Package org.biojava.nbio.structure

Class EntityInfo

java.lang.Object

org.biojava.nbio.structure.EntityInfo

All Implemented Interfaces:

Serializable

public class EntityInfo
extends Object
implements Serializable

An object to contain the info from the PDB header for a Molecule. In mmCIF dictionary, it is called an Entity. In the case of polymers it is defined as each group of sequence identical NCS-related chains Now PDB file format 3.2 aware - contains the new TAX_ID fields for the organism studied and the expression system.

Since:

1.5

Author:

Jules Jacobsen, Jose Duarte, Anthony Bradley

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
EntityInfo()
EntityInfo(EntityInfo c)	Constructs a new EntityInfo copying all data from the given one but not setting the Chains

Method Summary

Modifier and Type	Method	Description
void	addChain(Chain chain)	Add new Chain to this EntityInfo
int	getAlignedResIndex(Group g, Chain c)	Given a Group g of Chain c (member of this EntityInfo) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence.
String	getAtcc()
String	getBiologicalUnit()
String	getCell()
String	getCellLine()
String	getCellularLocation()
List<String>	getChainIds()	Return the list of member chain ids (asym ids) that are described by this EntityInfo, only unique chain IDs are contained in the list.
List<Chain>	getChains()	Get the list of chains that are part of this EntityInfo.
String	getDescription()
String	getDetails()
List<String>	getEcNums()
String	getEngineered()
String	getExpressionSystem()
String	getExpressionSystemAtccNumber()
String	getExpressionSystemCell()
String	getExpressionSystemCellLine()
String	getExpressionSystemCellularLocation()
String	getExpressionSystemGene()
String	getExpressionSystemOrgan()
String	getExpressionSystemOrganelle()
String	getExpressionSystemOtherDetails()
String	getExpressionSystemPlasmid()
String	getExpressionSystemStrain()
String	getExpressionSystemTaxId()
String	getExpressionSystemTissue()
String	getExpressionSystemVariant()
String	getExpressionSystemVector()
String	getExpressionSystemVectorType()
String	getFragment()
String	getGene()
String	getHeaderVars()
Long	getId()	get the ID used by Hibernate
int	getMolId()	Return the molecule identifier, called entity_id in mmCIF dictionary.
String	getMutation()
String	getNumRes()
String	getOrgan()
String	getOrganelle()
String	getOrganismCommon()
String	getOrganismScientific()
String	getOrganismTaxId()
String	getRefChainId()	Return the ref chain id value.
Chain	getRepresentative()	Get the representative Chain for this EntityInfo.
String	getResNames()
String	getSecretion()
String	getStrain()
List<String>	getSynonyms()
String	getSynthetic()
String	getTissue()
String	getTitle()
EntityType	getType()	Get the type of entity this EntityInfo describes.
String	getVariant()
void	setAtcc(String atcc)
void	setBiologicalUnit(String biologicalUnit)
void	setCell(String cell)
void	setCellLine(String cellLine)
void	setCellularLocation(String cellularLocation)
void	setChains(List<Chain> chains)	Set the chains for this EntityInfo
void	setDescription(String molName)
void	setDetails(String details)
void	setEcNums(List<String> ecNums)
void	setEngineered(String engineered)
void	setExpressionSystem(String expressionSystem)
void	setExpressionSystemAtccNumber(String expressionSystemAtccNumber)
void	setExpressionSystemCell(String expressionSystemCell)
void	setExpressionSystemCellLine(String expressionSystemCellLine)
void	setExpressionSystemCellularLocation(String expressionSystemCellularLocation)
void	setExpressionSystemGene(String expressionSystemGene)
void	setExpressionSystemOrgan(String expressionSystemOrgan)
void	setExpressionSystemOrganelle(String expressionSystemOrganelle)
void	setExpressionSystemOtherDetails(String expressionSystemOtherDetails)
void	setExpressionSystemPlasmid(String expressionSystemPlasmid)
void	setExpressionSystemStrain(String expressionSystemStrain)
void	setExpressionSystemTaxId(String expressionSystemTaxId)
void	setExpressionSystemTissue(String expressionSystemTissue)
void	setExpressionSystemVariant(String expressionSystemVariant)
void	setExpressionSystemVector(String expressionSystemVector)
void	setExpressionSystemVectorType(String expressionSystemVectorType)
void	setFragment(String fragment)
void	setGene(String gene)
void	setHeaderVars(String headerVars)
void	setId(Long id)	set the ID used by Hibernate
void	setMolId(int molId)	Set the molecule identifier, called entity_id in mmCIF dictionary.
void	setMutation(String mutation)
void	setNumRes(String numRes)
void	setOrgan(String organ)
void	setOrganelle(String organelle)
void	setOrganismCommon(String organismCommon)
void	setOrganismScientific(String organismScientific)
void	setOrganismTaxId(String organismTaxId)
void	setRefChainId(String refChainId)	Return the ref chain id value.
void	setResNames(String resNames)
void	setSecretion(String secretion)
void	setStrain(String strain)
void	setSynonyms(List<String> synonyms)
void	setSynthetic(String synthetic)
void	setTissue(String tissue)
void	setTitle(String title)
void	setType(EntityType type)	Set the type of entity this EntityInfo describes.
void	setVariant(String variant)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

EntityInfo

public EntityInfo()

EntityInfo

public EntityInfo(EntityInfo c)

Constructs a new EntityInfo copying all data from the given one but not setting the Chains

Parameters:

c -

Method Details

toString

public String toString()

Overrides:

toString in class Object

getRepresentative

public Chain getRepresentative()

Get the representative Chain for this EntityInfo. We choose the Chain with the first asym_id chain identifier after lexicographical sorting (case insensitive), e.g. chain A if EntityInfo is composed of chains A,B,C,D,E

Returns:

getId

public Long getId()

get the ID used by Hibernate

Returns:

the ID used by Hibernate

setId

public void setId(Long id)

set the ID used by Hibernate

Parameters:

id -

getChainIds

public List<String> getChainIds()

Return the list of member chain ids (asym ids) that are described by this EntityInfo, only unique chain IDs are contained in the list. Note that in the case of multimodel structures this will return just the unique chain identifiers whilst getChains() will return a corresponding chain per model.

Returns:

the list of unique ChainIDs that are described by this EnityInfo

See Also:

• setChains(List)
• getChains()

getAlignedResIndex

public int getAlignedResIndex(Group g,
 Chain c)

Given a Group g of Chain c (member of this EntityInfo) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e. the index (1-based) in the SEQRES sequence. This allows for comparisons of residues belonging to different chains of the same EntityInfo (entity).

Note this method should only be used for entities of type EntityType.POLYMER

If FileParsingParameters.setAlignSeqRes(boolean) is not used or SEQRES not present, a mapping will not be available and this method will return ResidueNumber.getSeqNum() for all residues, which in some cases will be correctly aligned indices (when no insertion codes are used and when all chains within the entity are numbered in the same way), but in general they will be neither unique (because of insertion codes) nor aligned.

Parameters:

g - the group

c - the chain

Returns:

the aligned residue index (1 to n), if no SEQRES groups are available at all then ResidueNumber.getSeqNum() is returned as a fall-back, if the group is not found in the SEQRES groups then -1 is returned for the given group and chain

Throws:

IllegalArgumentException - if the given Chain is not a member of this EntityInfo

See Also:

• Chain.getSeqResGroup(int)

getRefChainId

public String getRefChainId()

Return the ref chain id value.

Returns:

the RefChainID

See Also:

• setRefChainId(String)

setRefChainId

public void setRefChainId(String refChainId)

Return the ref chain id value.

Parameters:

refChainId - the RefChainID

See Also:

• getRefChainId()

getMolId

public int getMolId()

Return the molecule identifier, called entity_id in mmCIF dictionary.

Returns:

the molecule id

See Also:

• setMolId(int)

setMolId

public void setMolId(int molId)

Set the molecule identifier, called entity_id in mmCIF dictionary.

Parameters:

molId - the molecule id

See Also:

• getMolId()

getDescription

public String getDescription()

setDescription

public void setDescription(String molName)

getTitle

public String getTitle()

setTitle

public void setTitle(String title)

getSynonyms

public List<String> getSynonyms()

setSynonyms

public void setSynonyms(List<String> synonyms)

getEcNums

public List<String> getEcNums()

setEcNums

public void setEcNums(List<String> ecNums)

getEngineered

public String getEngineered()

setEngineered

public void setEngineered(String engineered)

getMutation

public String getMutation()

setMutation

public void setMutation(String mutation)

getBiologicalUnit

public String getBiologicalUnit()

setBiologicalUnit

public void setBiologicalUnit(String biologicalUnit)

getDetails

public String getDetails()

setDetails

public void setDetails(String details)

getNumRes

public String getNumRes()

setNumRes

public void setNumRes(String numRes)

getResNames

public String getResNames()

setResNames

public void setResNames(String resNames)

getHeaderVars

public String getHeaderVars()

setHeaderVars

public void setHeaderVars(String headerVars)

getSynthetic

public String getSynthetic()

setSynthetic

public void setSynthetic(String synthetic)

getFragment

public String getFragment()

setFragment

public void setFragment(String fragment)

getOrganismScientific

public String getOrganismScientific()

setOrganismScientific

public void setOrganismScientific(String organismScientific)

getOrganismTaxId

public String getOrganismTaxId()

setOrganismTaxId

public void setOrganismTaxId(String organismTaxId)

getOrganismCommon

public String getOrganismCommon()

setOrganismCommon

public void setOrganismCommon(String organismCommon)

getStrain

public String getStrain()

setStrain

public void setStrain(String strain)

getVariant

public String getVariant()

setVariant

public void setVariant(String variant)

getCellLine

public String getCellLine()

setCellLine

public void setCellLine(String cellLine)

getAtcc

public String getAtcc()

setAtcc

public void setAtcc(String atcc)

getOrgan

public String getOrgan()

setOrgan

public void setOrgan(String organ)

getTissue

public String getTissue()

setTissue

public void setTissue(String tissue)

getCell

public String getCell()

setCell

public void setCell(String cell)

getOrganelle

public String getOrganelle()

setOrganelle

public void setOrganelle(String organelle)

getSecretion

public String getSecretion()

setSecretion

public void setSecretion(String secretion)

getGene

public String getGene()

setGene

public void setGene(String gene)

getCellularLocation

public String getCellularLocation()

setCellularLocation

public void setCellularLocation(String cellularLocation)

getExpressionSystem

public String getExpressionSystem()

getExpressionSystemTaxId

public String getExpressionSystemTaxId()

setExpressionSystemTaxId

public void setExpressionSystemTaxId(String expressionSystemTaxId)

setExpressionSystem

public void setExpressionSystem(String expressionSystem)

getExpressionSystemStrain

public String getExpressionSystemStrain()

setExpressionSystemStrain

public void setExpressionSystemStrain(String expressionSystemStrain)

getExpressionSystemVariant

public String getExpressionSystemVariant()

setExpressionSystemVariant

public void setExpressionSystemVariant(String expressionSystemVariant)

getExpressionSystemCellLine

public String getExpressionSystemCellLine()

setExpressionSystemCellLine

public void setExpressionSystemCellLine(String expressionSystemCellLine)

getExpressionSystemAtccNumber

public String getExpressionSystemAtccNumber()

setExpressionSystemAtccNumber

public void setExpressionSystemAtccNumber(String expressionSystemAtccNumber)

getExpressionSystemOrgan

public String getExpressionSystemOrgan()

setExpressionSystemOrgan

public void setExpressionSystemOrgan(String expressionSystemOrgan)

getExpressionSystemTissue

public String getExpressionSystemTissue()

setExpressionSystemTissue

public void setExpressionSystemTissue(String expressionSystemTissue)

getExpressionSystemCell

public String getExpressionSystemCell()

setExpressionSystemCell

public void setExpressionSystemCell(String expressionSystemCell)

getExpressionSystemOrganelle

public String getExpressionSystemOrganelle()

setExpressionSystemOrganelle

public void setExpressionSystemOrganelle(String expressionSystemOrganelle)

getExpressionSystemCellularLocation

public String getExpressionSystemCellularLocation()

setExpressionSystemCellularLocation

public void setExpressionSystemCellularLocation(String expressionSystemCellularLocation)

getExpressionSystemVectorType

public String getExpressionSystemVectorType()

setExpressionSystemVectorType

public void setExpressionSystemVectorType(String expressionSystemVectorType)

getExpressionSystemVector

public String getExpressionSystemVector()

setExpressionSystemVector

public void setExpressionSystemVector(String expressionSystemVector)

getExpressionSystemPlasmid

public String getExpressionSystemPlasmid()

setExpressionSystemPlasmid

public void setExpressionSystemPlasmid(String expressionSystemPlasmid)

getExpressionSystemGene

public String getExpressionSystemGene()

setExpressionSystemGene

public void setExpressionSystemGene(String expressionSystemGene)

getExpressionSystemOtherDetails

public String getExpressionSystemOtherDetails()

setExpressionSystemOtherDetails

public void setExpressionSystemOtherDetails(String expressionSystemOtherDetails)

getChains

public List<Chain> getChains()

Get the list of chains that are part of this EntityInfo. Note that for multi-model structures chains from all models are returned.

Returns:

a List of Chain objects

addChain

public void addChain(Chain chain)

Add new Chain to this EntityInfo

Parameters:

chain -

setChains

public void setChains(List<Chain> chains)

Set the chains for this EntityInfo

Parameters:

chains -

getType

public EntityType getType()

Get the type of entity this EntityInfo describes. Options are polymer, non-polymer or water.

Returns:

a string describing the type of entity. (polymer, non-polymer or water).

setType

public void setType(EntityType type)

Set the type of entity this EntityInfo describes. Options are polymer, non-polymer or water.

Parameters:

type - a string describing the type of entity. (polymer, non-polymer or water).