org.helm.notation2.tools

Class SMILES

java.lang.Object

org.helm.notation2.tools.SMILES

public final class SMILES
extends Object

SMILES class to generate SMILES

Author:

hecht

Constructor Summary

Constructors

Constructor and Description
SMILES()

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	containsGenericStructurePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers) method if the any of the given PolymerNotation contains generic structures
static String	convertMolToSMILESWithAtomMapping(String molfile, List<Attachment> attachments) Converts molfile with the given attachments in smiles with atom mapping
static String	getCanonicalSMILESForAll(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to generate canonical smiles for the whole HELMNotation
static String	getCanonicalSMILESForPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to generate canonical smiles for one single PolymerNotation
static String	getSMILESForAll(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to generate smiles for the whole HELMNotation
static String	getSMILESforPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) method to generate smiles for one single PolymerNotation
static String	getUniqueExtendedSMILES(String smiles)

Methods inherited from class java.lang.Object

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

Constructor Detail

SMILES

public SMILES()

Method Detail

getSMILESForAll

public static String getSMILESForAll(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                              throws BuilderMoleculeException,
                                     org.helm.chemtoolkit.CTKException,
                                     ChemistryException

method to generate smiles for the whole HELMNotation

Parameters:

helm2notation - input HELMNotation

Returns:

smiles for the whole HELMNotation

Throws:

BuilderMoleculeException - if the molecule can't be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if the Chemistry Engine can not be initialized

getCanonicalSMILESForAll

public static String getCanonicalSMILESForAll(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                                       throws BuilderMoleculeException,
                                              org.helm.chemtoolkit.CTKSmilesException,
                                              org.helm.chemtoolkit.CTKException,
                                              NotationException,
                                              ChemistryException

method to generate canonical smiles for the whole HELMNotation

Parameters:

helm2notation - input HELMNotation

Returns:

canonical smiles for the whole HELMNotation

Throws:

BuilderMoleculeException - if the molecule can't be built

org.helm.chemtoolkit.CTKSmilesException - if it contains an invalid smiles

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

containsGenericStructurePolymer

public static boolean containsGenericStructurePolymer(List<org.helm.notation2.parser.notation.polymer.PolymerNotation> polymers)
                                               throws HELM2HandledException,
                                                      ChemistryException,
                                                      IOException,
                                                      org.helm.chemtoolkit.CTKException

method if the any of the given PolymerNotation contains generic structures

Parameters:

polymers - list of polymernotations

Returns:

true, if it contains generic structure, false otherwise

Throws:

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

ChemistryException - if chemistry engine can not be initialized

IOException - if monomer can not be read by chemistry

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

getUniqueExtendedSMILES

public static String getUniqueExtendedSMILES(String smiles)

Parameters:

smiles - given smiles

Returns:

unique extended smiles

getCanonicalSMILESForPolymer

public static String getCanonicalSMILESForPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                           throws BuilderMoleculeException,
                                                  HELM2HandledException,
                                                  org.helm.chemtoolkit.CTKSmilesException,
                                                  org.helm.chemtoolkit.CTKException,
                                                  NotationException,
                                                  ChemistryException

method to generate canonical smiles for one single PolymerNotation

Parameters:

polymer - PolymerNotation

Returns:

smiles for the sinlge given PolymerNotation

Throws:

BuilderMoleculeException - if the molecule can't be built

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

org.helm.chemtoolkit.CTKSmilesException - if it contains an invalid smiles

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

getSMILESforPolymer

public static String getSMILESforPolymer(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)
                                  throws BuilderMoleculeException,
                                         HELM2HandledException,
                                         org.helm.chemtoolkit.CTKSmilesException,
                                         org.helm.chemtoolkit.CTKException,
                                         NotationException,
                                         ChemistryException

method to generate smiles for one single PolymerNotation

Parameters:

polymer - PolymerNotation

Returns:

smiles for the sinlge given PolymerNotation

Throws:

BuilderMoleculeException - if the molecule can't be built

HELM2HandledException - if it contains HELM2 specific features, so that it can not be casted to HELM1 Format

org.helm.chemtoolkit.CTKSmilesException - if it contains an invalid smiles

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

convertMolToSMILESWithAtomMapping

public static String convertMolToSMILESWithAtomMapping(String molfile,
                                       List<Attachment> attachments)
                                                throws org.helm.chemtoolkit.CTKException,
                                                       ChemistryException

Converts molfile with the given attachments in smiles with atom mapping

Parameters:

molfile - given molfile

attachments - given attachments of the molfile

Returns:

smiles with atom mapping

Throws:

org.helm.chemtoolkit.CTKException - if the molfile can not be converted to smiles

ChemistryException - if the Chemistry Engine can not be initialized