com.im.df.api.chem
Class MarvinStructure

java.lang.Object
  com.im.df.api.chem.Structure<Molecule>
      com.im.df.api.chem.MarvinStructure

public class MarvinStructure
extends Structure<Molecule>

A representation of a molecular structure that uses the ChemAxon Molecule as its native format.

Field Summary

static String	STANDARDIZED_2D
static String	STANDARDIZED_NATIVE

Constructor Summary

MarvinStructure()
Creates a new instance of MarvinStructure with an empty Molecule

MarvinStructure(Molecule mol)
Create a new instance with a molecule specified as a Marvin Molecule instance.

MarvinStructure(String mol)
Create a new instance with the structure specified as a String.

MarvinStructure(String molecule, boolean validate)
Create, but optionally check that the molecule is a valid.

Method Summary

String	asSimpleText(DFOperator operator) Format the structure as appropriate in smiles or smarts fromat, according to the search orerator (if available).
boolean	equals(Object obj)
Molecule[]	getAllMolecules()
Molecule[]	getAllNative2D()
Molecule	getNative() Get the molecule in its native format Never returns null.
Molecule	getNative2D() Get the Molecule in 2 dimensional representation
int	hashCode()
Exception	parseExceptionException()
String	toString()

Methods inherited from class com.im.df.api.chem.Structure

getEncodedMol, retrieveMolecule, retrieveMolecules, setEncodedMol, storeMolecule, storeMolecules

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

STANDARDIZED_2D

public static final String STANDARDIZED_2D

See Also:

Constant Field Values

STANDARDIZED_NATIVE

public static final String STANDARDIZED_NATIVE

See Also:

Constant Field Values

Constructor Detail

MarvinStructure

public MarvinStructure()

Creates a new instance of MarvinStructure with an empty Molecule

MarvinStructure

public MarvinStructure(String mol)

Create a new instance with the structure specified as a String. No validation of the format is performed, and if an invalid structure is used exception will occur later when the molecule needs to be converted. Only use this approach if you are sure that the structures are valid. Use the 2 argument constructor is you want to perform validation.

Parameters:

mol - The molecule, in one of the formats that Marvin recognises.

MarvinStructure

public MarvinStructure(Molecule mol)

Create a new instance with a molecule specified as a Marvin Molecule instance. This is the internal representation that is used by MarvinStructure

Parameters:

The - Molecule instance

MarvinStructure

public MarvinStructure(String molecule,
                       boolean validate)

Create, but optionally check that the molecule is a valid. Throws an IllegalArgumentException if the string can't be converted into a Marvin Molecule object using MolImporter

Parameters:

molecule - The structure

validate - Whether to validate the structure. If so the native form of the molecule is created immediately.

Throws:

IllegalArgumentException - if structure is invalid

Method Detail

toString

public String toString()

Overrides:

toString in class Structure<Molecule>

getNative

public Molecule getNative()

Description copied from class: Structure

Get the molecule in its native format Never returns null.

Specified by:

getNative in class Structure<Molecule>

Returns:

The source Molecule. this is not a clone, so do not edit this unless you want your changes to be permanent. Clone it instead.

getAllMolecules

public Molecule[] getAllMolecules()

parseExceptionException

public Exception parseExceptionException()

Returns:

The exception if parsing of melecule failed

asSimpleText

public String asSimpleText(DFOperator operator)

Description copied from class: Structure

Format the structure as appropriate in smiles or smarts fromat, according to the search orerator (if available). ChemAxon extended smiles/smarts will be used if it is not possible to describe the structure in Daylight smiles/smarts.

The decission on smiles vs. smarts is taken based on the operator. For perfect, similarity and superstructure type smiles is used, for other types smarts is used. If operator is not specified then smarts format is returned.

To convert Molecule you can use also these two methods: ChemUtils.convertToSmilesRepresentation(chemaxon.struc.Molecule) and ChemUtils.convertToSmartsRepresentation(chemaxon.struc.Molecule).

Specified by:

asSimpleText in class Structure<Molecule>

Parameters:

operator - The search operator if it's available. It's allowed to put null here

Returns:

The smiles/smarts string

getNative2D

public Molecule getNative2D()

Get the Molecule in 2 dimensional representation

Specified by:

getNative2D in class Structure<Molecule>

Returns:

The Molecule in 2 dimensional representation. If the original is in 3D or less than 2D then it will be converted to 2D. If its already in 2D then a copy of the molecule is returned to prevent unwanted modification to the original.

getAllNative2D

public Molecule[] getAllNative2D()

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object