Package org.biojava.nbio.structure.symmetry.internal

Class CeSymmResult

java.lang.Object
org.biojava.nbio.structure.symmetry.internal.CeSymmResult
public class CeSymmResult extends Object
This Class stores all the relevant information of an internal symmetry result obtained with CeSymm. The purpose is to carry all the information packed during the calculations and return a single object.
Since:
4.2.0
Author:
Aleix Lafita

  • Constructor Details

    • CeSymmResult

      public CeSymmResult()

  • Method Details

    • isSignificant

      public boolean isSignificant()
      Conditions checked are: score above the threshold, number of repeats higher than 1 and refinement succeeded.
      Returns:
      true if significant, false otherwise

    • getRepeatsID

      public List<StructureIdentifier> getRepeatsID() throws StructureException
      Return the symmetric repeats as structure identifiers, if the result is symmetric and it was refined, return null otherwise.
      Returns:
      List of StructureIdentifiers or null if not defined
      Throws:
      StructureException

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getMultipleAlignment

      public MultipleAlignment getMultipleAlignment()

    • setMultipleAlignment

      public void setMultipleAlignment(MultipleAlignment multipleAlignment)

    • getSelfAlignment

      public AFPChain getSelfAlignment()

    • setSelfAlignment

      public void setSelfAlignment(AFPChain selfAlignment)

    • getParams

      public CESymmParameters getParams()

    • setParams

      public void setParams(CESymmParameters params)

    • getAxes

      public SymmetryAxes getAxes()

    • setAxes

      public void setAxes(SymmetryAxes axes)

    • getNumRepeats

      public int getNumRepeats()
      Return the symmetry order determined by the order detector if the symmetry is significant. Return 1 otherwise.
      Returns:
      the order of symmetry if the result is significant

    • setNumRepeats

      public void setNumRepeats(int symmOrder)

    • isRefined

      public boolean isRefined()

    • setRefined

      public void setRefined(boolean refined)

    • getSymmGroup

      public String getSymmGroup()

    • setSymmGroup

      public void setSymmGroup(String symmGroup)

    • getAtoms

      public Atom[] getAtoms()

    • setAtoms

      public void setAtoms(Atom[] atoms)

    • getSymmLevels

      public int getSymmLevels()

    • getStructureId

      public StructureIdentifier getStructureId()

    • setStructureId

      public void setStructureId(StructureIdentifier structureId)

    • getReason

      public String getReason()
      Return a String describing the reasons for the CE-Symm final decision in this particular result.
      Returns:
      String decision reason