Package com.im.df.api.chem

Class ChemUtils

java.lang.Object

com.im.df.api.chem.ChemUtils

public final class ChemUtils
extends java.lang.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.

Author:

Petr Hamernik

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ChemUtils.MolCoreDescriptor

Method Summary

Modifier and Type	Method	Description
static java.lang.String	convertToSmartsRepresentation(chemaxon.struc.Molecule m)	Generates the simplest smarts representation of the molecule.
static java.lang.String	convertToSmilesRepresentation(chemaxon.struc.Molecule m)	Generates the simplest smiles representation of the molecule.
static java.lang.String	convertToStringRepresentation(chemaxon.struc.Molecule m)	Generates the simplest smiles representation of the molecule.
static java.lang.String	convertToStringRepresentation(chemaxon.struc.Molecule m, java.lang.String... formats)	Converts given molecule into a format.
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 chemaxon.standardizer.Standardizer	getStandardizer(JChemEntityCapability cap)	Gets standardizer from JChemEntityCapability.
static chemaxon.standardizer.Standardizer	getStandardizer(DFEntity entity)	Gets standardizer from entity based on JChemEntityCapability.
static com.google.common.base.Optional<DFField>	getStructureField(DFEntity entity)
static void	setDissimilarityScore(chemaxon.struc.Molecule target, float dissimilarity)	Sets dissimilarity score property to target molecule.
static DFOperator	toStructureOperator(int jchemSearchType)	Converts JChemSearch search type to structure DFOperator.

Methods inherited from class java.lang.Object

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

Method Detail

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

toStructureOperator

public static DFOperator toStructureOperator(int jchemSearchType)

Converts JChemSearch search type to structure DFOperator. It is an inverse method to genSearchType.

Parameters:

jchemSearchType - JChemSearch search type constant

Returns:

structure DFOperator

convertToSmilesRepresentation

public static java.lang.String convertToSmilesRepresentation(chemaxon.struc.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:

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

convertToSmartsRepresentation

public static java.lang.String convertToSmartsRepresentation(chemaxon.struc.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:

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

convertToStringRepresentation

public static java.lang.String convertToStringRepresentation(chemaxon.struc.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:

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

convertToStringRepresentation

public static java.lang.String convertToStringRepresentation(chemaxon.struc.Molecule m,
                                                             java.lang.String... formats)

Converts given molecule into a format. Tries format by format in given order.

Parameters:

m - the molecule

formats - export formats like "smiles", "smarts", "mrv", ...

Returns:

the first succesfull result

Throws:

java.lang.IllegalArgumentException - if none of the given format is supported. Your code should expect this to happen on occasion.

Since:

18.15.0

getStructureField

public static com.google.common.base.Optional<DFField> getStructureField(DFEntity entity)

Parameters:

entity - JChemBase entity

Returns:

structure field

getStandardizer

public static chemaxon.standardizer.Standardizer getStandardizer(DFEntity entity)

Gets standardizer from entity based on JChemEntityCapability.

Parameters:

entity - structure entity

Returns:

standardizer or null if entity doesn't have JChemEntityCapability

getStandardizer

public static chemaxon.standardizer.Standardizer getStandardizer(JChemEntityCapability cap)

Gets standardizer from JChemEntityCapability.

Parameters:

cap - JChemEntityCapability, cannot be null

Returns:

standardizer, never null

setDissimilarityScore

public static void setDissimilarityScore(chemaxon.struc.Molecule target,
                                         float dissimilarity)

Sets dissimilarity score property to target molecule. For example HitDisplayTool is able to pick it up from there.

Parameters:

target - the molecule which will obtain the new property

dissimilarity - new dissimilarity score