EcodDomain (biojava 5.0.0 API)

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:

Serialized Form

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected Object`	`clone()`
`boolean`	`equals(Object obj)`
`String`	`getArchitectureName()`
`Long`	`getAssemblyId()`
`String`	`getChainId()`
`String`	`getDomainId()`
`Integer`	`getFGroup()`
`String`	`getFGroupName()`
`Integer`	`getHGroup()`
`String`	`getHGroupName()`
`String`	`getIdentifier()` Get the String form of this identifier.
`Set<String>`	`getLigands()`
`Boolean`	`getManual()`
`String`	`getPdbId()`
`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).
`List<ResidueRange>`	`getResidueRanges()`
`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.
`Integer`	`getTGroup()`
`String`	`getTGroupName()`
`Long`	`getUid()`
`Integer`	`getXGroup()`
`String`	`getXGroupName()`
`int`	`hashCode()`
`Structure`	`loadStructure(AtomCache cache)` Loads a structure encompassing the structure identified.
`Structure`	`reduce(Structure input)` Takes a complete structure as input and reduces it to the substructure represented by this StructureIdentifier.
`void`	`setArchitectureName(String architectureName)`
`void`	`setAssemblyId(Long assemblyId)`
`void`	`setChainId(String chainId)`
`void`	`setDomainId(String domainId)`
`void`	`setFGroup(Integer fGroup)`
`void`	`setFGroupName(String fGroupName)`
`void`	`setGroupName(String tGroupName)`
`void`	`setHGroup(Integer hGroup)`
`void`	`setHGroupName(String hGroupName)`
`void`	`setLigands(Set<String> ligands)`
`void`	`setManual(Boolean manual)`
`void`	`setPdbId(String pdbId)`
`void`	`setRange(String range)`
`void`	`setSeqIdRange(String seqIdRange)`
`void`	`setTGroup(Integer tGroup)`
`void`	`setUid(Long uid)`
`void`	`setXGroup(Integer xGroup)`
`void`	`setXGroupName(String xGroupName)`
`SubstructureIdentifier`	`toCanonical()` Convert to a canonical SubstructureIdentifier.
`String`	`toString()`

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

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

EcodDomain

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

EcodDomain

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

EcodDomain
```
public EcodDomain(String domainId)
```

EcodDomain
```
public EcodDomain(EcodDomain o)
```

Method Detail
- 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:
  
  StructureTools.getReducedStructure(Structure, String)
- 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

Class EcodDomain

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

EcodDomain

EcodDomain

EcodDomain

EcodDomain

EcodDomain

Method Detail

clone

getUid

setUid

getDomainId

setDomainId

getManual

setManual

getXGroup

setXGroup

getHGroup

setHGroup

getTGroup

setTGroup

getFGroup

setFGroup

getPdbId

setPdbId

getChainId

setChainId

getRange

setRange

getSeqIdRange

setSeqIdRange

getArchitectureName

setArchitectureName

getXGroupName

setXGroupName

getHGroupName

setHGroupName

getTGroupName

setGroupName

getFGroupName

setFGroupName

getAssemblyId

setAssemblyId

getLigands

setLigands

toString

hashCode

equals

getIdentifier

getResidueRanges

toCanonical

reduce

loadStructure