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Rosetta 3.5
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Rosetta 3.5
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Classes | |
| class | ProteinBackboneBuildPoint |
| class | OriginalBackboneBuildPoint |
| class | ProteinSCSampler |
| 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 | 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 | 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 | FullChiSampleSet |
| class | ProteinUpstreamBuilder |
| 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 basic::Tracer | TR ("protocols.match.upstream.ProteinUpstreamBuilder") |
Variables | |
| BuildSet | b |
| dummy return value More... | |
| typedef utility::pointer::owning_ptr< DunbrackSCSampler const > protocols::match::upstream::DunbrackSCSamplerCOP |
Definition at line 33 of file ProteinSCSampler.fwd.hh.
| typedef utility::pointer::owning_ptr< DunbrackSCSampler > protocols::match::upstream::DunbrackSCSamplerOP |
Definition at line 30 of file ProteinSCSampler.fwd.hh.
| typedef utility::pointer::owning_ptr< OriginalBackboneBuildPoint const > protocols::match::upstream::OriginalBackboneBuildPointCOP |
Definition at line 32 of file OriginalScaffoldBuildPoint.fwd.hh.
| typedef utility::pointer::owning_ptr< OriginalBackboneBuildPoint > protocols::match::upstream::OriginalBackboneBuildPointOP |
Definition at line 30 of file OriginalScaffoldBuildPoint.fwd.hh.
| typedef utility::pointer::owning_ptr< ProteinBackboneBuildPoint const > protocols::match::upstream::ProteinBackboneBuildPointCOP |
Definition at line 28 of file OriginalScaffoldBuildPoint.fwd.hh.
| typedef utility::pointer::owning_ptr< ProteinBackboneBuildPoint > protocols::match::upstream::ProteinBackboneBuildPointOP |
Definition at line 26 of file OriginalScaffoldBuildPoint.fwd.hh.
| typedef utility::pointer::owning_ptr< ProteinSCSampler const > protocols::match::upstream::ProteinSCSamplerCOP |
Definition at line 28 of file ProteinSCSampler.fwd.hh.
| typedef utility::pointer::owning_ptr< ProteinSCSampler > protocols::match::upstream::ProteinSCSamplerOP |
Definition at line 25 of file ProteinSCSampler.fwd.hh.
| typedef utility::pointer::owning_ptr< ProteinUpstreamBuilder const > protocols::match::upstream::ProteinUpstreamBuilderCOP |
Definition at line 48 of file ProteinUpstreamBuilder.fwd.hh.
| typedef utility::pointer::owning_ptr< ProteinUpstreamBuilder > protocols::match::upstream::ProteinUpstreamBuilderOP |
Definition at line 46 of file ProteinUpstreamBuilder.fwd.hh.
| typedef utility::pointer::owning_ptr< ScaffoldBuildPoint const > protocols::match::upstream::ScaffoldBuildPointCOP |
Definition at line 28 of file ScaffoldBuildPoint.fwd.hh.
| typedef utility::pointer::owning_ptr< ScaffoldBuildPoint > protocols::match::upstream::ScaffoldBuildPointOP |
Definition at line 26 of file ScaffoldBuildPoint.fwd.hh.
| typedef utility::pointer::owning_ptr< UpstreamBuilder const > protocols::match::upstream::UpstreamBuilderCOP |
Definition at line 27 of file UpstreamBuilder.fwd.hh.
| typedef utility::pointer::owning_ptr< UpstreamBuilder > protocols::match::upstream::UpstreamBuilderOP |
Definition at line 25 of file UpstreamBuilder.fwd.hh.
| typedef utility::pointer::owning_ptr< UpstreamResidueProcessor const > protocols::match::upstream::UpstreamResidueProcessorCOP |
Definition at line 31 of file UpstreamBuilder.fwd.hh.
| typedef utility::pointer::owning_ptr< UpstreamResidueProcessor > protocols::match::upstream::UpstreamResidueProcessorOP |
Definition at line 29 of file UpstreamBuilder.fwd.hh.
| typedef utility::pointer::owning_ptr< UpstreamResTypeGeometry const > protocols::match::upstream::UpstreamResTypeGeometryCOP |
Definition at line 41 of file ProteinUpstreamBuilder.fwd.hh.
| typedef utility::pointer::owning_ptr< UpstreamResTypeGeometry > protocols::match::upstream::UpstreamResTypeGeometryOP |
Definition at line 38 of file ProteinUpstreamBuilder.fwd.hh.
Definition at line 25 of file ProteinUpstreamBuilder.fwd.hh.
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static |
Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build().
| BuildSet protocols::match::upstream::b |
dummy return value
Definition at line 57 of file ProteinUpstreamBuilder.cc.
Referenced by protocols::toolbox::task_operations::ThreadSequenceOperation::allow_design_around(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::sparta::ANN::applyVecNormalization(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::assemble_datamatrix(), 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(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::calc_dipscore(), protocols::sparta::PDB::calc_ElectricField(), protocols::sparta::PDB::calc_HN_S2(), protocols::simple_moves::BBConRotMover::calc_jacobian_cartesians(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::calc_ordermatrix(), protocols::sparta::PDB::calcSurface(), core::pose::carbohydrates::calculate_carbohydrate_phi(), protocols::sic_dock::Rose::clashes(), protocols::simple_moves::BBConRotMover::closure(), protocols::sparta::PDB::collect_HN_S2_and_EF(), protocols::rigid::RigidBodyMotionMover::compute_bias(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), core::scoring::packing::compute_holes_deriv(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score_res(), core::scoring::packing::compute_holes_surfs(), protocols::sic_dock::Rose::contacts(), core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesDihedral(), protocols::simple_filters::RelativePoseFilter::copy_stretch(), protocols::pockets::dD_dv1(), protocols::pockets::dD_dv2(), protocols::pockets::dD_dv3(), protocols::simple_filters::FileRemoveFilter::delete_content_only(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::design_only_target_residues(), core::scoring::constraints::FadeFunc::dfunc(), core::kinematics::distance(), protocols::frag_picker::scores::AmbigCSScore::do_caching(), protocols::frag_picker::scores::CSScore::do_caching(), core::optimization::symmetry::DOF_Node_sorter(), core::optimization::DOF_Node_sorter(), protocols::genetic_algorithm::eq_OP_deref(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::eval_dipolar(), core::scoring::etable::Etable::eval_spline(), protocols::canonical_sampling::ParallelTempering::finalize_simulation(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), protocols::protein_interface_design::movers::AddChainBreak::find_automatically(), protocols::pockets::Find_Closest_Intersect_SQ(), protocols::sparta::PDB::findNeighors(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), core::scoring::constraints::FadeFunc::func(), protocols::ligand_docking::generate_unique_name(), core::scoring::rna::RNA_Mg_Energy::get_cos_theta(), core::scoring::rna::RNA_FullAtomStackingEnergy::get_fa_stack_deriv(), core::scoring::rna::RNA_FullAtomStackingEnergy::get_fa_stack_score(), core::scoring::rna::get_fade_correction(), protocols::vip::VIP_Mover::get_neighbors(), protocols::rna::RNA_StructureParameters::get_pairings_from_line(), protocols::nonlocal::HelixRotate::get_rotation_parameters(), core::scoring::packing::get_surf_tot(), core::scoring::packing::get_surf_vol(), core::scoring::packing::get_surf_vol_deriv(), protocols::sparta::PDB::getOrbitalShift(), protocols::fldsgn::NcontactsCalculator::ignore_loops(), protocols::fldsgn::NcontactsCalculator::ignore_same_sheet(), protocols::fldsgn::NcontactsCalculator::ignore_same_sselement(), protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation::include_trp(), protocols::toolbox::task_operations::LimitAromaChi2Operation::include_trp(), core::scoring::saxs::DistanceHistogram::insert(), core::kinematics::AtomTree::insert_single_fragment(), protocols::evaluation::PCA::jacobi(), protocols::frag_picker::scores::RDCScore::jacobi(), protocols::toolbox::jacobi(), core::scoring::jacobi(), core::scoring::jacobi3(), core::kinematics::jump_distance(), protocols::hybridization::TMalign::Kabsch(), core::scoring::dna::lsf_normal(), protocols::genetic_algorithm::lt_OP_deref(), protocols::toolbox::SelectResiduesByLayer::make_rasmol_format_file(), protocols::toolbox::task_operations::LayerOperations::make_rasmol_format_file(), protocols::simple_filters::Sigmoid::negate(), protocols::simple_filters::Operator::negate(), core::kinematics::operator!=(), protocols::jd2::operator!=(), core::scoring::hbonds::operator!=(), core::conformation::symmetry::operator!=(), core::scoring::methods::operator!=(), core::scoring::packstat::HTL_EventX::operator()(), protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::prevent_repacking(), protocols::frag_picker::JCouplingIO::read(), protocols::jumping::read_disulf_pairing_list(), core::scoring::dssp::read_pairing_list(), protocols::topology_broker::PseudocontactShiftEnergyController::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(), core::sequence::ChemicalShiftScoringScheme::score(), protocols::outputter::SilentFileOutputter::score_only(), protocols::hotspot_hashing::ComposeSearchPatterns::Searchpoints(), protocols::genetic_algorithm::GeneticAlgorithm::set_checkpoint_gzip(), protocols::genetic_algorithm::GeneticAlgorithm::set_checkpoint_rename(), protocols::pockets::NonPlaidFingerprint::set_origin_away_from_eggshell_plane(), protocols::flxbb::LayerDesignOperation::set_restrict_restypes(), core::kinematics::AtomTree::set_stub_transform(), protocols::flxbb::LayerDesignOperation::set_verbose(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), protocols::design_opt::ParetoOptMutationMover::shuffle_order(), protocols::design_opt::GreedyOptMutationMover::shuffle_order(), protocols::ddg::sort_numerically_ascending(), core::scoring::etable::Etable::spline_deriv(), protocols::hotspot_hashing::stub_from_points(), protocols::hotspot_hashing::stub_to_points(), protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::svbksb(), protocols::protein_interface_design::filters::Torsion::task_factory_set(), core::kinematics::tree::Atom_::transform_Ax_plus_b_recursive(), protocols::simple_filters::RelativePoseFilter::unbound(), protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias(), protocols::fldsgn::NcontactsCalculator::use_only_calpha(), and protocols::fldsgn::filters::InterlockingAromaFilter::verbose().
1.8.4