Class AFPAlignmentDisplay

Method Details

• getRotMax

  public static Matrix getRotMax(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException

  Throws:

  StructureException

• getTranslation

  public static Atom getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws StructureException

  Throws:

  StructureException

• getAlignedAtoms1

  public static Atom[] getAlignedAtoms1(AFPChain afpChain, Atom[] ca1)

• getAlignedAtoms2

  public static Atom[] getAlignedAtoms2(AFPChain afpChain, Atom[] ca2)

• getAlign

  public static void getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

  Extract the alignment output

  eg

   STWNTWACTWHLKQP--WSTILILA
   111111111111     22222222
   SQNNTYACSWKLKSWNNNSTILILG
   

  Those position pairs labeled by 1 and 2 are equivalent positions, belongs to two blocks 1 and 2. The residues between labeled residues are non-equivalent, with '-' filling in their resulting gaps.

  The three lines can be accessed using AFPChain.getAlnseq1(), AFPChain.getAlnsymb(), and AFPChain.getAlnseq2().

• getAlign

  public static void getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showSeq)

  Sets the following properties:

  • The alignment strings alnseq1, alnseq2, and alnsymb
  • alnbeg1 and 2
  • alnLength and gapLen

  Expects the following properties to be previously computed:

  • AFPChain.getOptAln() and lengths

  Known Bugs

  Expects the alignment to have linear topology. May give odd results for circular permutations and other complicated topologies.

  Parameters:

  afpChain - Alignment between ca1 and ca2

  ca1 - CA atoms of the first protein

  ca2 - CA atoms of the second protein

  showSeq - Use symbols reflecting sequence similarity: '|' for identical, ':' for similar, '.' for dissimilar. Otherwise, use the block number to show aligned residues.

• aaScore

  public static int aaScore(char a, char b)

• calcIdSimilarity

  public static Map<String,Double> calcIdSimilarity(char[] seq1, char[] seq2, int alnLength)

• createArtificalStructure

  public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException

  Parameters:

  afpChain -

  ca1 -

  ca2 -

  Returns:

  Throws:

  ClassNotFoundException - If an error occurs when invoking jmol

  NoSuchMethodException - If an error occurs when invoking jmol

  InvocationTargetException - If an error occurs when invoking jmol

  IllegalAccessException - If an error occurs when invoking jmol

• getBlockNrForAlignPos

  public static int getBlockNrForAlignPos(AFPChain afpChain, int aligPos)

  get the block number for an aligned position

  Parameters:

  afpChain -

  aligPos -

  Returns: