Package org.rcsb.cif.model.generated

Class PdbxEntitySrcGenClone

java.lang.Object

org.rcsb.cif.model.BaseCategory

org.rcsb.cif.model.generated.PdbxEntitySrcGenClone

All Implemented Interfaces:

Category

@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class PdbxEntitySrcGenClone
extends BaseCategory

This category contains details for the cloning steps used in the overall protein production process. Each row in PDBX_ENTITY_SRC_GEN_CLONE should have an equivalent row in either PDBX_ENTITY_SRC_GEN_CLONE_LIGATION or PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION. If only summary information is provided data in the later two categories may be omitted.

Field Summary

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

isText, textFields

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
StrColumn	getDate()	The date of this production step.
StrColumn	getEndConstructId()	This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category.
StrColumn	getEntityId()	The value of _pdbx_entity_src_gen_clone.entity_id uniquely identifies each protein contained in the project target protein complex whose structure is to be determined.
StrColumn	getEntryId()	The value of _pdbx_entity_src_gen_clone.entry_id uniquely identifies a sample consisting of one or more proteins whose structure is to be determined.
StrColumn	getGeneInsertMethod()	The method used to insert the gene into the vector.
StrColumn	getMarker()	The type of marker included to allow selection of transformed cells
IntColumn	getNextStepId()	This item unique identifier for the next production step.
StrColumn	getPurificationDetails()	Details of any purification of the product.
StrColumn	getRobotId()	This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category.
IntColumn	getStepId()	This item is the unique identifier for this cloning step.
StrColumn	getSummary()	Summary of ligation or recombionation cloning used, the associated verification method and any purification of the product.
StrColumn	getTransformationMethod()	The method used to transform the expression cell line with the vector
StrColumn	getVectorDetails()	Details of any modifications made to the named vector.
StrColumn	getVectorName()	The name of the vector used in this cloning step.
StrColumn	getVerificationMethod()	The method used to verify that the incorporated gene is correct

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

PdbxEntitySrcGenClone

public PdbxEntitySrcGenClone(String name,
                             Map<String,Column> columns)

PdbxEntitySrcGenClone

public PdbxEntitySrcGenClone(String name,
                             int rowCount,
                             Object[] encodedColumns)

PdbxEntitySrcGenClone

public PdbxEntitySrcGenClone(String name)

Method Detail

getEntryId

public StrColumn getEntryId()

The value of _pdbx_entity_src_gen_clone.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_clone.entity_id uniquely identifies each protein contained in the project target protein complex 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 cloning 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 nucleic acid sequence is that of the cloned 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 this production step.

Returns:

StrColumn

getGeneInsertMethod

public StrColumn getGeneInsertMethod()

The method used to insert the gene into the vector. For 'Ligation', an PDBX_ENTITY_SRC_GEN_CLONE_LIGATION entry with matching .step_id is expected. For 'Recombination', an PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION entry with matching .step_id is expected.

Returns:

StrColumn

getVectorName

public StrColumn getVectorName()

The name of the vector used in this cloning step.

Returns:

StrColumn

getVectorDetails

public StrColumn getVectorDetails()

Details of any modifications made to the named vector.

Returns:

StrColumn

getTransformationMethod

public StrColumn getTransformationMethod()

The method used to transform the expression cell line with the vector

Returns:

StrColumn

getMarker

public StrColumn getMarker()

The type of marker included to allow selection of transformed cells

Returns:

StrColumn

getVerificationMethod

public StrColumn getVerificationMethod()

The method used to verify that the incorporated gene is correct

Returns:

StrColumn

getPurificationDetails

public StrColumn getPurificationDetails()

Details of any purification of the product.

Returns:

StrColumn

getSummary

public StrColumn getSummary()

Summary of ligation or recombionation cloning used, the associated verification method and any purification of the product.

Returns:

StrColumn