Class ScopDomain

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, StructureIdentifier

    public class ScopDomain
    extends java.lang.Object
    implements java.io.Serializable, java.lang.Cloneable, StructureIdentifier
    Container for the information for a domain. Contains a line in the file dir.cla.scop.txt_1.75 e.g d1dlwa_ 1dlw A: a.1.1.1 14982 cl=46456,cf=46457,sf=46458,fa=46459,dm=46460,sp=46461,px=14982 Instantiated using ScopDatabase.getDomainByScopID(String)
    Author:
    Andreas Prlic
    See Also:
    Serialized Form
    • Constructor Detail

      • ScopDomain

        public ScopDomain()
    • Method Detail

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • getScopId

        public java.lang.String getScopId()
      • setScopId

        public void setScopId​(java.lang.String scopId)
      • getPdbId

        public java.lang.String getPdbId()
      • setPdbId

        public void setPdbId​(java.lang.String pdbId)
      • getRanges

        public java.util.List<java.lang.String> getRanges()
      • setRanges

        public void setRanges​(java.util.List<java.lang.String> ranges)
      • getClassificationId

        public java.lang.String getClassificationId()
      • setClassificationId

        public void setClassificationId​(java.lang.String classificationId)
      • getSunid

        public java.lang.Integer getSunid()
      • setSunid

        public void setSunid​(java.lang.Integer sunid)
      • getClassId

        public int getClassId()
      • setClassId

        public void setClassId​(int classId)
      • getFoldId

        public int getFoldId()
      • setFoldId

        public void setFoldId​(int foldId)
      • getSuperfamilyId

        public int getSuperfamilyId()
      • setSuperfamilyId

        public void setSuperfamilyId​(int superfamilyId)
      • getFamilyId

        public int getFamilyId()
      • setFamilyId

        public void setFamilyId​(int familyId)
      • getDomainId

        public int getDomainId()
      • setDomainId

        public void setDomainId​(int domainId)
      • getSpeciesId

        public int getSpeciesId()
      • setSpeciesId

        public void setSpeciesId​(int speciesId)
      • getPx

        public int getPx()
      • setPx

        public void setPx​(int px)
      • clone

        protected java.lang.Object clone()
                                  throws java.lang.CloneNotSupportedException
        Overrides:
        clone in class java.lang.Object
        Throws:
        java.lang.CloneNotSupportedException
      • getChains

        public java.util.Set<java.lang.String> getChains()
        Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
      • getIdentifier

        public java.lang.String getIdentifier()
        Description copied from interface: StructureIdentifier
        Get the String form of this identifier. It is recommended that the #toString() method also return the identifier, for consistency during serialization.
        Specified by:
        getIdentifier in interface StructureIdentifier
        Returns:
        The String form of this identifier
      • getResidueRanges

        public java.util.List<ResidueRange> getResidueRanges()
      • loadStructure

        public Structure loadStructure​(AtomCache cache)
                                throws StructureException,
                                       java.io.IOException
        Description copied from interface: StructureIdentifier
        Loads a structure encompassing the structure identified. The Structure returned should be suitable for passing as the input to StructureIdentifier.reduce(Structure). It is recommended that the most complete structure available be returned (e.g. the full PDB) to allow processing of unselected portions where appropriate.
        Specified by:
        loadStructure in interface StructureIdentifier
        Returns:
        A Structure containing at least the atoms identified by this, or null if Structures are not applicable.
        Throws:
        StructureException - For errors loading and parsing the structure
        java.io.IOException - Errors reading the structure from disk