com.im.df.api.chem
Class ChemUtils

java.lang.Object
  com.im.df.api.chem.ChemUtils

public class ChemUtils
extends Object

Utilities related to chemical classes. Currently support to search of the core when molecule search is executed. UI can color the molecule core using different color.

Nested Class Summary

static class

ChemUtils.MolCoreDescriptor

Constructor Summary

ChemUtils()

Method Summary

static String	convertToSmartsRepresentation(Molecule m) Generates the simplest smarts representation of the molecule.
static String	convertToSmilesRepresentation(Molecule m) Generates the simplest smiles representation of the molecule.
static String	convertToStringRepresentation(Molecule m) Generates the simplest smiles representation of the molecule.
static JChemSearchOptions	createJChemSearchOptions(DFOperator op, JChemEntityCapability jchemCapability) Temporary method for creating JChemSearchOptions instances for the specific operator and setting some default values
static ChemUtils.MolCoreDescriptor	findMolCoreDescriptor(DFTermExpression expression, DFField field)
static int	genSearchType(DFOperator op) Temporary method finding appropriate JChemSearch search type constant for the given operator.
static Molecule	getLastQueryEditedStructure()
static Molecule	getMoleculeForQuery(Molecule previousMol)
static void	setLastQueryEditedStructure(Molecule mol)
static void	updateJChemSearchOptions(JChemSearchOptions jchemOpts, DFOperator op, JChemEntityCapability jchemCapability) Temporary method for creating JChemSearchOptions instances for the specific operator and setting some default values

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ChemUtils

public ChemUtils()

Method Detail

setLastQueryEditedStructure

public static void setLastQueryEditedStructure(Molecule mol)

getLastQueryEditedStructure

public static Molecule getLastQueryEditedStructure()

getMoleculeForQuery

public static Molecule getMoleculeForQuery(Molecule previousMol)

findMolCoreDescriptor

public static ChemUtils.MolCoreDescriptor findMolCoreDescriptor(DFTermExpression expression,
                                                                DFField field)

genSearchType

public static int genSearchType(DFOperator op)

Temporary method finding appropriate JChemSearch search type constant for the given operator.

Parameters:

op - Operator must be a structure operator

Returns:

The one of JChemSearch search type constant

createJChemSearchOptions

public static JChemSearchOptions createJChemSearchOptions(DFOperator op,
                                                          JChemEntityCapability jchemCapability)

Temporary method for creating JChemSearchOptions instances for the specific operator and setting some default values

Parameters:

op - The operator is filled inside JChemSearchOptions (this property must be set first and can't be changed)

jchemCapability - The JChem capability which determines some of the default settings

Returns:

The new JChemSearchOptions instance

updateJChemSearchOptions

public static void updateJChemSearchOptions(JChemSearchOptions jchemOpts,
                                            DFOperator op,
                                            JChemEntityCapability jchemCapability)

Temporary method for creating JChemSearchOptions instances for the specific operator and setting some default values

Parameters:

op - The operator is filled inside JChemSearchOptions (this property must be set first and can't be changed)

jchemCapability - The JChem capability which determines some of the default settings

convertToSmilesRepresentation

public static String convertToSmilesRepresentation(Molecule m)

Generates the simplest smiles representation of the molecule. It tries in this order: Daylight smiles, Chemaxon Extended smiles, Daylight smarts, Chemaxon Extended smarts.

Parameters:

m - The molecule

Returns:

The first smiles variant that is supported

Throws:

IllegalArgumentException - If none of the smiles variants are supported. Your code should expect this to happen on occasion.

convertToSmartsRepresentation

public static String convertToSmartsRepresentation(Molecule m)

Generates the simplest smarts representation of the molecule. It tries in this order: Daylight smarts, Chemaxon Extended smarts.

Parameters:

m - The molecule

Returns:

The first smarts variant that is supported

Throws:

IllegalArgumentException - If none of the smiles variants are supported. Your code should expect this to happen on occasion.

convertToStringRepresentation

public static String convertToStringRepresentation(Molecule m)

Generates the simplest smiles representation of the molecule. It tries in this order: Daylight smiles, Chemaxon Extended smiles, Daylight smarts, Chemaxon Extended smarts.

Parameters:

m - The molecule

Returns:

The first smiles variant that is supported

Throws:

IllegalArgumentException - If none of the smiles variants are supported. Your code should expect this to happen on occasion.