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frag_picker Directory Reference
Directory dependency graph for frag_picker:
src/protocols/frag_picker

Directories

directory  nonlocal
 
directory  quota
 
directory  scores
 

Files

file  BestTotalScoreSelector.cc
 
file  BestTotalScoreSelector.fwd.hh
 
file  BestTotalScoreSelector.hh
 provides a selector that picks best fragments based on their total score
 
file  BoundedCollector.fwd.hh
 
file  BoundedCollector.hh
 
file  CandidatesCollector.fwd.hh
 Forward declaration for CandidatesCollector.
 
file  CandidatesCollector.hh
 Pure virtual base class for a container holding fragment candidates.
 
file  CommonFragmentComparators.fwd.hh
 provides a few ways to compare fragment candidates (forward definitions)
 
file  CommonFragmentComparators.hh
 provides a few ways to compare fragment candidates
 
file  CompositeFragmentSelector.cc
 provides a selector that picks best fragments based on their total score
 
file  CompositeFragmentSelector.hh
 provides a selector that picks best fragments based on their total score
 
file  Contact.fwd.hh
 
file  Contact.hh
 A contact.
 
file  ContactCounts.fwd.hh
 
file  ContactCounts.hh
 Contact counts.
 
file  ContactTypes.cc
 fragment picker contact types
 
file  ContactTypes.hh
 fragment picker type declarations
 
file  CS2ndShift.cc
 
file  CS2ndShift.hh
 
file  CSTalosIO.cc
 
file  CSTalosIO.hh
 Class that converts Talos object into secondary shifts list.
 
file  CustomScoreSelector.cc
 
file  CustomScoreSelector.fwd.hh
 
file  CustomScoreSelector.hh
 provides a selector that picks best fragments based on their total score
 
file  DiversifyCrmsdByClustering.cc
 
file  DiversifyCrmsdByClustering.hh
 provides a selector that picks fragments diversified by crmsd (by means of hierarchical clustering)
 
file  DiversifyCrmsdSelector.cc
 
file  DiversifyCrmsdSelector.hh
 provides a selector that picks best fragments based on their total score
 
file  DiversifyDihedralsSelector.cc
 
file  DiversifyDihedralsSelector.hh
 provides a selector that picks best fragments based on their total score
 
file  Faraggi_SA.cc
 Faraggi maximum SA values from Faraggi et al. Proteins 2008.
 
file  Faraggi_SA.hh
 Faraggi maximum SA values from Faraggi et al. Proteins 2008.
 
file  FragmentCandidate.cc
 
file  FragmentCandidate.fwd.hh
 
file  FragmentCandidate.hh
 Something that might become a fragment if its scores will be good enough.
 
file  FragmentComparatorBase.fwd.hh
 
file  FragmentComparatorBase.hh
 defines a base class for all fragment comparators
 
file  FragmentPicker.cc
 Fragment picker - the core part of picking machinery.
 
file  FragmentPicker.fwd.hh
 Fragment picker - forward declaration.
 
file  FragmentPicker.hh
 Fragment picker - the core part of picking machinery.
 
file  FragmentScoreFilter.cc
 This filter analyzes fragment quality. How it does so is highly customizeable, but it is reccommended that you average the RMSD of all 200 fragments picked at every position. This is also the default behavior. It requires paths to external programs like SPARKS-X and blast-pgp, depending on your method of fragment picking.
 
file  FragmentScoreFilter.fwd.hh
 
file  FragmentScoreFilter.hh
 
file  FragmentScoreFilterCreator.hh
 FilterCreators for the FragmentScoreFilterCreator.
 
file  FragmentSelectingRule.fwd.hh
 
file  FragmentSelectingRule.hh
 provides a selector that picks best fragments based on their total score
 
file  GrabAllCollector.hh
 
file  JCouplingIO.cc
 
file  JCouplingIO.hh
 
file  LAMBEGO_IO.cc
 
file  LAMBEGO_IO.hh
 reader for a probability distribution over A,B,E,G,O torsion bins.
 
file  LazySortedVector1.hh
 
file  PdbIdChunkFilter.cc
 
file  PdbIdChunkFilter.fwd.hh
 
file  PdbIdChunkFilter.hh
 
file  PhiPsiTalosIO.cc
 
file  PhiPsiTalosIO.hh
 Class that reads and writes Phi-Psi in TALOS format.
 
file  SidechainContactDistCutoff.cc
 Defines sidechain contact distance cutoffs.
 
file  SidechainContactDistCutoff.fwd.hh
 
file  SidechainContactDistCutoff.hh
 Defines sidechain contact distance cutoffs.
 
file  TorsionBinIO.cc
 
file  TorsionBinIO.hh
 reader for a probability distribution over A,B,E,G,O torsion bins.
 
file  VallChunk.cc
 a contiguous chunk of residues taken from a vall.
 
file  VallChunk.fwd.hh
 forward declaration for VallChunk
 
file  VallChunk.hh
 a contiguous chunk of residues taken from a vall.
 
file  VallChunkFilter.fwd.hh
 forward declaration for VallChunkFilter
 
file  VallChunkFilter.hh
 defines two basic chunk filters based on pdb id
 
file  VallProvider.cc
 reads a vall library and serves the data in chunks
 
file  VallProvider.fwd.hh
 forward declaration for VallProvider
 
file  VallProvider.hh
 reads a vall library and serves the data in chunks
 
file  VallResidue.cc
 class for managing a line of the Vall fragment library
 
file  VallResidue.fwd.hh
 forward declaration for core::fragment::picking::vall:VallResidue
 
file  VallResidue.hh
 class for managing a line of the Vall fragment library