose const &pose, core::Size const level)
	utility for getting abego More...
static basic::Tracer	TR ("protocols.toolbox.disulfide_util")
void	rebuild_disulfide (Pose &pose, Size lower_res, Size upper_res, PackerTaskOP packer_task, ScoreFunctionOP packer_score, MoveMapOP mm, ScoreFunctionOP minimizer_score)
void	rebuild_disulfide (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > disulfides, core::pack::task::PackerTaskOP packer_task=0, core::scoring::ScoreFunctionOP packer_score=0, core::kinematics::MoveMapOP mm=0, core::scoring::ScoreFunctionOP minimizer_score=0)
	Rebuild a number of pairs of cysteines (and possibly surrounding residues) so that they form near-ideal disulfide bonds. More...
void	rebuild_disulfide (core::pose::Pose &pose, core::Size lower_res, core::Size upper_res, core::pack::task::PackerTaskOP packer_task=0, core::scoring::ScoreFunctionOP packer_score=0, core::kinematics::MoveMapOP mm=0, core::scoring::ScoreFunctionOP minimizer_score=0)
	Rebuild a pair of cysteines (and possibly surrounding residues) so that they form a near-ideal disulfide bond. More...
void	add_cutpoint_variants (core::pose::Pose *pose)
	Returns true if pose has a chainbreak, false otherwise. More...
void	remove_cutpoint_variants (core::pose::Pose *pose)
	Removes cutpoint variants from pose by scanning the fold tree. More...
static basic::Tracer	TR ("core.util.switchresiduetypeset")
void	switch_to_residue_type_set (core::pose::Pose &pose, std::string const &type_set_name, bool allow_sloppy_match)

Typedef Documentation

typedef utility::pointer::owning_ptr<ABEGOManager const> core::util::ABEGOManagerCOP

Definition at line 26 of file ABEGOManager.fwd.hh.

typedef utility::pointer::owning_ptr<ABEGOManager> core::util::ABEGOManagerOP

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

Function Documentation

void core::util::add_cutpoint_variants

(

core::pose::Pose *

pose)

Returns true if pose has a chainbreak, false otherwise.

Adds cutpoint variants to pose by scanning the fold tree

Definition at line 28 of file kinematics_util.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), and core::pose::Pose::total_residue().

Referenced by protocols::medal::MedalMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::util::ChainbreakUtil::has_chainbreak(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::star::StarAbinitio::setup_kinematics(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

utility::vector1< std::string > core::util::get_abego	(	core::pose::Pose const &	pose,
		core::Size const	level
	)

utility for getting abego

Definition at line 462 of file ABEGOManager.cc.

References core::util::ABEGOManager::get_symbols().

void core::util::rebuild_disulfide	(	core::pose::Pose &	pose,
		core::Size	lower_res,
		core::Size	upper_res,
		core::pack::task::PackerTaskOP	packer_task = 0,
		core::scoring::ScoreFunctionOP	packer_score = 0,
		core::kinematics::MoveMapOP	mm = 0,
		core::scoring::ScoreFunctionOP	minimizer_score = 0
	)

Rebuild a pair of cysteines (and possibly surrounding residues) so that they form a near-ideal disulfide bond.

void core::util::rebuild_disulfide	(	Pose &	pose,
		Size	lower_res,
		Size	upper_res,
		PackerTaskOP	packer_task,
		ScoreFunctionOP	packer_score,
		MoveMapOP	mm,
		ScoreFunctionOP	minimizer_score
	)

A convenience function for calling core::util:: rebuild_disulfide() with only a single disulfide bond

Definition at line 73 of file disulfide_util.cc.

Referenced by protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::forge::remodel::RemodelDesignMover::make_disulfide(), and switch_to_residue_type_set().

void core::util::rebuild_disulfide	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > >	disulfides,
		core::pack::task::PackerTaskOP	packer_task,
		core::scoring::ScoreFunctionOP	packer_score,
		core::kinematics::MoveMapOP	mm,
		core::scoring::ScoreFunctionOP	minimizer_score
	)

Rebuild a number of pairs of cysteines (and possibly surrounding residues) so that they form near-ideal disulfide bonds.

Precondition

The two residues specified should already be cysteines with a bond defined between the SG atoms. This can be accomplished by first calling protocols::toolbox::form_disulfide().

To provide the most flexibility, this function does not restrict the degrees of freedom in the repacking and minimization steps. This is needed in some cases where the backbone position is not optimal for making a disulfide bond. However, if this function needs to be reasonably fast you should prevent repacking on all residues except the two targets.

Parameters

pose[in,out]	The pose to modify with a disulfides
lower_res[in]	The first residue of the disulfide
upper_res[in]	The second residue of the disulfide
packer_task[in]	A task to control repacking. Defaults to repacking lower_res & upper_res if ommitted or NULL.
packer_score[in]	A scoring function to use while repacking. Defaults to score12 if ommitted or NULL.
mm[in]	A MoveMap to control minimization. Defaults to full degrees of freedom if ommitted or NULL.
minimizer_score[in]	The score to use for minimization. Defaults to packer_score if ommitted or NULL.

Definition at line 106 of file disulfide_util.cc.

References core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), core::pack::task::EX_SIX_QUARTER_STEP_STDDEVS, core::scoring::getScoreFunction(), core::conformation::is_disulfide_bond(), core::pack::pack_rotamers(), core::optimization::AtomTreeMinimizer::run(), core::pose::Pose::total_residue(), TR(), and core::pose::Pose::update_residue_neighbors().

void core::util::remove_cutpoint_variants

(

core::pose::Pose *

pose)

Removes cutpoint variants from pose by scanning the fold tree.

Definition at line 39 of file kinematics_util.cc.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::pose::remove_variant_type_from_pose_residue(), and core::pose::Pose::total_residue().

Referenced by protocols::medal::MedalMover::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::LoopRebuild::build_random_loops(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::seeded_abinitio::CloseFold::fast_loopclose(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::forge::build::Bridge::modify_impl(), protocols::seeded_abinitio::CloseFold::quick_closure(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), and protocols::star::StarAbinitio::tear_down_kinematics().

void core::util::switch_to_residue_type_set	(	core::pose::Pose &	pose,
		std::string const &	type_set_name,
		bool	allow_sloppy_match
	)

the function allows a pose to use a different residue_type_set to represent all its residues, such as from fullatom residues to centroid residues, or vice versa. During the switch, corresponding atoms will be copied. Redundant atoms will be removed (in case from fullatom to centroid) and missing atoms will be built by ideal geometry (in the case from centroid to fullatom).

Definition at line 66 of file SwitchResidueTypeSet.cc.

References core::chemical::aa_unk, core::scoring::Energies::clear(), core::pose::Pose::conformation(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::pack::task::TaskFactory::create_packer_task(), core::conformation::ResidueFactory::create_residue(), core::conformation::disulfide_bonds(), core::pose::Pose::energies(), core::chemical::ChemicalManager::get_instance(), core::pose::Pose::is_fullatom(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name3(), rebuild_disulfide(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::abinitio::StructureStore::add(), protocols::relax::MiniRelax::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::simple_filters::JScoreEvaluator::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::medal::MedalMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::FastGapMover::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::relax::FastRelax::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::relax::FastRelax::batch_apply(), protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::swa::StepWiseScreener::convert_to_centroid(), protocols::swa::protein::StepWiseProteinScreener::convert_to_centroid(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::noesy_assign::NoesyModule::generate_constraint_files(), protocols::seeded_abinitio::GrowPeptides::grow_from_verteces(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::topology_broker::RigidChunkClaimer::init_after_reading(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::topology_broker::RigidChunkClaimer::new_decoy(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::RBSegmentRelaxImpl::RBSegmentRelaxImpl(), protocols::comparative_modeling::rebuild_loops_until_closed(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::recompute(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), protocols::topology_broker::RigidChunkClaimer::RigidChunkClaimer(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::abinitio::AbrelaxApplication::setup(), protocols::abinitio::ResolutionSwitcher::start_pose(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::switch_residue_type_set(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), protocols::star::to_centroid(), protocols::nonlocal::SingleFragmentMover::to_centroid(), protocols::medal::to_centroid(), and protocols::jobdist::universal_main().

static basic::Tracer core::util::TR ( "core.util.switchresiduetypeset"  )

static

static basic::Tracer core::util::TR ( "protocols.toolbox.disulfide_util"  )

static

Referenced by core::util::ABEGOManager::index2symbol(), rebuild_disulfide(), switch_to_residue_type_set(), core::util::ABEGOManager::symbol2index(), and core::util::ABEGOManager::torsion2index().