Class SnpEffCmdPdb

  • All Implemented Interfaces:
    CommandLine

    public class SnpEffCmdPdb
    extends SnpEff
    PDB distance analysis References: http://biojava.org/wiki/BioJava:CookBook:PDB:read
    Author:
    pcingola
    • Field Detail

      • DEFAULT_ID_MAP_FILE

        public static final java.lang.String DEFAULT_ID_MAP_FILE
        See Also:
        Constant Field Values
      • DEFAULT_INTERACT_FILE

        public static final java.lang.String DEFAULT_INTERACT_FILE
        See Also:
        Constant Field Values
      • PDB_EXTS

        public static final java.lang.String[] PDB_EXTS
      • PROTEIN_INTERACTION_FILE

        public static final java.lang.String PROTEIN_INTERACTION_FILE
        See Also:
        Constant Field Values
      • UNIPROT_DATABASE

        public static final java.lang.String UNIPROT_DATABASE
        See Also:
        Constant Field Values
      • DEFAULT_DISTANCE_THRESHOLD

        public static final double DEFAULT_DISTANCE_THRESHOLD
        See Also:
        Constant Field Values
      • DEFAULT_MAX_MISMATCH_RATE

        public static final double DEFAULT_MAX_MISMATCH_RATE
        See Also:
        Constant Field Values
      • DEFAULT_PDB_MIN_AA_SEPARATION

        public static final int DEFAULT_PDB_MIN_AA_SEPARATION
        See Also:
        Constant Field Values
      • DEFAULT_PDB_ORGANISM_COMMON

        public static final java.lang.String DEFAULT_PDB_ORGANISM_COMMON
        See Also:
        Constant Field Values
      • DEFAULT_PDB_ORGANISM_SCIENTIFIC

        public static final java.lang.String DEFAULT_PDB_ORGANISM_SCIENTIFIC
        See Also:
        Constant Field Values
      • DEFAULT_PDB_RESOLUTION

        public static final double DEFAULT_PDB_RESOLUTION
        See Also:
        Constant Field Values
      • EMPTY_DISTANCES

        public static final java.util.ArrayList<DistanceResult> EMPTY_DISTANCES
    • Constructor Detail

      • SnpEffCmdPdb

        public SnpEffCmdPdb()
    • Method Detail

      • getDistanceResults

        public java.util.List<DistanceResult> getDistanceResults()
      • initialize

        public void initialize()
        Load all data
      • loadIdMapper

        public void loadIdMapper()
      • parseArgs

        public void parseArgs​(java.lang.String[] args)
        Parse command line arguments
        Specified by:
        parseArgs in interface CommandLine
        Overrides:
        parseArgs in class SnpEff
      • 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)
      • pdbAnalysis

        protected void pdbAnalysis​(java.lang.String pdbFileName)
        Analyze a PDB file
      • readPdbFile

        public org.biojava.nbio.structure.Structure readPdbFile​(java.lang.String pdbFileName)
        Read and parse PDB file
      • run

        public boolean run()
        Description copied from class: SnpEff
        Run according to command line options
        Specified by:
        run in interface CommandLine
        Overrides:
        run in class SnpEff
      • run

        public boolean run​(boolean storeResults)
      • setDistanceThresholdNon

        public void setDistanceThresholdNon​(double distanceThresholdNon)
      • usage

        public void usage​(java.lang.String message)
        Show 'usage;' message and exit with an error code '-1'
        Specified by:
        usage in interface CommandLine
        Overrides:
        usage in class SnpEff
        Parameters:
        message -