Package org.rcsb.cif.schema.mm

Class PdbxEntitySrcGenExpress

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PdbxEntitySrcGenExpress
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxEntitySrcGenExpress
extends DelegatingCategory
This category contains details for the EXPRESSION steps used in the overall protein production process. It is hoped that this category will cover all forms of cell-based expression by reading induction as induction/transformation/transfection.

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • getEntryId

      public StrColumn getEntryId()
      The value of _pdbx_entity_src_gen_express.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to _entry.id. This item may be a site dependent bar code.
      Returns:
      StrColumn

    • getEntityId

      public StrColumn getEntityId()
      The value of _pdbx_entity_src_gen_express.entity_id uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to _entity.id in the ENTITY category. This item may be a site dependent bar code.
      Returns:
      StrColumn

    • getStepId

      public IntColumn getStepId()
      This item is the unique identifier for this expression step.
      Returns:
      IntColumn

    • getNextStepId

      public IntColumn getNextStepId()
      This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product.
      Returns:
      IntColumn

    • getEndConstructId

      public StrColumn getEndConstructId()
      This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product.
      Returns:
      StrColumn

    • getRobotId

      public StrColumn getRobotId()
      This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category.
      Returns:
      StrColumn

    • getDate

      public StrColumn getDate()
      The date of production step.
      Returns:
      StrColumn

    • getPromoterType

      public StrColumn getPromoterType()
      The nature of the promoter controlling expression of the gene.
      Returns:
      StrColumn

    • getPlasmidId

      public StrColumn getPlasmidId()
      This item is a pointer to _pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced entry will contain the nucleotide sequence that is to be expressed, including tags.
      Returns:
      StrColumn

    • getVectorType

      public StrColumn getVectorType()
      Identifies the type of vector used (plasmid, virus, or cosmid) in the expression system.
      Returns:
      StrColumn

    • getNTerminalSeqTag

      public StrColumn getNTerminalSeqTag()
      Any N-terminal sequence tag as a string of one letter amino acid codes.
      Returns:
      StrColumn

    • getCTerminalSeqTag

      public StrColumn getCTerminalSeqTag()
      Any C-terminal sequence tag as a string of one letter amino acid codes
      Returns:
      StrColumn

    • getHostOrgScientificName

      public StrColumn getHostOrgScientificName()
      The scientific name of the organism that served as host for the expression system. It is expected that either this item or _pdbx_entity_src_gen_express.host_org_tax_id should be populated.
      Returns:
      StrColumn

    • getHostOrgCommonName

      public StrColumn getHostOrgCommonName()
      The common name of the organism that served as host for the expression system. Where _pdbx_entity_src_gen_express.host_org_tax_id is populated it is expected that this item may be derived by look up against the taxonomy database.
      Returns:
      StrColumn

    • getHostOrgVariant

      public StrColumn getHostOrgVariant()
      The vairant of the organism that served as host for the expression system. Where _pdbx_entity_src_gen_express.host_org_tax_id is populated it is expected that this item may be derived by a look up against the taxonomy database.
      Returns:
      StrColumn

    • getHostOrgStrain

      public StrColumn getHostOrgStrain()
      The strain of the organism that served as host for the expression system. Where _pdbx_entity_src_gen_express.host_org_tax_id is populated it is expected that this item may be derived by a look up against the taxonomy database.
      Returns:
      StrColumn

    • getHostOrgTissue

      public StrColumn getHostOrgTissue()
      The specific tissue which expressed the molecule.
      Returns:
      StrColumn

    • getHostOrgCultureCollection

      public StrColumn getHostOrgCultureCollection()
      Culture collection of the expression system
      Returns:
      StrColumn

    • getHostOrgCellLine

      public StrColumn getHostOrgCellLine()
      A specific line of cells used as the expression system
      Returns:
      StrColumn

    • getHostOrgTaxId

      public StrColumn getHostOrgTaxId()
      The id for the NCBI taxonomy node corresponding to the organism that served as host for the expression system.
      Returns:
      StrColumn

    • getHostOrgDetails

      public StrColumn getHostOrgDetails()
      A description of special aspects of the organism that served as host for the expression system.
      Returns:
      StrColumn

    • getCultureBaseMedia

      public StrColumn getCultureBaseMedia()
      The name of the base media in which the expression host was grown.
      Returns:
      StrColumn

    • getCultureAdditives

      public StrColumn getCultureAdditives()
      Any additives to the base media in which the expression host was grown.
      Returns:
      StrColumn

    • getCultureVolume

      public FloatColumn getCultureVolume()
      The volume of media in milliliters in which the expression host was grown.
      Returns:
      FloatColumn

    • getCultureTime

      public FloatColumn getCultureTime()
      The time in hours for which the expression host was allowed to grow prior to induction/transformation/transfection.
      Returns:
      FloatColumn

    • getCultureTemperature

      public FloatColumn getCultureTemperature()
      The temperature in degrees celsius at which the expression host was allowed to grow prior to induction/transformation/transfection.
      Returns:
      FloatColumn

    • getInducer

      public StrColumn getInducer()
      The chemical name of the inducing agent.
      Returns:
      StrColumn

    • getInducerConcentration

      public FloatColumn getInducerConcentration()
      Concentration of the inducing agent.
      Returns:
      FloatColumn

    • getInductionDetails

      public StrColumn getInductionDetails()
      Details of induction/transformation/transfection.
      Returns:
      StrColumn

    • getMultiplicityOfInfection

      public FloatColumn getMultiplicityOfInfection()
      The multiplicity of infection for genes introduced by transfection, eg. for baculovirus-based expression.
      Returns:
      FloatColumn

    • getInductionTimepoint

      public FloatColumn getInductionTimepoint()
      The time in hours after induction/transformation/transfection at which the optical density of the culture was measured.
      Returns:
      FloatColumn

    • getInductionTemperature

      public FloatColumn getInductionTemperature()
      The temperature in celsius at which the induced/transformed/transfected cells were grown.
      Returns:
      FloatColumn

    • getHarvestingDetails

      public StrColumn getHarvestingDetails()
      Details of the harvesting protocol.
      Returns:
      StrColumn

    • getStorageDetails

      public StrColumn getStorageDetails()
      Details of how the harvested culture was stored.
      Returns:
      StrColumn

    • getSummary

      public StrColumn getSummary()
      Summary of the details of the expression steps used in protein production.
      Returns:
      StrColumn