Package org.rcsb.cif.model.generated

Class PdbxReferenceMolecule

java.lang.Object

org.rcsb.cif.model.BaseCategory

org.rcsb.cif.model.generated.PdbxReferenceMolecule

All Implemented Interfaces:

Category

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

Data items in the PDBX_REFERENCE_MOLECULE category record reference information about small polymer molecules.

Field Summary

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

isText, textFields

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
StrColumn	getChemCompId()	For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule.
StrColumn	getClassEvidenceCode()	Evidence for the assignment of _pdbx_reference_molecule.class
StrColumn	getClazz()	Broadly defines the function of the entity.
StrColumn	getCompoundDetails()	Special details about this molecule.
StrColumn	getDescription()	Description of this molecule.
StrColumn	getFormula()	The formula for the reference entity.
FloatColumn	getFormulaWeight()	Formula mass in daltons of the entity.
StrColumn	getName()	A name of the entity.
StrColumn	getPrdId()	The value of _pdbx_reference_molecule.prd_id is the unique identifier for the reference molecule in this family.
StrColumn	getReleaseStatus()	Defines the current PDB release status for this molecule definition.
StrColumn	getReplacedBy()	Assigns the identifier of the reference molecule that has replaced this molecule.
StrColumn	getReplaces()	Assigns the identifier for the reference molecule which have been replaced by this reference molecule.
StrColumn	getRepresentAs()	Defines how this entity is represented in PDB data files.
StrColumn	getRepresentativePDBIdCode()	The PDB accession code for the entry containing a representative example of this molecule.
StrColumn	getType()	Defines the structural classification of the entity.
StrColumn	getTypeEvidenceCode()	Evidence for the assignment of _pdbx_reference_molecule.type

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

PdbxReferenceMolecule

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

PdbxReferenceMolecule

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

PdbxReferenceMolecule

public PdbxReferenceMolecule(String name)

Method Detail

getPrdId

public StrColumn getPrdId()

The value of _pdbx_reference_molecule.prd_id is the unique identifier for the reference molecule in this family. By convention this ID uniquely identifies the reference molecule in in the PDB reference dictionary. The ID has the template form PRD_dddddd (e.g. PRD_000001)

Returns:

StrColumn

getFormulaWeight

public FloatColumn getFormulaWeight()

Formula mass in daltons of the entity.

Returns:

FloatColumn

getFormula

public StrColumn getFormula()

The formula for the reference entity. Formulae are written according to the rules: 1. Only recognised element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each element symbol and its count, but in general parentheses are not used. 4. The order of elements depends on whether or not carbon is present. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts.

Returns:

StrColumn

getType

public StrColumn getType()

Defines the structural classification of the entity.

Returns:

StrColumn

getTypeEvidenceCode

public StrColumn getTypeEvidenceCode()

Evidence for the assignment of _pdbx_reference_molecule.type

Returns:

StrColumn

getClazz

public StrColumn getClazz()

Broadly defines the function of the entity.

Returns:

StrColumn

getClassEvidenceCode

public StrColumn getClassEvidenceCode()

Evidence for the assignment of _pdbx_reference_molecule.class

Returns:

StrColumn

getName

public StrColumn getName()

A name of the entity.

Returns:

StrColumn

getRepresentAs

public StrColumn getRepresentAs()

Defines how this entity is represented in PDB data files.

Returns:

StrColumn

getChemCompId

public StrColumn getChemCompId()

For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule.

Returns:

StrColumn

getCompoundDetails

public StrColumn getCompoundDetails()

Special details about this molecule.

Returns:

StrColumn

getDescription

public StrColumn getDescription()

Description of this molecule.

Returns:

StrColumn

getRepresentativePDBIdCode

public StrColumn getRepresentativePDBIdCode()

The PDB accession code for the entry containing a representative example of this molecule.

Returns:

StrColumn

getReleaseStatus

public StrColumn getReleaseStatus()

Defines the current PDB release status for this molecule definition.

Returns:

StrColumn

getReplaces

public StrColumn getReplaces()

Assigns the identifier for the reference molecule which have been replaced by this reference molecule. Multiple molecule identifier codes should be separated by commas.

Returns:

StrColumn

getReplacedBy

public StrColumn getReplacedBy()

Assigns the identifier of the reference molecule that has replaced this molecule.

Returns:

StrColumn