org.biopax.paxtools.model.level2
Interface chemicalStructure

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, Level2Element, java.io.Serializable, utilityClass

public interface chemicalStructure
extends utilityClass

Describes a small molecule structure. Structure information is stored in the property STRUCTURE-DATA, in one of three formats: the CML format (see www.xml-cml.org), the SMILES format (see www.daylight.com/dayhtml/smiles/) or the InChI format (http://www.iupac.org/inchi/). The STRUCTURE-FORMAT property specifies which format is used.

Comment: By virtue of the expressivity of CML, an instance of this class can also provide additional information about a small molecule, such as its chemical formula, names, and synonyms, if CML is used as the structure format. Examples: The following SMILES string, which 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	getSTRUCTURE_DATA()
java.lang.String	getSTRUCTURE_FORMAT()
void	setSTRUCTURE_DATA(java.lang.String STRUCTURE_DATA)
void	setSTRUCTURE_FORMAT(java.lang.String STRUCTURE_FORMAT)

Methods inherited from interface org.biopax.paxtools.model.level2.Level2Element

addCOMMENT, getCOMMENT, removeCOMMENT, setCOMMENT

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

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getSTRUCTURE_DATA

java.lang.String getSTRUCTURE_DATA()

getSTRUCTURE_FORMAT

java.lang.String getSTRUCTURE_FORMAT()

setSTRUCTURE_DATA

void setSTRUCTURE_DATA(java.lang.String STRUCTURE_DATA)

setSTRUCTURE_FORMAT

void setSTRUCTURE_FORMAT(java.lang.String STRUCTURE_FORMAT)