org.biopax.paxtools.model.level3
Interface ChemicalStructure

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Level3Element, java.io.Serializable, UtilityClass

All Known Implementing Classes:

ChemicalStructureImpl

public interface ChemicalStructure
extends UtilityClass

Definition: The chemical structure of a small molecule.

Usage: Structure information is stored in the property structureData, in one of the three formats: CML, SMILES or InChI.The structureFormat property specifies which format is used.

Examples: The following SMILES string describes the structure of glucose-6-phosphate: 'C(OP(=O)(O)O)[CH]1([CH](O) [CH](O)[CH](O)[CH](O)O1)'.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

java.lang.String	getStructureData() This property holds a string defining chemical structure,in one of the three formats: CML, SMILES or InChI.
StructureFormatType	getStructureFormat() This property specifies which format is used to define chemical structure.
void	setStructureData(java.lang.String structureData) This property holds a string of data defining chemical structure,in one of the three formats: CML, SMILES or InChI.
void	setStructureFormat(StructureFormatType structureFormat) This property specifies which format is used to define chemical structure.

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getStructureData

java.lang.String getStructureData()

This property holds a string defining chemical structure,in one of the three formats: CML, SMILES or InChI. If, for example,the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.

Returns:

a string defining chemical structure

setStructureData

void setStructureData(java.lang.String structureData)

This property holds a string of data defining chemical structure,in one of the three formats: CML, SMILES or InChI. If, for example,the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.

Parameters:

structureData - a string defining chemical structure

getStructureFormat

StructureFormatType getStructureFormat()

This property specifies which format is used to define chemical structure.

Returns:

format used to define chemical structure

setStructureFormat

void setStructureFormat(StructureFormatType structureFormat)

This property specifies which format is used to define chemical structure.

Parameters:

structureFormat - format used to define chemical structure