Compound (biojava-structure 4.1.0 API)

java.lang.Object
- org.biojava.nbio.structure.Compound

All Implemented Interfaces:

Serializable
```
public class Compound
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

See Also:
Serialized Form

Constructor Summary

Constructors
Constructor and Description

Compound()

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

Constructors
Constructor and Description
`Compound()`
`Compound(Compound c)` Constructs a new Compound copying all data from the given one but not setting the Chains

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addChain(Chain chain)` Add new Chain to this Compound
`int`	`getAlignedResIndex(Group g, Chain c)` Given a Group g of Chain c (member of this Compound) return the corresponding position in the alignment of all member sequences (1-based numbering), i.e.
`String`	`getAtcc()`
`String`	`getBiologicalUnit()`
`String`	`getCell()`
`String`	`getCellLine()`
`String`	`getCellularLocation()`
`List<String>`	`getChainIds()` Return the list of member chain IDs that are described by this Compound, only unique chain IDs are contained in the list.
`List<Chain>`	`getChains()` Get the list of chains that are part of this Compound.
`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`	`getMolName()`
`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 Compound.
`String`	`getResNames()`
`String`	`getSecretion()`
`String`	`getStrain()`
`List<String>`	`getSynonyms()`
`String`	`getSynthetic()`
`String`	`getTissue()`
`String`	`getTitle()`
`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 Compound
`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`	`setMolName(String molName)`
`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`	`setVariant(String variant)`
`void`	`showCompound()`
`void`	`showHeader()` Print some debug statements to System.out
`void`	`showSource()`
`String`	`toString()`

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

Constructor Detail
- Compound
```
public Compound()
```
- Compound
```
public Compound(Compound c)
```
  Constructs a new Compound copying all data from the given one but not setting the Chains
  
  Parameters:
  c -

Method Detail

toString
```
public String toString()
```
Overrides:

toString in class Object

getRepresentative
```
public Chain getRepresentative()
```
Get the representative Chain for this Compound. We choose the Chain with the first chain identifier after lexicographical sorting (case insensitive), e.g. chain A if Compound 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 -

showHeader
```
public void showHeader()
```
Print some debug statements to System.out

showCompound
```
public void showCompound()
```

showSource
```
public void showSource()
```

getChainIds
```
public List<String> getChainIds()
```
Return the list of member chain IDs that are described by this Compound, 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 Compound
See Also:
setChains(List), getChains()

getAlignedResIndex
```
public int getAlignedResIndex(Group g,
                     Chain c)
```
Given a Group g of Chain c (member of this Compound) 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 Compound (entity).
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 -
c -

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 Compound
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()

getMolName
```
public String getMolName()
```

setMolName

public void setMolName(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 Compound. 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 Compound

Parameters:
chain -

setChains
```
public void setChains(List<Chain> chains)
```
Set the chains for this Compound

Parameters:
chains -

Class Compound

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Compound

Compound

Method Detail

toString

getRepresentative

getId

setId

showHeader

showCompound

showSource

getChainIds

getAlignedResIndex

getRefChainId

setRefChainId

getMolId

setMolId

getMolName

setMolName

getTitle

setTitle

getSynonyms

setSynonyms

getEcNums

setEcNums

getEngineered

setEngineered

getMutation

setMutation

getBiologicalUnit

setBiologicalUnit

getDetails

setDetails

getNumRes

setNumRes

getResNames

setResNames

getHeaderVars

setHeaderVars

getSynthetic

setSynthetic

getFragment

setFragment

getOrganismScientific

setOrganismScientific

getOrganismTaxId

setOrganismTaxId

getOrganismCommon

setOrganismCommon

getStrain

setStrain

getVariant

setVariant

getCellLine

setCellLine

getAtcc

setAtcc

getOrgan

setOrgan

getTissue

setTissue

getCell

setCell

getOrganelle

setOrganelle

getSecretion

setSecretion

getGene

setGene

getCellularLocation

setCellularLocation

getExpressionSystem

getExpressionSystemTaxId

setExpressionSystemTaxId

setExpressionSystem

getExpressionSystemStrain