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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::shared_ptr< ProteinBackboneBuildPointProteinBackboneBuildPointOP
 
typedef utility::pointer::shared_ptr< ProteinBackboneBuildPoint const > ProteinBackboneBuildPointCOP
 
typedef utility::pointer::shared_ptr< OriginalBackboneBuildPointOriginalBackboneBuildPointOP
 
typedef utility::pointer::shared_ptr< OriginalBackboneBuildPoint const > OriginalBackboneBuildPointCOP
 
typedef utility::pointer::shared_ptr< ProteinSCSamplerProteinSCSamplerOP
 
typedef utility::pointer::shared_ptr< ProteinSCSampler const > ProteinSCSamplerCOP
 
typedef utility::pointer::shared_ptr< DunbrackSCSamplerDunbrackSCSamplerOP
 
typedef utility::pointer::shared_ptr< DunbrackSCSampler const > DunbrackSCSamplerCOP
 
typedef utility::pointer::shared_ptr< UpstreamResTypeGeometryUpstreamResTypeGeometryOP
 
typedef utility::pointer::shared_ptr< UpstreamResTypeGeometry const > UpstreamResTypeGeometryCOP
 
typedef utility::pointer::shared_ptr< ProteinUpstreamBuilderProteinUpstreamBuilderOP
 
typedef utility::pointer::shared_ptr< ProteinUpstreamBuilder const > ProteinUpstreamBuilderCOP
 
typedef utility::pointer::shared_ptr< ScaffoldBuildPointScaffoldBuildPointOP
 
typedef utility::pointer::shared_ptr< ScaffoldBuildPoint const > ScaffoldBuildPointCOP
 
typedef utility::pointer::shared_ptr< UpstreamBuilderUpstreamBuilderOP
 
typedef utility::pointer::shared_ptr< UpstreamBuilder const > UpstreamBuilderCOP
 
typedef utility::pointer::shared_ptr< UpstreamResidueProcessorUpstreamResidueProcessorOP
 
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

◆ OriginalBackboneBuildPointOP

◆ ProteinBackboneBuildPointCOP

◆ 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

◆ ProteinUpstreamBuilderOP

◆ ScaffoldBuildPointCOP

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

◆ 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

◆ UpstreamResidueProcessorOP

◆ UpstreamResTypeGeometryCOP

◆ UpstreamResTypeGeometryOP

Enumeration Type Documentation

◆ 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

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(), 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