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:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
EcodDomain()	Default constructor with all null properties
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)
EcodDomain(EcodDomain o)

Method Summary

Modifier and Type	Method	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()
PdbId	getPdbId()	Gets the PdbId object. Before 6.0.0, this method used to return a String.
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	setPdbId(PdbId 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)

setPdbId

public void setPdbId(String pdbId)

getPdbId

public PdbId getPdbId()

Gets the PdbId object.
Before 6.0.0, this method used to return a String.

Returns:

the PdbId object associated with this domain.

Since:

6.0.0

setPdbId

public void setPdbId(PdbId pdbId)

Parameters:

pdbId -

Since:

6.0.0

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