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

Typedef Documentation

DunbrackSCSamplerCOP

typedef utility::pointer::shared_ptr< DunbrackSCSampler const > protocols::match::upstream::DunbrackSCSamplerCOP

DunbrackSCSamplerOP

typedef utility::pointer::shared_ptr< DunbrackSCSampler > protocols::match::upstream::DunbrackSCSamplerOP

OriginalBackboneBuildPointCOP

typedef utility::pointer::shared_ptr< OriginalBackboneBuildPoint const > protocols::match::upstream::OriginalBackboneBuildPointCOP

OriginalBackboneBuildPointOP

typedef utility::pointer::shared_ptr< OriginalBackboneBuildPoint > protocols::match::upstream::OriginalBackboneBuildPointOP

ProteinBackboneBuildPointCOP

typedef utility::pointer::shared_ptr< ProteinBackboneBuildPoint const > protocols::match::upstream::ProteinBackboneBuildPointCOP

ProteinBackboneBuildPointOP

typedef utility::pointer::shared_ptr< ProteinBackboneBuildPoint > protocols::match::upstream::ProteinBackboneBuildPointOP

ProteinSCSamplerCOP

typedef utility::pointer::shared_ptr< ProteinSCSampler const > protocols::match::upstream::ProteinSCSamplerCOP

ProteinSCSamplerOP

typedef utility::pointer::shared_ptr< ProteinSCSampler > protocols::match::upstream::ProteinSCSamplerOP

ProteinUpstreamBuilderCOP

typedef utility::pointer::shared_ptr< ProteinUpstreamBuilder const > protocols::match::upstream::ProteinUpstreamBuilderCOP

ProteinUpstreamBuilderOP

typedef utility::pointer::shared_ptr< ProteinUpstreamBuilder > protocols::match::upstream::ProteinUpstreamBuilderOP

ScaffoldBuildPointCOP

typedef utility::pointer::shared_ptr< ScaffoldBuildPoint const > protocols::match::upstream::ScaffoldBuildPointCOP

ScaffoldBuildPointOP

typedef utility::pointer::shared_ptr< ScaffoldBuildPoint > protocols::match::upstream::ScaffoldBuildPointOP

UpstreamBuilderCOP

typedef utility::pointer::shared_ptr< UpstreamBuilder const > protocols::match::upstream::UpstreamBuilderCOP

UpstreamBuilderOP

typedef utility::pointer::shared_ptr< UpstreamBuilder > protocols::match::upstream::UpstreamBuilderOP

UpstreamResidueProcessorCOP

typedef utility::pointer::shared_ptr< UpstreamResidueProcessor const > protocols::match::upstream::UpstreamResidueProcessorCOP

UpstreamResidueProcessorOP

typedef utility::pointer::shared_ptr< UpstreamResidueProcessor > protocols::match::upstream::UpstreamResidueProcessorOP

UpstreamResTypeGeometryCOP

typedef utility::pointer::shared_ptr< UpstreamResTypeGeometry const > protocols::match::upstream::UpstreamResTypeGeometryCOP

UpstreamResTypeGeometryOP

typedef utility::pointer::shared_ptr< UpstreamResTypeGeometry > protocols::match::upstream::UpstreamResTypeGeometryOP

Enumeration Type Documentation

ChiStrategy

enum protocols::match::upstream::ChiStrategy

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

TR()

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

static

Referenced by protocols::match::upstream::ProteinUpstreamBuilder::build().

Variable Documentation

b

BuildSet protocols::match::upstream::b

dummy return value

Referenced by protocols::cluster::calibur::__cmp(), protocols::protein_interface_design::movers::SetAtomTree::ab_fold_tree(), protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::splice::SpliceManager::add_sequence_constraints_only(), core::membrane::add_shell(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::task_operations::SelectResiduesWithinChainOperation::allow_design(), protocols::task_operations::DatabaseThread::allow_design_around(), protocols::task_operations::ThreadSequenceOperation::allow_design_around(), protocols::task_operations::SelectResiduesWithinChainOperation::allow_repacking(), protocols::environment::ang_delta(), protocols::loops::loop_mover::ang_delta(), protocols::rigid::angle_between(), protocols::abinitio::abscript::angle_diff(), core::scoring::motif::angle_distance(), protocols::normalmode::NormalModeRelaxMover::apply(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::apply(), protocols::simple_moves::ExplicitWaterMover::apply(), protocols::sparta::ANN::applyANNTransformation(), protocols::sparta::ANN::applyVecNormalization(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::assemble_datamatrix(), protocols::calc_taskop_filters::RelativePoseFilter::baseline(), protocols::simple_filters::DeltaFilter::baseline(), protocols::calc_taskop_filters::RelativePoseFilter::baseline_val(), core::scoring::motif::ResPairMotifMetaBinner::bin0_of_real(), protocols::motifs::bools_from_sizes(), protocols::simple_filters::NonSequentialNeighborsFilter::bound(), protocols::match::upstream::ProteinUpstreamBuilder::build_set(), protocols::denovo_design::architects::bulge_residues(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::calc_dipscore(), protocols::sparta::PDB::calc_ElectricField(), protocols::sparta::PDB::calc_HN_S2(), core::energy_methods::CCS_IMMSEnergy::calc_IMMS_score(), protocols::simple_moves::BBConRotMover::calc_jacobian_cartesians(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::calc_ordermatrix(), protocols::sparta::PDB::calcSurface(), protocols::inverse_folding::calculate_Cb_position(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::sic_dock::Rose::clashes(), protocols::simple_moves::BBConRotMover::closure(), protocols::pockets::GenPharmacophore::cluster_KeyFeatures(), protocols::loophash::cmp(), core::optimization::cmp_particles(), protocols::sparta::PDB::collect_HN_S2_and_EF(), protocols::membrane::com(), protocols::indexed_structure_store::ResidueEntry::comp_id(), protocols::indexed_structure_store::StructureEntry::comp_id(), protocols::hbnet::NetworkStateScoreComparator::compare(), core::scoring::compare_by_abs(), protocols::motif_grafting::movers::compare_motif2scaffold_data_by_scaffold_low2high(), protocols::topology_broker::compare_sequence_claim_priority(), core::chemical::sdf::MolWriter::compose_properties(), protocols::simple_filters::InterRepeatContactFilter::compute(), protocols::simple_filters::IntraRepeatContactFilter::compute(), protocols::rigid::RigidBodyMotionMover::compute_bias(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::compute_deltas(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), 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::splice::SampleRotamersFromPDB::concatenate_rot_matrix(), protocols::sic_dock::Rose::contacts(), core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper(), protocols::calc_taskop_filters::RelativePoseFilter::copy_stretch(), protocols::denovo_design::architects::StrandArchitect::create_motif(), core::kinematics::Stub::create_orthogonal(), protocols::pockets::dD_dv1(), protocols::pockets::dD_dv2(), protocols::pockets::dD_dv3(), protocols::splice::RBOutMover::debug(), protocols::task_operations::SeqprofConsensusOperation::debug(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores(), protocols::simple_filters::FileRemoveFilter::delete_content_only(), protocols::splice::Splice::delete_hairpin(), protocols::splice::SpliceOut::delete_hairpin(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::design_only_target_residues(), protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply(), core::scoring::func::FadeFunc::dfunc(), 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