Class CathDomain

    • Constructor Detail

      • CathDomain

        public CathDomain()
    • Method Detail

      • getDomainName

        public java.lang.String getDomainName()
      • setDomainName

        public void setDomainName​(java.lang.String domainName)
      • getPdbId

        @Deprecated
        public java.lang.String getPdbId()
        Deprecated.
        This method is poorly named; use getThePdbId() or getPdbIdAndChain() instead
        Returns a string of the form PDBID.CHAIN. For example: 1hiv.A.
      • getThePdbId

        public java.lang.String getThePdbId()
        Returns the PDB ID.
      • getPdbIdAndChain

        public java.lang.String getPdbIdAndChain()
        Returns a string of the form PDBID.CHAIN. For example: 1hiv.A.
      • getDomainId

        public java.lang.Integer getDomainId()
      • getClassId

        public java.lang.Integer getClassId()
      • setClassId

        public void setClassId​(java.lang.Integer classId)
      • getArchitectureId

        public java.lang.Integer getArchitectureId()
      • setArchitectureId

        public void setArchitectureId​(java.lang.Integer architectureId)
      • getTopologyId

        public java.lang.Integer getTopologyId()
      • setTopologyId

        public void setTopologyId​(java.lang.Integer topologyId)
      • getHomologyId

        public java.lang.Integer getHomologyId()
      • setHomologyId

        public void setHomologyId​(java.lang.Integer homologyId)
      • getSequenceFamilyId

        public java.lang.Integer getSequenceFamilyId()
      • setSequenceFamilyId

        public void setSequenceFamilyId​(java.lang.Integer sequenceFamilyId)
      • getOrthologousSequenceFamilyId

        public java.lang.Integer getOrthologousSequenceFamilyId()
      • setOrthologousSequenceFamilyId

        public void setOrthologousSequenceFamilyId​(java.lang.Integer orthologousSequenceFamilyId)
      • getLikeSequenceFamilyId

        public java.lang.Integer getLikeSequenceFamilyId()
      • setLikeSequenceFamilyId

        public void setLikeSequenceFamilyId​(java.lang.Integer likeSequenceFamilyId)
      • getIdenticalSequenceFamilyId

        public java.lang.Integer getIdenticalSequenceFamilyId()
      • setIdenticalSequenceFamilyId

        public void setIdenticalSequenceFamilyId​(java.lang.Integer identicalSequenceFamilyId)
      • getDomainCounter

        public java.lang.Integer getDomainCounter()
      • setDomainCounter

        public void setDomainCounter​(java.lang.Integer domainCounter)
      • getLength

        public java.lang.Integer getLength()
      • setLength

        public void setLength​(java.lang.Integer length)
      • getResolution

        public java.lang.Double getResolution()
      • setResolution

        public void setResolution​(java.lang.Double resolution)
      • setCATH

        public void setCATH​(java.lang.String cathCode)
      • getCATH

        public java.lang.String getCATH()
      • setSOLID

        public void setSOLID​(java.lang.String cathCode)
      • getSOILD

        public java.lang.String getSOILD()
      • getClassificationId

        public java.lang.Integer getClassificationId​(CathCategory cathCategory)
      • getFormat

        public java.lang.String getFormat()
      • setFormat

        public void setFormat​(java.lang.String format)
      • getVersion

        public java.lang.String getVersion()
      • setVersion

        public void setVersion​(java.lang.String version)
      • getDate

        public java.util.Date getDate()
      • setDate

        public void setDate​(java.util.Date date)
      • getName

        public java.lang.String getName()
      • setName

        public void setName​(java.lang.String name)
      • getSource

        public java.lang.String getSource()
      • setSource

        public void setSource​(java.lang.String source)
      • getSequenceHeader

        public java.lang.String getSequenceHeader()
      • setSequenceHeader

        public void setSequenceHeader​(java.lang.String sequenceHeader)
      • getSequence

        public java.lang.String getSequence()
      • setSequence

        public void setSequence​(java.lang.String sequence)
      • getSegments

        public java.util.List<CathSegment> getSegments()
      • setSegments

        public void setSegments​(java.util.List<CathSegment> segments)
      • getComment

        public java.lang.String getComment()
      • setComment

        public void setComment​(java.lang.String comment)
      • toString

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