Package org.biojava.nbio.structure
Class Compound
- java.lang.Object
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- org.biojava.nbio.structure.Compound
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- All Implemented Interfaces:
java.io.Serializable
public class Compound extends java.lang.Object implements java.io.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
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addChain(Chain chain)
Add new Chain to this Compoundint
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.java.lang.String
getAtcc()
java.lang.String
getBiologicalUnit()
java.lang.String
getCell()
java.lang.String
getCellLine()
java.lang.String
getCellularLocation()
java.util.List<java.lang.String>
getChainIds()
Return the list of member chain IDs that are described by this Compound, only unique chain IDs are contained in the list.java.util.List<Chain>
getChains()
Get the list of chains that are part of this Compound.java.lang.String
getDetails()
java.util.List<java.lang.String>
getEcNums()
java.lang.String
getEngineered()
java.lang.String
getExpressionSystem()
java.lang.String
getExpressionSystemAtccNumber()
java.lang.String
getExpressionSystemCell()
java.lang.String
getExpressionSystemCellLine()
java.lang.String
getExpressionSystemCellularLocation()
java.lang.String
getExpressionSystemGene()
java.lang.String
getExpressionSystemOrgan()
java.lang.String
getExpressionSystemOrganelle()
java.lang.String
getExpressionSystemOtherDetails()
java.lang.String
getExpressionSystemPlasmid()
java.lang.String
getExpressionSystemStrain()
java.lang.String
getExpressionSystemTaxId()
java.lang.String
getExpressionSystemTissue()
java.lang.String
getExpressionSystemVariant()
java.lang.String
getExpressionSystemVector()
java.lang.String
getExpressionSystemVectorType()
java.lang.String
getFragment()
java.lang.String
getGene()
java.lang.String
getHeaderVars()
java.lang.Long
getId()
get the ID used by Hibernateint
getMolId()
Return the molecule identifier, called entity_id in mmCIF dictionary.java.lang.String
getMolName()
java.lang.String
getMutation()
java.lang.String
getNumRes()
java.lang.String
getOrgan()
java.lang.String
getOrganelle()
java.lang.String
getOrganismCommon()
java.lang.String
getOrganismScientific()
java.lang.String
getOrganismTaxId()
java.lang.String
getRefChainId()
Return the ref chain id value.Chain
getRepresentative()
Get the representative Chain for this Compound.java.lang.String
getResNames()
java.lang.String
getSecretion()
java.lang.String
getStrain()
java.util.List<java.lang.String>
getSynonyms()
java.lang.String
getSynthetic()
java.lang.String
getTissue()
java.lang.String
getTitle()
java.lang.String
getVariant()
void
setAtcc(java.lang.String atcc)
void
setBiologicalUnit(java.lang.String biologicalUnit)
void
setCell(java.lang.String cell)
void
setCellLine(java.lang.String cellLine)
void
setCellularLocation(java.lang.String cellularLocation)
void
setChains(java.util.List<Chain> chains)
Set the chains for this Compoundvoid
setDetails(java.lang.String details)
void
setEcNums(java.util.List<java.lang.String> ecNums)
void
setEngineered(java.lang.String engineered)
void
setExpressionSystem(java.lang.String expressionSystem)
void
setExpressionSystemAtccNumber(java.lang.String expressionSystemAtccNumber)
void
setExpressionSystemCell(java.lang.String expressionSystemCell)
void
setExpressionSystemCellLine(java.lang.String expressionSystemCellLine)
void
setExpressionSystemCellularLocation(java.lang.String expressionSystemCellularLocation)
void
setExpressionSystemGene(java.lang.String expressionSystemGene)
void
setExpressionSystemOrgan(java.lang.String expressionSystemOrgan)
void
setExpressionSystemOrganelle(java.lang.String expressionSystemOrganelle)
void
setExpressionSystemOtherDetails(java.lang.String expressionSystemOtherDetails)
void
setExpressionSystemPlasmid(java.lang.String expressionSystemPlasmid)
void
setExpressionSystemStrain(java.lang.String expressionSystemStrain)
void
setExpressionSystemTaxId(java.lang.String expressionSystemTaxId)
void
setExpressionSystemTissue(java.lang.String expressionSystemTissue)
void
setExpressionSystemVariant(java.lang.String expressionSystemVariant)
void
setExpressionSystemVector(java.lang.String expressionSystemVector)
void
setExpressionSystemVectorType(java.lang.String expressionSystemVectorType)
void
setFragment(java.lang.String fragment)
void
setGene(java.lang.String gene)
void
setHeaderVars(java.lang.String headerVars)
void
setId(java.lang.Long id)
set the ID used by Hibernatevoid
setMolId(int molId)
Set the molecule identifier, called entity_id in mmCIF dictionary.void
setMolName(java.lang.String molName)
void
setMutation(java.lang.String mutation)
void
setNumRes(java.lang.String numRes)
void
setOrgan(java.lang.String organ)
void
setOrganelle(java.lang.String organelle)
void
setOrganismCommon(java.lang.String organismCommon)
void
setOrganismScientific(java.lang.String organismScientific)
void
setOrganismTaxId(java.lang.String organismTaxId)
void
setRefChainId(java.lang.String refChainId)
Return the ref chain id value.void
setResNames(java.lang.String resNames)
void
setSecretion(java.lang.String secretion)
void
setStrain(java.lang.String strain)
void
setSynonyms(java.util.List<java.lang.String> synonyms)
void
setSynthetic(java.lang.String synthetic)
void
setTissue(java.lang.String tissue)
void
setTitle(java.lang.String title)
void
setVariant(java.lang.String variant)
void
showCompound()
void
showHeader()
Print some debug statements to System.outvoid
showSource()
java.lang.String
toString()
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Constructor Detail
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Compound
public Compound()
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Compound
public Compound(Compound c)
Constructs a new Compound copying all data from the given one but not setting the Chains- Parameters:
c
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Method Detail
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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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:
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getId
public java.lang.Long getId()
get the ID used by Hibernate- Returns:
- the ID used by Hibernate
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setId
public void setId(java.lang.Long id)
set the ID used by Hibernate- Parameters:
id
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showHeader
public void showHeader()
Print some debug statements to System.out
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showCompound
public void showCompound()
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showSource
public void showSource()
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getChainIds
public java.util.List<java.lang.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 whilstgetChains()
will return a corresponding chain per model.- Returns:
- the list of unique ChainIDs that are described by this Compound
- See Also:
setChains(List)
,getChains()
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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 returnResidueNumber.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:
java.lang.IllegalArgumentException
- if the given Chain is not a member of this Compound
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getRefChainId
public java.lang.String getRefChainId()
Return the ref chain id value.- Returns:
- the RefChainID
- See Also:
setRefChainId(String)
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setRefChainId
public void setRefChainId(java.lang.String refChainId)
Return the ref chain id value.- Parameters:
refChainId
- the RefChainID- See Also:
getRefChainId()
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getMolId
public int getMolId()
Return the molecule identifier, called entity_id in mmCIF dictionary.- Returns:
- the molecule id
- See Also:
setMolId(int)
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setMolId
public void setMolId(int molId)
Set the molecule identifier, called entity_id in mmCIF dictionary.- Parameters:
molId
- the molecule id- See Also:
getMolId()
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getMolName
public java.lang.String getMolName()
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setMolName
public void setMolName(java.lang.String molName)
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getTitle
public java.lang.String getTitle()
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setTitle
public void setTitle(java.lang.String title)
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getSynonyms
public java.util.List<java.lang.String> getSynonyms()
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setSynonyms
public void setSynonyms(java.util.List<java.lang.String> synonyms)
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getEcNums
public java.util.List<java.lang.String> getEcNums()
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setEcNums
public void setEcNums(java.util.List<java.lang.String> ecNums)
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getEngineered
public java.lang.String getEngineered()
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setEngineered
public void setEngineered(java.lang.String engineered)
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getMutation
public java.lang.String getMutation()
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setMutation
public void setMutation(java.lang.String mutation)
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getBiologicalUnit
public java.lang.String getBiologicalUnit()
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setBiologicalUnit
public void setBiologicalUnit(java.lang.String biologicalUnit)
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getDetails
public java.lang.String getDetails()
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setDetails
public void setDetails(java.lang.String details)
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getNumRes
public java.lang.String getNumRes()
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setNumRes
public void setNumRes(java.lang.String numRes)
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getResNames
public java.lang.String getResNames()
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setResNames
public void setResNames(java.lang.String resNames)
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getHeaderVars
public java.lang.String getHeaderVars()
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setHeaderVars
public void setHeaderVars(java.lang.String headerVars)
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getSynthetic
public java.lang.String getSynthetic()
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setSynthetic
public void setSynthetic(java.lang.String synthetic)
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getFragment
public java.lang.String getFragment()
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setFragment
public void setFragment(java.lang.String fragment)
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getOrganismScientific
public java.lang.String getOrganismScientific()
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setOrganismScientific
public void setOrganismScientific(java.lang.String organismScientific)
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getOrganismTaxId
public java.lang.String getOrganismTaxId()
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setOrganismTaxId
public void setOrganismTaxId(java.lang.String organismTaxId)
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getOrganismCommon
public java.lang.String getOrganismCommon()
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setOrganismCommon
public void setOrganismCommon(java.lang.String organismCommon)
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getStrain
public java.lang.String getStrain()
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setStrain
public void setStrain(java.lang.String strain)
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getVariant
public java.lang.String getVariant()
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setVariant
public void setVariant(java.lang.String variant)
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getCellLine
public java.lang.String getCellLine()
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setCellLine
public void setCellLine(java.lang.String cellLine)
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getAtcc
public java.lang.String getAtcc()
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setAtcc
public void setAtcc(java.lang.String atcc)
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getOrgan
public java.lang.String getOrgan()
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setOrgan
public void setOrgan(java.lang.String organ)
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getTissue
public java.lang.String getTissue()
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setTissue
public void setTissue(java.lang.String tissue)
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getCell
public java.lang.String getCell()
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setCell
public void setCell(java.lang.String cell)
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getOrganelle
public java.lang.String getOrganelle()
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setOrganelle
public void setOrganelle(java.lang.String organelle)
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getSecretion
public java.lang.String getSecretion()
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setSecretion
public void setSecretion(java.lang.String secretion)
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getGene
public java.lang.String getGene()
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setGene
public void setGene(java.lang.String gene)
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getCellularLocation
public java.lang.String getCellularLocation()
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setCellularLocation
public void setCellularLocation(java.lang.String cellularLocation)
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getExpressionSystem
public java.lang.String getExpressionSystem()
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getExpressionSystemTaxId
public java.lang.String getExpressionSystemTaxId()
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setExpressionSystemTaxId
public void setExpressionSystemTaxId(java.lang.String expressionSystemTaxId)
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setExpressionSystem
public void setExpressionSystem(java.lang.String expressionSystem)
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getExpressionSystemStrain
public java.lang.String getExpressionSystemStrain()
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setExpressionSystemStrain
public void setExpressionSystemStrain(java.lang.String expressionSystemStrain)
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getExpressionSystemVariant
public java.lang.String getExpressionSystemVariant()
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setExpressionSystemVariant
public void setExpressionSystemVariant(java.lang.String expressionSystemVariant)
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getExpressionSystemCellLine
public java.lang.String getExpressionSystemCellLine()
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setExpressionSystemCellLine
public void setExpressionSystemCellLine(java.lang.String expressionSystemCellLine)
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getExpressionSystemAtccNumber
public java.lang.String getExpressionSystemAtccNumber()
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setExpressionSystemAtccNumber
public void setExpressionSystemAtccNumber(java.lang.String expressionSystemAtccNumber)
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getExpressionSystemOrgan
public java.lang.String getExpressionSystemOrgan()
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setExpressionSystemOrgan
public void setExpressionSystemOrgan(java.lang.String expressionSystemOrgan)
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getExpressionSystemTissue
public java.lang.String getExpressionSystemTissue()
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setExpressionSystemTissue
public void setExpressionSystemTissue(java.lang.String expressionSystemTissue)
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getExpressionSystemCell
public java.lang.String getExpressionSystemCell()
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setExpressionSystemCell
public void setExpressionSystemCell(java.lang.String expressionSystemCell)
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getExpressionSystemOrganelle
public java.lang.String getExpressionSystemOrganelle()
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setExpressionSystemOrganelle
public void setExpressionSystemOrganelle(java.lang.String expressionSystemOrganelle)
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getExpressionSystemCellularLocation
public java.lang.String getExpressionSystemCellularLocation()
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setExpressionSystemCellularLocation
public void setExpressionSystemCellularLocation(java.lang.String expressionSystemCellularLocation)
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getExpressionSystemVectorType
public java.lang.String getExpressionSystemVectorType()
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setExpressionSystemVectorType
public void setExpressionSystemVectorType(java.lang.String expressionSystemVectorType)
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getExpressionSystemVector
public java.lang.String getExpressionSystemVector()
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setExpressionSystemVector
public void setExpressionSystemVector(java.lang.String expressionSystemVector)
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getExpressionSystemPlasmid
public java.lang.String getExpressionSystemPlasmid()
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setExpressionSystemPlasmid
public void setExpressionSystemPlasmid(java.lang.String expressionSystemPlasmid)
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getExpressionSystemGene
public java.lang.String getExpressionSystemGene()
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setExpressionSystemGene
public void setExpressionSystemGene(java.lang.String expressionSystemGene)
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getExpressionSystemOtherDetails
public java.lang.String getExpressionSystemOtherDetails()
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setExpressionSystemOtherDetails
public void setExpressionSystemOtherDetails(java.lang.String expressionSystemOtherDetails)
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getChains
public java.util.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
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addChain
public void addChain(Chain chain)
Add new Chain to this Compound- Parameters:
chain
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setChains
public void setChains(java.util.List<Chain> chains)
Set the chains for this Compound- Parameters:
chains
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