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Rosetta Protocols
2015.09
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Rosetta Protocols
2015.09
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Classes | |
| class | BuildSet |
| A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom. More... | |
| class | DunbrackSCSampler |
| Basic class for sidechain sampling that pulls data from the Dunbrack rotamer library. The samples that are returned are the basic rotamers and do not include any expansions by the "ex" flags. More... | |
| class | FullChiSampleSet |
| class | OriginalBackboneBuildPoint |
| class | ProteinBackboneBuildPoint |
| class | ProteinSCSampler |
| class | ProteinUpstreamBuilder |
| class | SampleStrategyData |
| This class holds all of the data associated with the logic for generating extra samples for a particular chi angle. There are tons of ways concievable to build extra rotamers; the data in this class is intended to group all of that data into one place. This class is not responsible for building extra rotamer samples; that responsibility is given to class FullChiSampleSet. More... | |
| class | ScaffoldBuildPoint |
| class | UpstreamBuilder |
| class | UpstreamResidueProcessor |
| class | UpstreamResTypeGeometry |
| A simple class that describes the geometry for a particular residue type. It describes the coordinate frame geometry for the fourth atom defining each chi dihedral. The fourth atom is called the "chi tip" atom, as it's at the tip of the growing kinematic chain when building chi i. This class also describes the location of the atoms controlled by each chi which are not the chi-tip atoms; it measures their location in the coordinate frame of the chi-tip atom. More... | |
Functions | |
| static thread_local basic::Tracer | TR ("protocols.match.upstream.ProteinUpstreamBuilder") |
Variables | |
| BuildSet | b |
| dummy return value More... | |
| typedef utility::pointer::shared_ptr< DunbrackSCSampler const > protocols::match::upstream::DunbrackSCSamplerCOP |
| typedef utility::pointer::shared_ptr< DunbrackSCSampler > protocols::match::upstream::DunbrackSCSamplerOP |
| typedef utility::pointer::shared_ptr< OriginalBackboneBuildPoint const > protocols::match::upstream::OriginalBackboneBuildPointCOP |
| typedef utility::pointer::shared_ptr< OriginalBackboneBuildPoint > protocols::match::upstream::OriginalBackboneBuildPointOP |
| typedef utility::pointer::shared_ptr< ProteinBackboneBuildPoint const > protocols::match::upstream::ProteinBackboneBuildPointCOP |
| typedef utility::pointer::shared_ptr< ProteinBackboneBuildPoint > protocols::match::upstream::ProteinBackboneBuildPointOP |
| typedef utility::pointer::shared_ptr< ProteinSCSampler const > protocols::match::upstream::ProteinSCSamplerCOP |
| typedef utility::pointer::shared_ptr< ProteinSCSampler > protocols::match::upstream::ProteinSCSamplerOP |
| typedef utility::pointer::shared_ptr< ProteinUpstreamBuilder const > protocols::match::upstream::ProteinUpstreamBuilderCOP |
| typedef utility::pointer::shared_ptr< ProteinUpstreamBuilder > protocols::match::upstream::ProteinUpstreamBuilderOP |
| typedef utility::pointer::shared_ptr< ScaffoldBuildPoint const > protocols::match::upstream::ScaffoldBuildPointCOP |
| typedef utility::pointer::shared_ptr< ScaffoldBuildPoint > protocols::match::upstream::ScaffoldBuildPointOP |
| typedef utility::pointer::shared_ptr< UpstreamBuilder const > protocols::match::upstream::UpstreamBuilderCOP |
| typedef utility::pointer::shared_ptr< UpstreamBuilder > protocols::match::upstream::UpstreamBuilderOP |
| typedef utility::pointer::shared_ptr< UpstreamResidueProcessor const > protocols::match::upstream::UpstreamResidueProcessorCOP |
| typedef utility::pointer::shared_ptr< UpstreamResidueProcessor > protocols::match::upstream::UpstreamResidueProcessorOP |
| typedef utility::pointer::shared_ptr< UpstreamResTypeGeometry const > protocols::match::upstream::UpstreamResTypeGeometryCOP |
| typedef utility::pointer::shared_ptr< UpstreamResTypeGeometry > protocols::match::upstream::UpstreamResTypeGeometryOP |
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static |
Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build().
| BuildSet protocols::match::upstream::b |
dummy return value
Referenced by protocols::protein_interface_design::movers::SetAtomTree::ab_fold_tree(), protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::simple_filters::RepeatParameterFilter::align_to_frame(), protocols::toolbox::task_operations::SelectResiduesWithinChainOperation::allow_design(), protocols::toolbox::task_operations::DatabaseThread::allow_design_around(), protocols::toolbox::task_operations::ThreadSequenceOperation::allow_design_around(), protocols::toolbox::task_operations::SelectResiduesWithinChainOperation::allow_repacking(), protocols::sparta::ANN::applyVecNormalization(), protocols::simple_filters::DeltaFilter::baseline(), protocols::simple_filters::RelativePoseFilter::baseline(), protocols::simple_filters::RelativePoseFilter::baseline_val(), protocols::motifs::bools_from_sizes(), protocols::simple_filters::NonSequentialNeighborsFilter::bound(), protocols::match::upstream::ProteinUpstreamBuilder::build_set(), protocols::sparta::PDB::calc_ElectricField(), protocols::sparta::PDB::calc_HN_S2(), protocols::simple_moves::BBConRotMover::calc_jacobian_cartesians(), protocols::sparta::PDB::calcSurface(), protocols::sic_dock::Rose::clashes(), protocols::simple_moves::BBConRotMover::closure(), protocols::pockets::GenPharmacophore::cluster_KeyFeatures(), protocols::sparta::PDB::collect_HN_S2_and_EF(), protocols::simple_filters::InterRepeatContactFilter::compute(), protocols::simple_filters::IntraRepeatContactFilter::compute(), protocols::rigid::RigidBodyMotionMover::compute_bias(), protocols::sic_dock::Rose::contacts(), protocols::simple_filters::RelativePoseFilter::copy_stretch(), protocols::pockets::dD_dv1(), protocols::pockets::dD_dv2(), protocols::pockets::dD_dv3(), protocols::toolbox::task_operations::SeqprofConsensusOperation::debug(), protocols::simple_filters::FileRemoveFilter::delete_content_only(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::design_only_target_residues(), protocols::design_opt::GreedyOptMutationMover::diversify(), protocols::matdes::MatDesGreedyOptMutationMover::diversify(), protocols::frag_picker::scores::AmbigCSScore::do_caching(), protocols::frag_picker::scores::CSScore::do_caching(), protocols::genetic_algorithm::eq_OP_deref(), protocols::simple_filters::DdgFilter::extreme_value_removal(), protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values_with_type(), protocols::canonical_sampling::ParallelTempering::finalize_simulation(), protocols::protein_interface_design::movers::AddChainBreak::find_automatically(), protocols::pockets::Find_Closest_Intersect_SQ(), protocols::sparta::PDB::findNeighors(), protocols::ligand_docking::generate_unique_name(), protocols::pockets::UnionEdge::get_b(), protocols::vip::VIP_Mover::get_neighbors(), protocols::farna::RNA_StructureParameters::get_pairings_from_line(), protocols::nonlocal::HelixRotate::get_rotation_parameters(), protocols::sparta::PDB::getOrbitalShift(), protocols::fldsgn::NcontactsCalculator::ignore_loops(), protocols::fldsgn::NcontactsCalculator::ignore_same_sheet(), protocols::fldsgn::NcontactsCalculator::ignore_same_sselement(), protocols::design_opt::GreedyOptMutationMover::incl_nonopt(), protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt(), protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation::include_trp(), protocols::toolbox::task_operations::LimitAromaChi2Operation::include_trp(), protocols::evaluation::PCA::jacobi(), protocols::toolbox::jacobi(), protocols::hybridization::TMalign::Kabsch(), protocols::toolbox::task_operations::SeqprofConsensusOperation::keep_native(), protocols::simple_filters::Operator::logarithm(), protocols::genetic_algorithm::lt_OP_deref(), protocols::toolbox::SelectResiduesByLayer::make_rasmol_format_file(), protocols::toolbox::task_operations::SelectResiduesWithinChainOperation::modify_unselected_residues(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::multi_use(), protocols::simple_filters::Operator::negate(), protocols::simple_filters::Sigmoid::negate(), protocols::simple_moves::MinMover::omega(), protocols::jd2::operator!=(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::prevent_repacking(), protocols::simple_moves::AddChainMover::random_access(), protocols::protein_interface_design::PatchdockReader::random_entry(), protocols::frag_picker::JCouplingIO::read(), protocols::jumping::read_disulf_pairing_list(), protocols::topology_broker::PseudocontactShiftEnergyController::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::read_tag(), protocols::ligand_docking::RigidSearchMover::recover_low(), protocols::features::SaltBridgeFeatures::report_features(), protocols::hotspot_hashing::StubGenerator::residueStubOrientFrame(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::restrict_identities(), protocols::simple_filters::RelativePoseFilter::rtmin(), protocols::design_opt::ParetoOptMutationMover::rtmin(), protocols::design_opt::GreedyOptMutationMover::rtmin(), protocols::matdes::MatDesGreedyOptMutationMover::rtmin(), protocols::sic_dock::scores::MotifHashRigidScore::score(), protocols::outputter::SilentFileOutputter::score_only(), protocols::hotspot_hashing::ComposeSearchPatterns::Searchpoints(), protocols::pose_selectors::AndSelector::selection_operation(), protocols::pose_selectors::OrSelector::selection_operation(), protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_gzip(), protocols::genetic_algorithm::GeneticAlgorithmBase::set_checkpoint_rename(), protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell_plane(), protocols::flxbb::LayerDesignOperation::set_restrict_restypes(), protocols::flxbb::LayerDesignOperation::set_verbose(), protocols::design_opt::ParetoOptMutationMover::shuffle_order(), protocols::design_opt::GreedyOptMutationMover::shuffle_order(), protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order(), protocols::ddg::sort_numerically_ascending(), protocols::simple_filters::StemFinder::stems_are_neighbors(), protocols::simple_filters::StemFinder::stems_on_sse(), protocols::hotspot_hashing::stub_from_points(), protocols::hotspot_hashing::stub_to_points(), protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all(), protocols::protein_interface_design::movers::LoopLengthChange::tail(), protocols::protein_interface_design::filters::Torsion::task_factory_set(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::two_step(), protocols::simple_filters::RelativePoseFilter::unbound(), protocols::pockets::UnionEdge::UnionEdge(), protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias(), protocols::fldsgn::NcontactsCalculator::use_only_calpha(), protocols::toolbox::SelectResiduesByLayer::use_sidechain_neighbors(), and protocols::fldsgn::filters::InterlockingAromaFilter::verbose().
1.8.7