Package psidev.psi.mi.jami.model

Interface BioactiveEntity

All Superinterfaces:

Interactor, Molecule

All Known Implementing Classes:

DefaultBioactiveEntity, MitabBioactiveEntity, XmlBioactiveEntity, XmlBioactiveEntity, XmlBioactiveEntity

public interface BioactiveEntity
extends Molecule

Molecules showing activity in a living system and which can interact with other molecules

Since:

23/11/12

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	BIOACTIVE_ENTITY	Constant BIOACTIVE_ENTITY="bioactive entity"
static String	BIOACTIVE_ENTITY_MI	Constant BIOACTIVE_ENTITY_MI="MI:1100"
static String	POLYSACCHARIDE	Constant POLYSACCHARIDE="polysaccharide"
static String	POLYSACCHARIDE_MI	Constant POLYSACCHARIDE_MI="MI:0904"
static String	SMALL_MOLECULE	Constant SMALL_MOLECULE="small molecule"
static String	SMALL_MOLECULE_MI	Constant SMALL_MOLECULE_MI="MI:0328"

Fields inherited from interface psidev.psi.mi.jami.model.Interactor

UNKNOWN_INTERACTOR, UNKNOWN_INTERACTOR_MI

Method Summary

Modifier and Type	Method	Description
String	getChebi()	The CHEBI accession which identifies the bioactive entity.
String	getSmile()	The Simplified Molecular Input Line Entry System.
String	getStandardInchi()	The standard InChI for this chemical compound.
String	getStandardInchiKey()	The standard InChI Key for this chemical compound It is a shortcut which should point to the first standard Inchi key in the collection of checksums.
void	setChebi(String id)	Sets the CHEBI identifier.
void	setSmile(String smile)	Sets the smile of this small molecule.
void	setStandardInchi(String inchi)	Sets the standard InChI.
void	setStandardInchiKey(String key)	Sets the standard InChI key .

Methods inherited from interface psidev.psi.mi.jami.model.Interactor

getAliases, getAnnotations, getChecksums, getFullName, getIdentifiers, getInteractorType, getOrganism, getPreferredIdentifier, getPreferredName, getShortName, getXrefs, setFullName, setInteractorType, setOrganism, setShortName

Field Detail

BIOACTIVE_ENTITY

static final String BIOACTIVE_ENTITY

Constant BIOACTIVE_ENTITY="bioactive entity"

See Also:

Constant Field Values

BIOACTIVE_ENTITY_MI

static final String BIOACTIVE_ENTITY_MI

Constant BIOACTIVE_ENTITY_MI="MI:1100"

See Also:

Constant Field Values

SMALL_MOLECULE

static final String SMALL_MOLECULE

Constant SMALL_MOLECULE="small molecule"

See Also:

Constant Field Values

SMALL_MOLECULE_MI

static final String SMALL_MOLECULE_MI

Constant SMALL_MOLECULE_MI="MI:0328"

See Also:

Constant Field Values

POLYSACCHARIDE

static final String POLYSACCHARIDE

Constant POLYSACCHARIDE="polysaccharide"

See Also:

Constant Field Values

POLYSACCHARIDE_MI

static final String POLYSACCHARIDE_MI

Constant POLYSACCHARIDE_MI="MI:0904"

See Also:

Constant Field Values

Method Detail

getChebi

String getChebi()

The CHEBI accession which identifies the bioactive entity. It is a shortcut which should point to the first chebi identifier in the collection of identifiers. It can be null Ex: CHEBI:4991

Returns:

The CHEBI accession

setChebi

void setChebi(String id)

Sets the CHEBI identifier. It will remove the old chebi identifier from the collection of identifiers and replace it with the new chebi identifier. If the new chebi identifier is null, all the existing chebi identifiers will be removed from the collection of identifiers

Parameters:

id - : CHEBI identifier

getSmile

String getSmile()

The Simplified Molecular Input Line Entry System. It is a shortcut which should point to the first smile in the collection of checksums. It can be null Ex: OC1C[C@]2(O)CC(O)O[Fe]34(O1)(OC(O)C[C@](O)(CC(O)O3)C(O)O4)OC2O

Returns:

the smile

setSmile

void setSmile(String smile)

Sets the smile of this small molecule. It will remove the old smile from the collection of checksums and replace it with the new smile. If the new smile is null, all the existing smiles will be removed from the collection of checksums

Parameters:

smile - : the smile

getStandardInchiKey

String getStandardInchiKey()

The standard InChI Key for this chemical compound It is a shortcut which should point to the first standard Inchi key in the collection of checksums. It can be null. Ex: ISOHCBXAFHMIHK-UHFFFAOYSA-N

Returns:

the standard InChI key

setStandardInchiKey

void setStandardInchiKey(String key)

Sets the standard InChI key . It will remove the old standard inchi key from the collection of checksums and replace it with the new standard inchi key. If the new standard inchi key is null, all the existing standard inchi keys will be removed from the collection of checksums

Parameters:

key - : the standard inchi key

getStandardInchi

String getStandardInchi()

The standard InChI for this chemical compound. It is a shortcut which should point to the first standard Inchi in the collection of checksums. It can be null. Ex: InChI=1S/2C6H11O7.Fe/c2*7-3(8)1-6(13,5(11)12)2-4(9)10;/h2*3-5,7,9,11,13H,1-2H2;/q2*-3;+6

Returns:

the standard InChI

setStandardInchi

void setStandardInchi(String inchi)

Sets the standard InChI. It will remove the old standard inchi from the collection of checksums and replace it with the new standard inchi. If the new standard is null, all the existing standard inchi will be removed from the collection of checksums

Parameters:

inchi - : the standard InChI