Rosetta 3.4
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protocols::match::upstream Namespace Reference

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...

Typedefs

typedef
utility::pointer::owning_ptr
< ProteinBackboneBuildPoint
ProteinBackboneBuildPointOP
typedef
utility::pointer::owning_ptr
< ProteinBackboneBuildPoint
const > 
ProteinBackboneBuildPointCOP
typedef
utility::pointer::owning_ptr
< OriginalBackboneBuildPoint
OriginalBackboneBuildPointOP
typedef
utility::pointer::owning_ptr
< OriginalBackboneBuildPoint
const > 
OriginalBackboneBuildPointCOP
typedef
utility::pointer::owning_ptr
< ProteinSCSampler
ProteinSCSamplerOP
typedef
utility::pointer::owning_ptr
< ProteinSCSampler const > 
ProteinSCSamplerCOP
typedef
utility::pointer::owning_ptr
< DunbrackSCSampler
DunbrackSCSamplerOP
typedef
utility::pointer::owning_ptr
< DunbrackSCSampler const > 
DunbrackSCSamplerCOP
typedef
utility::pointer::owning_ptr
< UpstreamResTypeGeometry
UpstreamResTypeGeometryOP
typedef
utility::pointer::owning_ptr
< UpstreamResTypeGeometry
const > 
UpstreamResTypeGeometryCOP
typedef
utility::pointer::owning_ptr
< ProteinUpstreamBuilder
ProteinUpstreamBuilderOP
typedef
utility::pointer::owning_ptr
< ProteinUpstreamBuilder const > 
ProteinUpstreamBuilderCOP
typedef
utility::pointer::owning_ptr
< ScaffoldBuildPoint
ScaffoldBuildPointOP
typedef
utility::pointer::owning_ptr
< ScaffoldBuildPoint const > 
ScaffoldBuildPointCOP
typedef
utility::pointer::owning_ptr
< UpstreamBuilder
UpstreamBuilderOP
typedef
utility::pointer::owning_ptr
< UpstreamBuilder const > 
UpstreamBuilderCOP
typedef
utility::pointer::owning_ptr
< UpstreamResidueProcessor
UpstreamResidueProcessorOP
typedef
utility::pointer::owning_ptr
< UpstreamResidueProcessor
const > 
UpstreamResidueProcessorCOP

Enumerations

enum  ChiStrategy {
  no_samples, follow_EX_flags, rotameric_chi_mimic_EX_flags, rotameric_chi_step_by_value,
  rotameric_chi_step_wi_sd_range, rotameric_chi_partition_sd_range, nonrotameric_chi_sample_wi_nrchi_bin, nonrotameric_chi_sample_wi_nrchi_bin_to_lower_boundary
}

Functions

static basic::Tracer TR ("protocols.match.upstream.ProteinUpstreamBuilder")

Variables

BuildSet b
 dummy return value

Typedef Documentation


Enumeration Type Documentation

Enumerator:
no_samples 
follow_EX_flags 

In particular, for proton chi, leave them fixed at some arbitrary value.

rotameric_chi_mimic_EX_flags 
rotameric_chi_step_by_value 
rotameric_chi_step_wi_sd_range 
rotameric_chi_partition_sd_range 
nonrotameric_chi_sample_wi_nrchi_bin 
nonrotameric_chi_sample_wi_nrchi_bin_to_lower_boundary 

Function Documentation

static basic::Tracer protocols::match::upstream::TR ( "protocols.match.upstream.ProteinUpstreamBuilder"  ) [static]

Variable Documentation

dummy return value

Referenced by protocols::toolbox::task_operations::ThreadSequenceOperation::allow_design_around(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::sparta::ANN::applyVecNormalization(), protocols::protein_interface_design::filters::RelativePoseFilter::baseline(), protocols::protein_interface_design::filters::DeltaFilter::baseline(), protocols::protein_interface_design::filters::RelativePoseFilter::baseline_val(), protocols::motifs::bools_from_sizes(), protocols::match::upstream::ProteinUpstreamBuilder::build_set(), protocols::sparta::PDB::calc_ElectricField(), protocols::sparta::PDB::calc_HN_S2(), protocols::sparta::PDB::calcSurface(), protocols::sparta::PDB::collect_HN_S2_and_EF(), 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(), core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesDihedral(), protocols::protein_interface_design::filters::RelativePoseFilter::copy_stretch(), core::scoring::constraints::FadeFunc::dfunc(), core::kinematics::distance(), protocols::frag_picker::scores::CSScore::do_caching(), protocols::frag_picker::scores::AmbigCSScore::do_caching(), core::optimization::symmetry::DOF_Node_sorter(), core::optimization::DOF_Node_sorter(), protocols::genetic_algorithm::eq_OP_deref(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), protocols::protein_interface_design::movers::AddChainBreak::find_automatically(), protocols::pockets::PlaidFingerprint::Find_Intersect(), 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::get_fade_correction(), protocols::vip::VIP_Mover::get_neighbors(), 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(), core::scoring::saxs::DistanceHistogram::insert(), protocols::toolbox::jacobi(), core::scoring::jacobi(), core::scoring::jacobi3(), core::kinematics::jump_distance(), core::scoring::dna::lsf_normal(), protocols::genetic_algorithm::lt_OP_deref(), protocols::toolbox::SelectResiduesByLayer::make_rasmol_format_file(), core::scoring::methods::operator!=(), core::scoring::hbonds::operator!=(), core::kinematics::operator!=(), core::scoring::packstat::HTL_EventX::operator()(), 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::simple_moves::FragmentCost::score(), protocols::genetic_algorithm::GeneticAlgorithm::set_checkpoint_gzip(), protocols::genetic_algorithm::GeneticAlgorithm::set_checkpoint_rename(), core::kinematics::AtomTree::set_stub_transform(), protocols::flxbb::LayerDesignOperation::set_verbose(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), protocols::ddg::sort_numerically_ascending(), protocols::protein_interface_design::filters::RmsdFilter::superimpose_on_all(), protocols::protein_interface_design::filters::Torsion::task_factory_set(), core::kinematics::tree::Atom_::transform_Ax_plus_b_recursive(), protocols::protein_interface_design::filters::RelativePoseFilter::unbound(), protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias(), protocols::fldsgn::NcontactsCalculator::use_only_calpha(), and protocols::fldsgn::filters::InterlockingAromaFilter::verbose().

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