Package org.rcsb.strucmotif.config

Class MotifSearchConfig

java.lang.Object
org.rcsb.strucmotif.config.MotifSearchConfig
@Configuration @EnableConfigurationProperties @ConfigurationProperties(prefix="strucmotif") public class MotifSearchConfig extends Object
All properties used throughout the strucmotif-search application.

  • Field Details

    • STATE_KNOWN_LIST

      public static final String STATE_KNOWN_LIST
      List of all identifiers ever registered.
      See Also:

    • STATE_DIRTY_LIST

      public static final String STATE_DIRTY_LIST
      List of all identifiers needed to recover if update operation fails.
      See Also:

    • RENUMBERED_DIRECTORY

      public static final String RENUMBERED_DIRECTORY
      Name of the renumbered directory.
      See Also:

    • INDEX_DIRECTORY

      public static final String INDEX_DIRECTORY
      Name of the inverted index directory.
      See Also:

    • RCSB_ENTRY_LIST

      public static final String RCSB_ENTRY_LIST
      RCSB URL that reports currently present identifiers in archive.
      See Also:

  • Constructor Details

    • MotifSearchConfig

      public MotifSearchConfig()

  • Method Details

    • getDistanceCutoff

      public float getDistanceCutoff()
      Maximum distance of residue pairs.
      Returns:
      threshold in Angstrom

    • setDistanceCutoff

      public void setDistanceCutoff(float distanceCutoff)
      Set maximum distance of residue pairs.
      Parameters:
      distanceCutoff - threshold in Angstrom

    • getRootPath

      public String getRootPath()
      The root path where data is read/written.
      Returns:
      a path

    • setRootPath

      public void setRootPath(String rootPath)
      Set the root path where data is read/written.
      Parameters:
      rootPath - a path

    • getDataSource

      public String getDataSource()
      Optional path to a local collection of structure data. This will be used during update operations. If not set or not valid, corresponding data will be fetched from bcif-fetch-url. {id} refers to the PDB-ID, {middle} can be used to represent the middle hash of an ID (e.g. 'ab' for '1abc').
      Returns:
      a path

    • setDataSource

      public void setDataSource(String dataSource)
      Optional path to a local collection of structure data. This will be used during update operations. If not set or not valid, corresponding data will be fetched from bcif-fetch-url. {id} refers to the PDB-ID, {middle} can be used to represent the middle hash of an ID (e.g. 'ab' for '1abc').
      Parameters:
      dataSource - a path

    • getNumberThreads

      public int getNumberThreads()
      How many threads to use?
      Returns:
      an int

    • setNumberThreads

      public void setNumberThreads(int numberThreads)
      Set how many threads to use?
      Parameters:
      numberThreads - an int greater than 0

    • getMaxResults

      public int getMaxResults()
      Maximum number of results returned.
      Returns:
      an int

    • setMaxResults

      public void setMaxResults(int maxResults)
      Set maximum number of results returned.
      Parameters:
      maxResults - an int

    • getDecimalPlacesScore

      public int getDecimalPlacesScore()
      How many digits to write (e.g. for RMSD).
      Returns:
      an int

    • setDecimalPlacesScore

      public void setDecimalPlacesScore(int decimalPlacesScore)
      Set how many digits to write (e.g. for RMSD).
      Parameters:
      decimalPlacesScore - an int

    • getDecimalPlacesMatrix

      public int getDecimalPlacesMatrix()
      How many digits to write for matrices.
      Returns:
      an int

    • setDecimalPlacesMatrix

      public void setDecimalPlacesMatrix(int decimalPlacesMatrix)
      Set how many digits to write for matrices.
      Parameters:
      decimalPlacesMatrix - an int

    • getUpdateChunkSize

      public int getUpdateChunkSize()
      How many structures to process before flushing to inverted index.
      Returns:
      an int

    • setUpdateChunkSize

      public void setUpdateChunkSize(int updateChunkSize)
      Set how many structures to process before flushing to inverted index.
      Parameters:
      updateChunkSize - an int

    • getMaxMotifSize

      public int getMaxMotifSize()
      Maximum number of residues in a motif.
      Returns:
      an int

    • setMaxMotifSize

      public void setMaxMotifSize(int maxMotifSize)
      Set maximum number of residues in a motif.
      Parameters:
      maxMotifSize - an int

    • getCifFetchUrl

      public String getCifFetchUrl()
      The URL where (Binary)CIF data will be fetched from if not present locally. {id} refers to the PDB-ID, {middle} can be used to represent the middle hash of an ID (e.g. 'ab' for '1abc').
      Returns:
      a URL

    • setCifFetchUrl

      public void setCifFetchUrl(String cifFetchUrl)
      The URL where (Binary)CIF data will be fetched from if not present locally. {id} refers to the PDB-ID, {middle} can be used to represent the middle hash of an ID (e.g. 'ab' for '1abc').
      Parameters:
      cifFetchUrl - a URL

    • getSquaredDistanceCutoff

      public float getSquaredDistanceCutoff()
      Convenience method to get squared distance cutoff.
      Returns:
      a float

    • getRenumberedCoordinatePrecision

      public int getRenumberedCoordinatePrecision()
      How many digits to write for renumbered files.
      Returns:
      an int

    • setRenumberedCoordinatePrecision

      public void setRenumberedCoordinatePrecision(int renumberedCoordinatePrecision)
      Set how many digits to write for renumbered files.
      Parameters:
      renumberedCoordinatePrecision - an int

    • isRenumberedGzip

      public boolean isRenumberedGzip()
      Gzip renumbered files?
      Returns:
      a Boolean

    • setRenumberedGzip

      public void setRenumberedGzip(boolean renumberedGzip)
      Set gzip renumbered files?
      Parameters:
      renumberedGzip - a Boolean

    • getDownloadTries

      public int getDownloadTries()
      How many tries are allowed for connection failures/timeouts during update.
      Returns:
      an int

    • setDownloadTries

      public void setDownloadTries(int downloadTries)
      Set how many tries should be allowed for connection failures/timeouts during update.
      Parameters:
      downloadTries - an int

    • getInMemoryStrategy

      public InMemoryStrategy getInMemoryStrategy()
      How is index and structure data acquired at runtime?
      Returns:
      the InMemoryStrategy

    • setInMemoryStrategy

      public void setInMemoryStrategy(InMemoryStrategy inMemoryStrategy)
      Set how index and structure data is acquired at runtime.
      Parameters:
      inMemoryStrategy - the new value