Package org.biojava.nbio.structure.ecod

Class EcodDomain

java.lang.Object
org.biojava.nbio.structure.ecod.EcodDomain
All Implemented Interfaces:
Serializable, Cloneable, StructureIdentifier
public class EcodDomain extends Object implements Serializable, 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:

  • Constructor Details

  • Method Details

    • clone

      protected Object clone() throws CloneNotSupportedException
      Overrides:
      clone in class Object
      Throws:
      CloneNotSupportedException

    • getUid

      public Long getUid()

    • setUid

      public void setUid(Long uid)

    • getDomainId

      public String getDomainId()

    • setDomainId

      public void setDomainId(String domainId)

    • getManual

      public Boolean getManual()

    • setManual

      public void setManual(Boolean manual)

    • getXGroup

      public Integer getXGroup()

    • setXGroup

      public void setXGroup(Integer xGroup)

    • getHGroup

      public Integer getHGroup()

    • setHGroup

      public void setHGroup(Integer hGroup)

    • getTGroup

      public Integer getTGroup()

    • setTGroup

      public void setTGroup(Integer tGroup)

    • getFGroup

      public Integer getFGroup()

    • setFGroup

      public void setFGroup(Integer fGroup)

    • getPdbId

      public String getPdbId()

    • setPdbId

      public void setPdbId(String pdbId)

    • getChainId

      public String getChainId()

    • setChainId

      public void setChainId(String chainId)

    • getRange

      public 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(String range)

    • getSeqIdRange

      public 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(String seqIdRange)

    • getArchitectureName

      public String getArchitectureName()

    • setArchitectureName

      public void setArchitectureName(String architectureName)

    • getXGroupName

      public String getXGroupName()

    • setXGroupName

      public void setXGroupName(String xGroupName)

    • getHGroupName

      public String getHGroupName()

    • setHGroupName

      public void setHGroupName(String hGroupName)

    • getTGroupName

      public String getTGroupName()

    • setGroupName

      public void setGroupName(String tGroupName)

    • getFGroupName

      public String getFGroupName()

    • setFGroupName

      public void setFGroupName(String fGroupName)

    • getAssemblyId

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

    • setAssemblyId

      public void setAssemblyId(Long assemblyId)

    • getLigands

      public Set<String> getLigands()

    • setLigands

      public void setLigands(Set<String> ligands)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • getIdentifier

      public 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 List<ResidueRange> getResidueRanges()

    • toCanonical

      public SubstructureIdentifier toCanonical()
      Description copied from interface: StructureIdentifier
      Convert to a canonical SubstructureIdentifier.

      This allows all domains to be converted to a standard format String.

      Specified by:
      toCanonical in interface StructureIdentifier
      Returns:
      A SubstructureIdentifier equivalent to this

    • reduce

      public Structure reduce(Structure input) throws StructureException
      Description copied from interface: StructureIdentifier
      Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.

      The returned structure may be a shallow copy of the input, with shared Chains, Residues, etc.

      Specified by:
      reduce in interface StructureIdentifier
      Parameters:
      input - A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId(), if applicable.
      Returns:
      Throws:
      StructureException
      See Also:

    • loadStructure

      public Structure loadStructure(AtomCache cache) throws StructureException, 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
      IOException - Errors reading the structure from disk