Package org.snpeff.pdb

Class ProteinInteractions

java.lang.Object
org.snpeff.pdb.ProteinInteractions
public class ProteinInteractions extends Object
This class reads a set of protein structure (PDB) files, analyzes the structures, and creates a interactions file for a SnpEff genome database (interactions.bin)
Author:
pcingola

  • Field Details

  • Constructor Details

    • ProteinInteractions

      public ProteinInteractions()

  • Method Details

    • checkParams

      public String checkParams()

    • deleteOutputDb

      public void deleteOutputDb()

    • filterTranscript

      public boolean filterTranscript(String trId)
      Return true if the transcript passes the criteria (i.e. the ID is present in 'trancriptById' map)

    • findTranscriptIds

      public Set<String> findTranscriptIds(String pdbId)

    • getAaMinSeparation

      public int getAaMinSeparation()

    • setAaMinSeparation

      public void setAaMinSeparation(int aaMinSeparation)

    • getByProteinId

      public List<IdMapperEntry> getByProteinId(String proteinId)

    • getDistanceResults

      public List<DistanceResult> getDistanceResults()

    • getDistanceThreshold

      public double getDistanceThreshold()

    • setDistanceThreshold

      public void setDistanceThreshold(double distanceThreshold)

    • getDistanceThresholdNon

      public double getDistanceThresholdNon()

    • setDistanceThresholdNon

      public void setDistanceThresholdNon(double distanceThresholdNon)

    • getIdMapFile

      public String getIdMapFile()

    • setIdMapFile

      public void setIdMapFile(String idMapFile)

    • getMaxMismatchRate

      public double getMaxMismatchRate()

    • setMaxMismatchRate

      public void setMaxMismatchRate(double maxMismatchRate)

    • getPdbOrganismCommon

      public String getPdbOrganismCommon()

    • setPdbOrganismCommon

      public void setPdbOrganismCommon(String pdbOrganismCommon)

    • getPdbOrganismScientific

      public String getPdbOrganismScientific()

    • setPdbOrganismScientific

      public void setPdbOrganismScientific(String pdbOrganismScientific)

    • getPdbResolution

      public double getPdbResolution()

    • setPdbResolution

      public void setPdbResolution(double pdbResolution)

    • getTranscript

      public Transcript getTranscript(String trId)

    • incCountFilesPass

      public void incCountFilesPass()

    • incCountMapOk

      public void incCountMapOk()

    • incCountMapError

      public void incCountMapError()

    • initialize

      public void initialize(Config config)
      Initialize class (deferred initialization) Note: This is not done at construction because we don't have a 'Config' object ready (loaded) at the time

    • isDebug

      public boolean isDebug()

    • setDebug

      public void setDebug(boolean debug)

    • isVerbose

      public boolean isVerbose()

    • setVerbose

      public void setVerbose(boolean verbose)

    • loadIdMapper

      public void loadIdMapper()

    • pdb

      public void pdb()
      PDB analysis

    • pdbAnalysis

      protected void pdbAnalysis()
      Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e. AA sequence matches between transcript and PDB)

    • run

      public boolean run()
      Run analysis.

    • run

      public boolean run(boolean storeResults)

    • save

      public void save(List<DistanceResult> distResults)
      Save results

    • setConfig

      public void setConfig(Config config)

    • setGenomeVer

      public void setGenomeVer(String genomeVer)

    • setPdbDir

      public void setPdbDir(String pdbDir)