Class EcodDomain

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

    public class EcodDomain
    extends java.lang.Object
    implements java.io.Serializable, java.lang.Cloneable, StructureIdentifier
    An EcodDomain contains all the information of the ECOD database: id, classification groups (from higher to lower in the tree: X,H,T,F), PDB code, chain, residue ranges and status (manual or automatic classification).

    For detailed explanation about the ECOD information see the original article at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256011.

     Cheng H, Schaeffer RD, Liao Y, et al.
     ECOD: An Evolutionary Classification of Protein Domains.
     Elofsson A, ed. PLoS Computational Biology. 2014;10(12):e1003926.
     
    Author:
    Spencer Bliven
    See Also:
    Serialized Form
    • Constructor Summary

      Constructors 
      Constructor Description
      EcodDomain()
      Default constructor with all null properties
      EcodDomain​(java.lang.Long uid, java.lang.String domainId, java.lang.Boolean manual, java.lang.Integer xGroup, java.lang.Integer hGroup, java.lang.Integer tGroup, java.lang.Integer fGroup, java.lang.String pdbId, java.lang.String chainId, java.lang.String range, java.lang.String architectureName, java.lang.String xGroupName, java.lang.String hGroupName, java.lang.String tGroupName, java.lang.String fGroupName, java.lang.Long assemblyId, java.util.Set<java.lang.String> ligands)  
      EcodDomain​(java.lang.Long uid, java.lang.String domainId, java.lang.Boolean manual, java.lang.Integer xGroup, java.lang.Integer hGroup, java.lang.Integer tGroup, java.lang.Integer fGroup, java.lang.String pdbId, java.lang.String chainId, java.lang.String range, java.lang.String seqId, java.lang.String architectureName, java.lang.String xGroupName, java.lang.String hGroupName, java.lang.String tGroupName, java.lang.String fGroupName, java.lang.Long assemblyId, java.util.Set<java.lang.String> ligands)  
      EcodDomain​(java.lang.String domainId)  
      EcodDomain​(EcodDomain o)  
    • Constructor Detail

      • EcodDomain

        public EcodDomain()
        Default constructor with all null properties
      • EcodDomain

        public EcodDomain​(java.lang.Long uid,
                          java.lang.String domainId,
                          java.lang.Boolean manual,
                          java.lang.Integer xGroup,
                          java.lang.Integer hGroup,
                          java.lang.Integer tGroup,
                          java.lang.Integer fGroup,
                          java.lang.String pdbId,
                          java.lang.String chainId,
                          java.lang.String range,
                          java.lang.String architectureName,
                          java.lang.String xGroupName,
                          java.lang.String hGroupName,
                          java.lang.String tGroupName,
                          java.lang.String fGroupName,
                          java.lang.Long assemblyId,
                          java.util.Set<java.lang.String> ligands)
      • EcodDomain

        public EcodDomain​(java.lang.Long uid,
                          java.lang.String domainId,
                          java.lang.Boolean manual,
                          java.lang.Integer xGroup,
                          java.lang.Integer hGroup,
                          java.lang.Integer tGroup,
                          java.lang.Integer fGroup,
                          java.lang.String pdbId,
                          java.lang.String chainId,
                          java.lang.String range,
                          java.lang.String seqId,
                          java.lang.String architectureName,
                          java.lang.String xGroupName,
                          java.lang.String hGroupName,
                          java.lang.String tGroupName,
                          java.lang.String fGroupName,
                          java.lang.Long assemblyId,
                          java.util.Set<java.lang.String> ligands)
      • EcodDomain

        public EcodDomain​(java.lang.String domainId)
    • Method Detail

      • clone

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

        public java.lang.Long getUid()
      • setUid

        public void setUid​(java.lang.Long uid)
      • getDomainId

        public java.lang.String getDomainId()
      • setDomainId

        public void setDomainId​(java.lang.String domainId)
      • getManual

        public java.lang.Boolean getManual()
      • setManual

        public void setManual​(java.lang.Boolean manual)
      • getXGroup

        public java.lang.Integer getXGroup()
      • setXGroup

        public void setXGroup​(java.lang.Integer xGroup)
      • getHGroup

        public java.lang.Integer getHGroup()
      • setHGroup

        public void setHGroup​(java.lang.Integer hGroup)
      • getTGroup

        public java.lang.Integer getTGroup()
      • setTGroup

        public void setTGroup​(java.lang.Integer tGroup)
      • getFGroup

        public java.lang.Integer getFGroup()
      • setFGroup

        public void setFGroup​(java.lang.Integer fGroup)
      • getPdbId

        public java.lang.String getPdbId()
      • setPdbId

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

        public java.lang.String getChainId()
      • setChainId

        public void setChainId​(java.lang.String chainId)
      • getRange

        public java.lang.String getRange()
        Get the range of this domain, in PDB residue numbers (mmCif's _pdbx_poly_seq_scheme.pdb_seq_num and pdb_ins_code).
        Returns:
        The chain and residue range, e.g. "A:1-100"
      • setRange

        public void setRange​(java.lang.String range)
      • getSeqIdRange

        public java.lang.String getSeqIdRange()
        Get the range of this domain, in 1-based residue indices (mmCif's _pdbx_poly_seq_scheme.seq_id) Note that getRange() is used when constructing the domain.
        Returns:
        The chain and residue range, e.g. "A:1-100"
      • setSeqIdRange

        public void setSeqIdRange​(java.lang.String seqIdRange)
      • getArchitectureName

        public java.lang.String getArchitectureName()
      • setArchitectureName

        public void setArchitectureName​(java.lang.String architectureName)
      • getXGroupName

        public java.lang.String getXGroupName()
      • setXGroupName

        public void setXGroupName​(java.lang.String xGroupName)
      • getHGroupName

        public java.lang.String getHGroupName()
      • setHGroupName

        public void setHGroupName​(java.lang.String hGroupName)
      • getTGroupName

        public java.lang.String getTGroupName()
      • setGroupName

        public void setGroupName​(java.lang.String tGroupName)
      • getFGroupName

        public java.lang.String getFGroupName()
      • setFGroupName

        public void setFGroupName​(java.lang.String fGroupName)
      • getAssemblyId

        public java.lang.Long getAssemblyId()
        Returns:
        The assembly ID, or the DomainId if not in an assembly, or null if unknown.
      • setAssemblyId

        public void setAssemblyId​(java.lang.Long assemblyId)
      • getLigands

        public java.util.Set<java.lang.String> getLigands()
      • setLigands

        public void setLigands​(java.util.Set<java.lang.String> ligands)
      • toString

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

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object
      • equals

        public boolean equals​(java.lang.Object obj)
        Overrides:
        equals in class java.lang.Object
      • 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