java.lang.Object
- org.rcsb.cif.model.BaseCategory
- - org.rcsb.cif.model.generated.EntitySrcGen

All Implemented Interfaces:

Category
```
@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class EntitySrcGen
extends BaseCategory
```
Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).

Field Summary
- Fields inherited from class org.rcsb.cif.model.BaseCategory
  isText, textFields

Constructor Summary

Constructors
Constructor	Description
`EntitySrcGen(String name)`
`EntitySrcGen(String name, int rowCount, Object[] encodedColumns)`
`EntitySrcGen(String name, Map<String,Column> columns)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`StrColumn`	`getEntityId()`	This data item is a pointer to _entity.id in the ENTITY category.
`StrColumn`	`getExpressionSystemId()`	A unique identifier for the expression system.
`StrColumn`	`getGeneSrcCommonName()`	The common name of the natural organism from which the gene was obtained.
`StrColumn`	`getGeneSrcDetails()`	A description of special aspects of the natural organism from which the gene was obtained.
`StrColumn`	`getGeneSrcDevStage()`	A string to indicate the life-cycle or cell development cycle in which the gene is expressed and the mature protein is active.
`StrColumn`	`getGeneSrcGenus()`	The genus of the natural organism from which the gene was obtained.
`StrColumn`	`getGeneSrcSpecies()`	The species of the natural organism from which the gene was obtained.
`StrColumn`	`getGeneSrcStrain()`	The strain of the natural organism from which the gene was obtained, if relevant.
`StrColumn`	`getGeneSrcTissue()`	The tissue of the natural organism from which the gene was obtained.
`StrColumn`	`getGeneSrcTissueFraction()`	The subcellular fraction of the tissue of the natural organism from which the gene was obtained.
`StrColumn`	`getHostOrgCommonName()`	The common name of the organism that served as host for the production of the entity.
`StrColumn`	`getHostOrgDetails()`	A description of special aspects of the organism that served as host for the production of the entity.
`StrColumn`	`getHostOrgGenus()`	The genus of the organism that served as host for the production of the entity.
`StrColumn`	`getHostOrgSpecies()`	The species of the organism that served as host for the production of the entity.
`StrColumn`	`getHostOrgStrain()`	The strain of the organism in which the entity was expressed.
`StrColumn`	`getPdbxAltSourceFlag()`	This data item identifies cases in which an alternative source modeled.
`IntColumn`	`getPdbxBegSeqNum()`	The beginning polymer sequence position for the polymer section corresponding to this source.
`StrColumn`	`getPdbxDescription()`	Information on the source which is not given elsewhere.
`IntColumn`	`getPdbxEndSeqNum()`	The ending polymer sequence position for the polymer section corresponding to this source.
`StrColumn`	`getPdbxGeneSrcAtcc()`	American Type Culture Collection tissue culture number.
`StrColumn`	`getPdbxGeneSrcCell()`	Cell type.
`StrColumn`	`getPdbxGeneSrcCellLine()`	The specific line of cells.
`StrColumn`	`getPdbxGeneSrcCellularLocation()`	Identifies the location inside (or outside) the cell.
`StrColumn`	`getPdbxGeneSrcCultureCollection()`	Culture collection identifier.
`StrColumn`	`getPdbxGeneSrcFragment()`	A domain or fragment of the molecule.
`StrColumn`	`getPdbxGeneSrcGene()`	Identifies the gene.
`StrColumn`	`getPdbxGeneSrcNcbiTaxonomyId()`	NCBI Taxonomy identifier for the gene source organism.
`StrColumn`	`getPdbxGeneSrcOrgan()`	Organized group of tissues that carries on a specialized function.
`StrColumn`	`getPdbxGeneSrcOrganelle()`	Organized structure within cell.
`StrColumn`	`getPdbxGeneSrcPlasmid()`	The source plasmid.
`StrColumn`	`getPdbxGeneSrcPlasmidName()`	The source plasmid.
`StrColumn`	`getPdbxGeneSrcScientificName()`	Scientific name of the organism.
`StrColumn`	`getPdbxGeneSrcVariant()`	Identifies the variant.
`StrColumn`	`getPdbxHostOrgAtcc()`	Americal Tissue Culture Collection of the expression system.
`StrColumn`	`getPdbxHostOrgCell()`	Cell type from which the gene is derived.
`StrColumn`	`getPdbxHostOrgCellLine()`	A specific line of cells used as the expression system.
`StrColumn`	`getPdbxHostOrgCellularLocation()`	Identifies the location inside (or outside) the cell which expressed the molecule.
`StrColumn`	`getPdbxHostOrgCultureCollection()`	Culture collection of the expression system.
`StrColumn`	`getPdbxHostOrgGene()`	Specific gene which expressed the molecule.
`StrColumn`	`getPdbxHostOrgNcbiTaxonomyId()`	NCBI Taxonomy identifier for the expression system organism.
`StrColumn`	`getPdbxHostOrgOrgan()`	Specific organ which expressed the molecule.
`StrColumn`	`getPdbxHostOrgOrganelle()`	Specific organelle which expressed the molecule.
`StrColumn`	`getPdbxHostOrgScientificName()`	The scientific name of the organism that served as host for the production of the entity.
`StrColumn`	`getPdbxHostOrgStrain()`	The strain of the organism in which the entity was expressed.
`StrColumn`	`getPdbxHostOrgTissue()`	The specific tissue which expressed the molecule.
`StrColumn`	`getPdbxHostOrgTissueFraction()`	The fraction of the tissue which expressed the molecule.
`StrColumn`	`getPdbxHostOrgVariant()`	Variant of the organism used as the expression system.
`StrColumn`	`getPdbxHostOrgVector()`	Identifies the vector used.
`StrColumn`	`getPdbxHostOrgVectorType()`	Identifies the type of vector used (plasmid, virus, or cosmid).
`StrColumn`	`getPdbxSeqType()`	This data item povides additional information about the sequence type.
`IntColumn`	`getPdbxSrcId()`	This data item is an ordinal identifier for entity_src_gen data records.
`StrColumn`	`getPlasmidDetails()`	A description of special aspects of the plasmid that produced the entity in the host organism.
`StrColumn`	`getPlasmidName()`	The name of the plasmid that produced the entity in the host organism.
`StrColumn`	`getStartConstructId()`	A pointer to _pdbx_construct.id in the PDBX_CONSTRUCT category.

Methods inherited from class org.rcsb.cif.model.BaseCategory
getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined

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

Methods inherited from interface org.rcsb.cif.model.Category
columnNames, columns, get

- Constructor Detail
  - EntitySrcGen
```
public EntitySrcGen(String name,
                    Map<String,Column> columns)
```
  - EntitySrcGen
```
public EntitySrcGen(String name,
                    int rowCount,
                    Object[] encodedColumns)
```
  - EntitySrcGen
```
public EntitySrcGen(String name)
```
- Method Detail
  - getEntityId
```
public StrColumn getEntityId()
```
    This data item is a pointer to _entity.id in the ENTITY category.
    
    Returns:
    
    StrColumn
  - getGeneSrcCommonName
```
public StrColumn getGeneSrcCommonName()
```
    The common name of the natural organism from which the gene was obtained.
    
    Returns:
    
    StrColumn
  - getGeneSrcDetails
```
public StrColumn getGeneSrcDetails()
```
    A description of special aspects of the natural organism from which the gene was obtained.
    
    Returns:
    
    StrColumn
  - getGeneSrcGenus
```
public StrColumn getGeneSrcGenus()
```
    The genus of the natural organism from which the gene was obtained.
    
    Returns:
    
    StrColumn
  - getGeneSrcSpecies
```
public StrColumn getGeneSrcSpecies()
```
    The species of the natural organism from which the gene was obtained.
    
    Returns:
    
    StrColumn
  - getGeneSrcStrain
```
public StrColumn getGeneSrcStrain()
```
    The strain of the natural organism from which the gene was obtained, if relevant.
    
    Returns:
    
    StrColumn
  - getGeneSrcTissue
```
public StrColumn getGeneSrcTissue()
```
    The tissue of the natural organism from which the gene was obtained.
    
    Returns:
    
    StrColumn
  - getGeneSrcTissueFraction
```
public StrColumn getGeneSrcTissueFraction()
```
    The subcellular fraction of the tissue of the natural organism from which the gene was obtained.
    
    Returns:
    
    StrColumn
  - getHostOrgGenus
```
public StrColumn getHostOrgGenus()
```
    The genus of the organism that served as host for the production of the entity.
    
    Returns:
    
    StrColumn
  - getHostOrgSpecies
```
public StrColumn getHostOrgSpecies()
```
    The species of the organism that served as host for the production of the entity.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcFragment
```
public StrColumn getPdbxGeneSrcFragment()
```
    A domain or fragment of the molecule.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcGene
```
public StrColumn getPdbxGeneSrcGene()
```
    Identifies the gene.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcScientificName
```
public StrColumn getPdbxGeneSrcScientificName()
```
    Scientific name of the organism.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcVariant
```
public StrColumn getPdbxGeneSrcVariant()
```
    Identifies the variant.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcCellLine
```
public StrColumn getPdbxGeneSrcCellLine()
```
    The specific line of cells.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcAtcc
```
public StrColumn getPdbxGeneSrcAtcc()
```
    American Type Culture Collection tissue culture number.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcOrgan
```
public StrColumn getPdbxGeneSrcOrgan()
```
    Organized group of tissues that carries on a specialized function.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcOrganelle
```
public StrColumn getPdbxGeneSrcOrganelle()
```
    Organized structure within cell.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcPlasmid
```
public StrColumn getPdbxGeneSrcPlasmid()
```
    The source plasmid.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcPlasmidName
```
public StrColumn getPdbxGeneSrcPlasmidName()
```
    The source plasmid.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcCell
```
public StrColumn getPdbxGeneSrcCell()
```
    Cell type.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcCellularLocation
```
public StrColumn getPdbxGeneSrcCellularLocation()
```
    Identifies the location inside (or outside) the cell.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgGene
```
public StrColumn getPdbxHostOrgGene()
```
    Specific gene which expressed the molecule.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgOrgan
```
public StrColumn getPdbxHostOrgOrgan()
```
    Specific organ which expressed the molecule.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgOrganelle
```
public StrColumn getPdbxHostOrgOrganelle()
```
    Specific organelle which expressed the molecule.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgCellularLocation
```
public StrColumn getPdbxHostOrgCellularLocation()
```
    Identifies the location inside (or outside) the cell which expressed the molecule.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgStrain
```
public StrColumn getPdbxHostOrgStrain()
```
    The strain of the organism in which the entity was expressed.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgTissueFraction
```
public StrColumn getPdbxHostOrgTissueFraction()
```
    The fraction of the tissue which expressed the molecule.
    
    Returns:
    
    StrColumn
  - getPdbxDescription
```
public StrColumn getPdbxDescription()
```
    Information on the source which is not given elsewhere.
    
    Returns:
    
    StrColumn
  - getHostOrgCommonName
```
public StrColumn getHostOrgCommonName()
```
    The common name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item be derived from _entity_src_gen_express.host_org_common_name or via _entity_src_gen_express.host_org_tax_id
    
    Returns:
    
    StrColumn
  - getHostOrgDetails
```
public StrColumn getHostOrgDetails()
```
    A description of special aspects of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would derived from _entity_src_gen_express.host_org_details
    
    Returns:
    
    StrColumn
  - getHostOrgStrain
```
public StrColumn getHostOrgStrain()
```
    The strain of the organism in which the entity was expressed. Where full details of the protein production are available it would be expected that this item be derived from _entity_src_gen_express.host_org_strain or via _entity_src_gen_express.host_org_tax_id
    
    Returns:
    
    StrColumn
  - getPlasmidDetails
```
public StrColumn getPlasmidDetails()
```
    A description of special aspects of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from _pdbx_construct.details of the construct pointed to from _entity_src_gen_express.plasmid_id.
    
    Returns:
    
    StrColumn
  - getPlasmidName
```
public StrColumn getPlasmidName()
```
    The name of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from _pdbx_construct.name of the construct pointed to from _entity_src_gen_express.plasmid_id.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgVariant
```
public StrColumn getPdbxHostOrgVariant()
```
    Variant of the organism used as the expression system. Where full details of the protein production are available it would be expected that this item be derived from entity_src_gen_express.host_org_variant or via _entity_src_gen_express.host_org_tax_id
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgCellLine
```
public StrColumn getPdbxHostOrgCellLine()
```
    A specific line of cells used as the expression system. Where full details of the protein production are available it would be expected that this item would be derived from entity_src_gen_express.host_org_cell_line
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgAtcc
```
public StrColumn getPdbxHostOrgAtcc()
```
    Americal Tissue Culture Collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.host_org_culture_collection
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgCultureCollection
```
public StrColumn getPdbxHostOrgCultureCollection()
```
    Culture collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived somehwere, but exactly where is not clear.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgCell
```
public StrColumn getPdbxHostOrgCell()
```
    Cell type from which the gene is derived. Where entity.target_id is provided this should be derived from details of the target.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgScientificName
```
public StrColumn getPdbxHostOrgScientificName()
```
    The scientific name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.host_org_scientific_name or via _entity_src_gen_express.host_org_tax_id
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgTissue
```
public StrColumn getPdbxHostOrgTissue()
```
    The specific tissue which expressed the molecule. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.host_org_tissue
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgVector
```
public StrColumn getPdbxHostOrgVector()
```
    Identifies the vector used. Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_clone.vector_name.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgVectorType
```
public StrColumn getPdbxHostOrgVectorType()
```
    Identifies the type of vector used (plasmid, virus, or cosmid). Where full details of the protein production are available it would be expected that this item would be derived from _entity_src_gen_express.vector_type.
    
    Returns:
    
    StrColumn
  - getExpressionSystemId
```
public StrColumn getExpressionSystemId()
```
    A unique identifier for the expression system. This should be extracted from a local list of expression systems.
    
    Returns:
    
    StrColumn
  - getGeneSrcDevStage
```
public StrColumn getGeneSrcDevStage()
```
    A string to indicate the life-cycle or cell development cycle in which the gene is expressed and the mature protein is active.
    
    Returns:
    
    StrColumn
  - getStartConstructId
```
public StrColumn getStartConstructId()
```
    A pointer to _pdbx_construct.id in the PDBX_CONSTRUCT category. The indentified sequence is the initial construct.
    
    Returns:
    
    StrColumn
  - getPdbxGeneSrcNcbiTaxonomyId
```
public StrColumn getPdbxGeneSrcNcbiTaxonomyId()
```
    NCBI Taxonomy identifier for the gene source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
    
    Returns:
    
    StrColumn
  - getPdbxHostOrgNcbiTaxonomyId
```
public StrColumn getPdbxHostOrgNcbiTaxonomyId()
```
    NCBI Taxonomy identifier for the expression system organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18.
    
    Returns:
    
    StrColumn
  - getPdbxSrcId
```
public IntColumn getPdbxSrcId()
```
    This data item is an ordinal identifier for entity_src_gen data records.
    
    Returns:
    
    IntColumn
  - getPdbxAltSourceFlag
```
public StrColumn getPdbxAltSourceFlag()
```
    This data item identifies cases in which an alternative source modeled.
    
    Returns:
    
    StrColumn
  - getPdbxSeqType
```
public StrColumn getPdbxSeqType()
```
    This data item povides additional information about the sequence type.
    
    Returns:
    
    StrColumn
  - getPdbxBegSeqNum
```
public IntColumn getPdbxBegSeqNum()
```
    The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category.
    
    Returns:
    
    IntColumn
  - getPdbxEndSeqNum
```
public IntColumn getPdbxEndSeqNum()
```
    The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category.
    
    Returns:
    
    IntColumn
  - getPdbxGeneSrcCultureCollection
```
public StrColumn getPdbxGeneSrcCultureCollection()
```
    Culture collection identifier.
    
    Returns:
    
    StrColumn

Class EntitySrcGen

Field Summary

Fields inherited from class org.rcsb.cif.model.BaseCategory

Constructor Summary

Method Summary

Methods inherited from class org.rcsb.cif.model.BaseCategory

Methods inherited from class java.lang.Object

Methods inherited from interface org.rcsb.cif.model.Category

Constructor Detail

EntitySrcGen

EntitySrcGen

EntitySrcGen

Method Detail

getEntityId

getGeneSrcCommonName

getGeneSrcDetails

getGeneSrcGenus

getGeneSrcSpecies

getGeneSrcStrain

getGeneSrcTissue

getGeneSrcTissueFraction

getHostOrgGenus

getHostOrgSpecies

getPdbxGeneSrcFragment

getPdbxGeneSrcGene

getPdbxGeneSrcScientificName

getPdbxGeneSrcVariant

getPdbxGeneSrcCellLine

getPdbxGeneSrcAtcc

getPdbxGeneSrcOrgan

getPdbxGeneSrcOrganelle

getPdbxGeneSrcPlasmid

getPdbxGeneSrcPlasmidName

getPdbxGeneSrcCell

getPdbxGeneSrcCellularLocation

getPdbxHostOrgGene

getPdbxHostOrgOrgan

getPdbxHostOrgOrganelle

getPdbxHostOrgCellularLocation

getPdbxHostOrgStrain

getPdbxHostOrgTissueFraction

getPdbxDescription

getHostOrgCommonName

getHostOrgDetails

getHostOrgStrain

getPlasmidDetails

getPlasmidName

getPdbxHostOrgVariant

getPdbxHostOrgCellLine

getPdbxHostOrgAtcc

getPdbxHostOrgCultureCollection

getPdbxHostOrgCell

getPdbxHostOrgScientificName

getPdbxHostOrgTissue

getPdbxHostOrgVector

getPdbxHostOrgVectorType

getExpressionSystemId

getGeneSrcDevStage

getStartConstructId

getPdbxGeneSrcNcbiTaxonomyId

getPdbxHostOrgNcbiTaxonomyId

getPdbxSrcId

getPdbxAltSourceFlag

getPdbxSeqType

getPdbxBegSeqNum

getPdbxEndSeqNum

getPdbxGeneSrcCultureCollection