Rosetta 3.4
Classes | Typedefs | Functions
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
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.
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.
void add_cutpoint_variants (core::pose::Pose *pose)
 Returns true if `pose` has a chainbreak, false otherwise.
void remove_cutpoint_variants (core::pose::Pose *pose)
 Removes cutpoint variants from `pose` by scanning the fold tree.
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


Function Documentation

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

utility for getting abego

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

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.

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::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 
)
void core::util::remove_cutpoint_variants ( core::pose::Pose pose)
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).

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::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::simple_filters::JScoreEvaluator::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::relax::MiniRelax::apply(), protocols::relax::FastRelax::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::medal::MedalMover::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::loophash::FastGapMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::relax::FastRelax::batch_apply(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::protein_interface_design::EnergyPerResidueFilter::compute(), protocols::protein_interface_design::ScoreTypeFilter::compute(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::noesy_assign::NoesyModule::generate_constraint_files(), protocols::noesy_assign::CrossPeakList::generate_constraints(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::topology_broker::RigidChunkClaimer::init_after_reading(), protocols::topology_broker::RigidChunkClaimer::new_decoy(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::RBSegmentRelax_main(), 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::topology_broker::TopologyBroker::switch_to_fullatom(), protocols::star::to_centroid(), protocols::medal::to_centroid(), and protocols::jobdist::universal_main().

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