Class Compound

Method Details

• 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

• 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 -