Package csb :: Package bio :: Package fragments
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Package fragments

source code

APIs for working with protein structure fragments and libraries.

This package contains the nuts and bolts of HHfrag. Everything here revolves around the Target class, which describes a protein structure prediction target. One typically assigns fragments (Assignments) to the target and then builds a fragment library with RosettaFragsetFactory.


Note: Internal or legacy objects are intentionally left undocumented. This typically indicates experimental code.

Submodules

Classes
  AdaptedAssignment
  Assignment
Represents a match between a fragment and its target.
  AssignmentFactory
  BenchmarkAdapter
  ChemShiftAssignment
  ChemShiftAssignmentFactory
  ChemShiftTarget
  ChemShiftTargetResidue
  ClusterDivergingError
  ClusterEmptyError
  ClusterExhaustedError
  ClusterNode
Cluster node.
  ClusterRep
Cluster's representative (centroid) node.
  FragmentCluster
Provides clustering/filtering of the fragments, covering a common residue in the target.
  FragmentMatch
Base class, representing a match between a fragment and its target.
  FragmentTypes
  Metrics
  Prediction
  PredictionContainer
  ResidueAssignmentInfo
  ResidueEventInfo
  RosettaFragsetFactory
Simplifies the construction of fragment libraries.
  SmoothFragmentMap
  Target
Represents a protein structure prediction target.
  TargetResidue
Wrapper around Target's native residues.
  TargetSegment
  TorsionAnglesPredictor
Fragment-based phi/psi angles predictor.
  TorsionPredictionInfo
Struct container for a single torsion angle prediction.
Variables
  RANDOM_RMSD = {5: 1.87490058573, 6: 2.43142836863, 7: 2.902113...
  __package__ = 'csb.bio.fragments'
Variables Details

RANDOM_RMSD

Value:
{5: 1.87490058573,
 6: 2.43142836863,
 7: 2.90211352678,
 8: 3.24777162002,
 9: 3.5469606556,
 10: 3.82954655245,
 11: 4.13431071141,
 12: 4.37616979291,
...