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protocols::match::upstream Namespace Reference

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...
 

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

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< ProteinSCSampler const > protocols::match::upstream::ProteinSCSamplerCOP
typedef utility::pointer::shared_ptr< ProteinSCSampler > protocols::match::upstream::ProteinSCSamplerOP
typedef utility::pointer::shared_ptr< ScaffoldBuildPoint const > protocols::match::upstream::ScaffoldBuildPointCOP
typedef utility::pointer::shared_ptr< UpstreamBuilder const > protocols::match::upstream::UpstreamBuilderCOP
typedef utility::pointer::shared_ptr< UpstreamBuilder > protocols::match::upstream::UpstreamBuilderOP

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

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::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::normalmode::NormalModeRelaxMover::apply(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::apply(), protocols::simple_moves::ExplicitWaterMover::apply(), protocols::sparta::ANN::applyVecNormalization(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::assemble_datamatrix(), protocols::simple_filters::DeltaFilter::baseline(), 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