Package org.biojava.nbio.structure.align.model

Class AfpChainWriter

java.lang.Object
org.biojava.nbio.structure.align.model.AfpChainWriter
public class AfpChainWriter extends Object
A class to convert the data in an AfpChain object to various String outputs.
Author:
Andreas Prlic

  • Field Details

    • newline

      public static final String newline

  • Constructor Details

    • AfpChainWriter

      public AfpChainWriter()

  • Method Details

    • toFatCat

      public static String toFatCat(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

    • toScoresList

      public static String toScoresList(AFPChain afpChain)

    • 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:

    • 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.

    • toDBSearchResult

      public static String toDBSearchResult(AFPChain afpChain)

    • toRotMat

      public static String toRotMat(AFPChain afpChain)

    • toCE

      public static String toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)