001package org.biopax.paxtools.model.level3; 002 003 004/** 005 * Definition: The chemical structure of a small molecule. 006 * 007 * Usage: Structure information is stored in the property structureData, in one of the three formats: 008 * <a href="www.xml-cml.org">CML</a>, <a href="www.daylight.com/dayhtml/smiles/">SMILES</a> or 009 * <a href="http://www.iupac.org/inchi/">InChI</a>.The structureFormat property specifies which format is used. 010 * 011 * Examples: The following SMILES string describes the structure of glucose-6-phosphate: 'C(OP(=O)(O)O)[CH]1([CH](O) 012 * [CH](O)[CH](O)[CH](O)O1)'. 013 */ 014public interface ChemicalStructure extends UtilityClass 015{ 016 017 018 /** 019 * This property holds a string defining chemical structure,in one of the three formats: 020 * <a href ="www.xml-cml.org">CML</a>, <a href = "www.daylight.com/dayhtml/smiles/">SMILES</a> or 021 * <a href="http://www.iupac.org/inchi/">InChI</a>. If, for example,the CML format is used, 022 * then the value of this property is a string containing the XML encoding of the CML data. 023 * @return a string defining chemical structure 024 */ 025 String getStructureData(); 026 027 /** 028 * This property holds a string of data defining chemical structure,in one of the three formats: 029 * <a href ="www.xml-cml.org">CML</a>, <a href = "www.daylight.com/dayhtml/smiles/">SMILES</a> or 030 * <a href="http://www.iupac.org/inchi/">InChI</a>. If, for example,the CML format is used, 031 * then the value of this property is a string containing the XML encoding of the CML data. 032 * @param structureData a string defining chemical structure 033 */ 034 void setStructureData(String structureData); 035 036 037 /** 038 * This property specifies which format is used to define chemical structure. 039 * @return format used to define chemical structure 040 */ 041 StructureFormatType getStructureFormat(); 042 043 /** 044 * This property specifies which format is used to define chemical structure. 045 * @param structureFormat format used to define chemical structure 046 */ 047 void setStructureFormat(StructureFormatType structureFormat); 048 049}