Class AfpChainWriter


  • public class AfpChainWriter
    extends Object
    A class to convert the data in an AfpChain object to various String outputs.
    Author:
    Andreas Prlic
    • Method Detail

      • toFatCatCore

        public static String toFatCatCore​(AFPChain afpChain,
                                          Atom[] ca1,
                                          Atom[] ca2,
                                          boolean printLegend,
                                          boolean longHeader,
                                          boolean showHTML,
                                          boolean showAlignmentBlock)
        Output in FatCatCore format

        Note that if a circular permutation has occured the residue numbers may be innaccurate.

        Parameters:
        afpChain -
        ca1 -
        ca2 -
        printLegend -
        longHeader -
        showHTML -
        showAlignmentBlock -
        Returns:
      • printScoresInLines

        public static void printScoresInLines​(AFPChain afpChain,
                                              int blockNum,
                                              int optLength,
                                              double totalRmsdOpt,
                                              double alignScore,
                                              int alnLength,
                                              int gapLen,
                                              double identity,
                                              double similarity,
                                              StringBuffer txt)
      • toWebSiteDisplay

        public static String toWebSiteDisplay​(AFPChain afpChain,
                                              Atom[] ca1,
                                              Atom[] ca2)
        Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
        Parameters:
        afpChain -
        ca1 -
        ca2 -
        Returns:
        a String representation as it is used on the RCSB PDB web site for display.
      • toWebSiteDisplay

        public static String toWebSiteDisplay​(AFPChain afpChain,
                                              Atom[] ca1,
                                              Atom[] ca2,
                                              boolean showAlignmentBlock)
        Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
        Parameters:
        afpChain -
        ca1 -
        ca2 -
        Returns:
        a String representation as it is used on the RCSB PDB web site for display.
      • toAlignedPairs

        public static String toAlignedPairs​(AFPChain afpChain,
                                            Atom[] ca1,
                                            Atom[] ca2)
        Prints the alignment in the simplest form: a list of aligned residues. Format is one line per residue pair, tab delimited:
        • 1. PDB number. Includes insertion code
        • 1. Chain.
        • 1. Amino Acid. Three letter code.
        • 2. PDB number.
        • 2. Chain.
        • 2. Amino Acid.
        example: 152 A ALA 161S A VAL

        Note that this format loses information about blocks.

        Parameters:
        afpChain -
        ca1 -
        ca2 -
        Returns:
        a String representation of the aligned pairs.