Package org.biojava.nbio.structure.symmetry.core

Class UniqueSequenceList

java.lang.Object
org.biojava.nbio.structure.symmetry.core.UniqueSequenceList
All Implemented Interfaces:
Cloneable
public class UniqueSequenceList extends Object implements Cloneable
Bean for a single sequence. These are intended to be unique sequences (100% id) as an imput to clustering.

  • Constructor Details

    • UniqueSequenceList

      public UniqueSequenceList(Atom[] cAlphaAtoms, String chainId, int modelNumber, int structureId, String seqResSequence)

  • Method Details

    • isMatch

      public boolean isMatch(Atom[] caAlphaAtoms)
      Return true is the sequence and residues numbers of the passed in array of atoms matches those of this unique sequence list
      Parameters:
      caAlphaAtoms -
      Returns:

    • getChainId

      public String getChainId()

    • getModelNumber

      public int getModelNumber()

    • getStructureId

      public int getStructureId()

    • getCalphaAtoms

      public Atom[] getCalphaAtoms()

    • getSeqResSequence

      public String getSeqResSequence()

    • setSequenceString

      public void setSequenceString(String sequenceString)
      Parameters:
      sequenceString - the sequenceString to set

    • getAlignment1

      public List<Integer> getAlignment1()
      Returns:
      the alignment1

    • setAlignment1

      public void setAlignment1(List<Integer> alignment1)
      Parameters:
      alignment1 - the alignment1 to set

    • getAlignment2

      public List<Integer> getAlignment2()
      Returns:
      the alignment2

    • setAlignment2

      public void setAlignment2(List<Integer> alignment2)
      Parameters:
      alignment2 - the alignment2 to set

    • clone

      public Object clone()
      Overrides:
      clone in class Object

    • getSequenceString

      public static String getSequenceString(Atom[] caAlphaAtoms)

    • toString

      public String toString()
      Overrides:
      toString in class Object