Class Compound

  • 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
    • 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 java.lang.String toString()
        Overrides:
        toString in class java.lang.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 java.lang.Long getId()
        get the ID used by Hibernate
        Returns:
        the ID used by Hibernate
      • setId

        public void setId​(java.lang.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 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 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:
        java.lang.IllegalArgumentException - if the given Chain is not a member of this Compound
      • getRefChainId

        public java.lang.String getRefChainId()
        Return the ref chain id value.
        Returns:
        the RefChainID
        See Also:
        setRefChainId(String)
      • setRefChainId

        public void setRefChainId​(java.lang.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 java.lang.String getMolName()
      • setMolName

        public void setMolName​(java.lang.String molName)
      • getTitle

        public java.lang.String getTitle()
      • setTitle

        public void setTitle​(java.lang.String title)
      • getSynonyms

        public java.util.List<java.lang.String> getSynonyms()
      • setSynonyms

        public void setSynonyms​(java.util.List<java.lang.String> synonyms)
      • getEcNums

        public java.util.List<java.lang.String> getEcNums()
      • setEcNums

        public void setEcNums​(java.util.List<java.lang.String> ecNums)
      • getEngineered

        public java.lang.String getEngineered()
      • setEngineered

        public void setEngineered​(java.lang.String engineered)
      • getMutation

        public java.lang.String getMutation()
      • setMutation

        public void setMutation​(java.lang.String mutation)
      • getBiologicalUnit

        public java.lang.String getBiologicalUnit()
      • setBiologicalUnit

        public void setBiologicalUnit​(java.lang.String biologicalUnit)
      • getDetails

        public java.lang.String getDetails()
      • setDetails

        public void setDetails​(java.lang.String details)
      • getNumRes

        public java.lang.String getNumRes()
      • setNumRes

        public void setNumRes​(java.lang.String numRes)
      • getResNames

        public java.lang.String getResNames()
      • setResNames

        public void setResNames​(java.lang.String resNames)
      • getHeaderVars

        public java.lang.String getHeaderVars()
      • setHeaderVars

        public void setHeaderVars​(java.lang.String headerVars)
      • getSynthetic

        public java.lang.String getSynthetic()
      • setSynthetic

        public void setSynthetic​(java.lang.String synthetic)
      • getFragment

        public java.lang.String getFragment()
      • setFragment

        public void setFragment​(java.lang.String fragment)
      • getOrganismScientific

        public java.lang.String getOrganismScientific()
      • setOrganismScientific

        public void setOrganismScientific​(java.lang.String organismScientific)
      • getOrganismTaxId

        public java.lang.String getOrganismTaxId()
      • setOrganismTaxId

        public void setOrganismTaxId​(java.lang.String organismTaxId)
      • getOrganismCommon

        public java.lang.String getOrganismCommon()
      • setOrganismCommon

        public void setOrganismCommon​(java.lang.String organismCommon)
      • getStrain

        public java.lang.String getStrain()
      • setStrain

        public void setStrain​(java.lang.String strain)
      • getVariant

        public java.lang.String getVariant()
      • setVariant

        public void setVariant​(java.lang.String variant)
      • getCellLine

        public java.lang.String getCellLine()
      • setCellLine

        public void setCellLine​(java.lang.String cellLine)
      • getAtcc

        public java.lang.String getAtcc()
      • setAtcc

        public void setAtcc​(java.lang.String atcc)
      • getOrgan

        public java.lang.String getOrgan()
      • setOrgan

        public void setOrgan​(java.lang.String organ)
      • getTissue

        public java.lang.String getTissue()
      • setTissue

        public void setTissue​(java.lang.String tissue)
      • getCell

        public java.lang.String getCell()
      • setCell

        public void setCell​(java.lang.String cell)
      • getOrganelle

        public java.lang.String getOrganelle()
      • setOrganelle

        public void setOrganelle​(java.lang.String organelle)
      • getSecretion

        public java.lang.String getSecretion()
      • setSecretion

        public void setSecretion​(java.lang.String secretion)
      • getGene

        public java.lang.String getGene()
      • setGene

        public void setGene​(java.lang.String gene)
      • getCellularLocation

        public java.lang.String getCellularLocation()
      • setCellularLocation

        public void setCellularLocation​(java.lang.String cellularLocation)
      • getExpressionSystem

        public java.lang.String getExpressionSystem()
      • getExpressionSystemTaxId

        public java.lang.String getExpressionSystemTaxId()
      • setExpressionSystemTaxId

        public void setExpressionSystemTaxId​(java.lang.String expressionSystemTaxId)
      • setExpressionSystem

        public void setExpressionSystem​(java.lang.String expressionSystem)
      • getExpressionSystemStrain

        public java.lang.String getExpressionSystemStrain()
      • setExpressionSystemStrain

        public void setExpressionSystemStrain​(java.lang.String expressionSystemStrain)
      • getExpressionSystemVariant

        public java.lang.String getExpressionSystemVariant()
      • setExpressionSystemVariant

        public void setExpressionSystemVariant​(java.lang.String expressionSystemVariant)
      • getExpressionSystemCellLine

        public java.lang.String getExpressionSystemCellLine()
      • setExpressionSystemCellLine

        public void setExpressionSystemCellLine​(java.lang.String expressionSystemCellLine)
      • getExpressionSystemAtccNumber

        public java.lang.String getExpressionSystemAtccNumber()
      • setExpressionSystemAtccNumber

        public void setExpressionSystemAtccNumber​(java.lang.String expressionSystemAtccNumber)
      • getExpressionSystemOrgan

        public java.lang.String getExpressionSystemOrgan()
      • setExpressionSystemOrgan

        public void setExpressionSystemOrgan​(java.lang.String expressionSystemOrgan)
      • getExpressionSystemTissue

        public java.lang.String getExpressionSystemTissue()
      • setExpressionSystemTissue

        public void setExpressionSystemTissue​(java.lang.String expressionSystemTissue)
      • getExpressionSystemCell

        public java.lang.String getExpressionSystemCell()
      • setExpressionSystemCell

        public void setExpressionSystemCell​(java.lang.String expressionSystemCell)
      • getExpressionSystemOrganelle

        public java.lang.String getExpressionSystemOrganelle()
      • setExpressionSystemOrganelle

        public void setExpressionSystemOrganelle​(java.lang.String expressionSystemOrganelle)
      • getExpressionSystemCellularLocation

        public java.lang.String getExpressionSystemCellularLocation()
      • setExpressionSystemCellularLocation

        public void setExpressionSystemCellularLocation​(java.lang.String expressionSystemCellularLocation)
      • getExpressionSystemVectorType

        public java.lang.String getExpressionSystemVectorType()
      • setExpressionSystemVectorType

        public void setExpressionSystemVectorType​(java.lang.String expressionSystemVectorType)
      • getExpressionSystemVector

        public java.lang.String getExpressionSystemVector()
      • setExpressionSystemVector

        public void setExpressionSystemVector​(java.lang.String expressionSystemVector)
      • getExpressionSystemPlasmid

        public java.lang.String getExpressionSystemPlasmid()
      • setExpressionSystemPlasmid

        public void setExpressionSystemPlasmid​(java.lang.String expressionSystemPlasmid)
      • getExpressionSystemGene

        public java.lang.String getExpressionSystemGene()
      • setExpressionSystemGene

        public void setExpressionSystemGene​(java.lang.String expressionSystemGene)
      • getExpressionSystemOtherDetails

        public java.lang.String getExpressionSystemOtherDetails()
      • setExpressionSystemOtherDetails

        public void setExpressionSystemOtherDetails​(java.lang.String expressionSystemOtherDetails)
      • 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
      • addChain

        public void addChain​(Chain chain)
        Add new Chain to this Compound
        Parameters:
        chain -
      • setChains

        public void setChains​(java.util.List<Chain> chains)
        Set the chains for this Compound
        Parameters:
        chains -