A B C D F G I M O R S T V

A

AbstractChemistryManipulator - Class in org.helm.chemtoolkit

AbstractChemistryManipulator() - Constructor for class org.helm.chemtoolkit.AbstractChemistryManipulator

AbstractChemistryManipulator.OutputType - Enum in org.helm.chemtoolkit

OutputType image type

AbstractChemistryManipulator.StType - Enum in org.helm.chemtoolkit

StType chemical notation type

AbstractMolecule - Class in org.helm.chemtoolkit

AbstractMolecule() - Constructor for class org.helm.chemtoolkit.AbstractMolecule

AbstractMolecule.Flag - Enum in org.helm.chemtoolkit

addIBase(IChemObjectBase) - Method in class org.helm.chemtoolkit.AbstractMolecule

atoms - Variable in class org.helm.chemtoolkit.AbstractMolecule

Attachment - Class in org.helm.chemtoolkit

Attachment(String, String, String, String) - Constructor for class org.helm.chemtoolkit.Attachment

AttachmentList - Class in org.helm.chemtoolkit

AttachmentList() - Constructor for class org.helm.chemtoolkit.AttachmentList

attachments - Variable in class org.helm.chemtoolkit.AbstractMolecule

B

bindAtoms(IAtomBase, IAtomBase) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

buildManipulator(String) - Static method in class org.helm.chemtoolkit.ManipulatorFactory

C

canonicalize(String) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

returns canonical smiles

changeAtomLabel(int, int) - Method in class org.helm.chemtoolkit.AbstractMolecule

changeIndex(int) - Method in class org.helm.chemtoolkit.Attachment

clearFlags() - Method in class org.helm.chemtoolkit.AbstractMolecule

cloneAttachment() - Method in class org.helm.chemtoolkit.Attachment

cloneList() - Method in class org.helm.chemtoolkit.AttachmentList

cloneMolecule() - Method in class org.helm.chemtoolkit.AbstractMolecule

compare(Object) - Method in class org.helm.chemtoolkit.IAtomBase

compareTo(Attachment) - Method in class org.helm.chemtoolkit.Attachment

convert(String, AbstractChemistryManipulator.StType) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

convert input notation to another

convertExtendedSmiles(String) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

convert extended smiles format to smiles with atom mappings

convertMolecule(AbstractMolecule, AbstractChemistryManipulator.StType) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

produces chemical notation for input molecule

CTKException - Exception in org.helm.chemtoolkit

CTKException(String) - Constructor for exception org.helm.chemtoolkit.CTKException

Constructs a new CTKException with the given message.

CTKException(String, Throwable) - Constructor for exception org.helm.chemtoolkit.CTKException

Constructs a new CTKException with the given message and the Exception as cause.

CTKSmilesException - Exception in org.helm.chemtoolkit

CTKSmilesException(String) - Constructor for exception org.helm.chemtoolkit.CTKSmilesException

Constructs a new ChemToolkitException with the given message.

CTKSmilesException(String, Throwable) - Constructor for exception org.helm.chemtoolkit.CTKSmilesException

Constructs a new CTKSmilesException with the given message and the Exception as cause.

D

dearomatize() - Method in class org.helm.chemtoolkit.AbstractMolecule

F

flag - Variable in class org.helm.chemtoolkit.IAtomBase

G

generateCoordinates(int) - Method in class org.helm.chemtoolkit.AbstractMolecule

get(int) - Method in class org.helm.chemtoolkit.AttachmentList

getAttachments() - Method in class org.helm.chemtoolkit.AbstractMolecule

getCurrentIndex() - Method in class org.helm.chemtoolkit.Attachment

getExactMass() - Method in class org.helm.chemtoolkit.MoleculeInfo

getExtension(String) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

getFlag() - Method in class org.helm.chemtoolkit.IAtomBase

getIAtno() - Method in class org.helm.chemtoolkit.IAtomBase

getIAtom1() - Method in interface org.helm.chemtoolkit.IBondBase

getIAtom2() - Method in interface org.helm.chemtoolkit.IBondBase

getIAtomArray() - Method in class org.helm.chemtoolkit.AbstractMolecule

getIBond(int) - Method in class org.helm.chemtoolkit.IAtomBase

getIBondArray() - Method in class org.helm.chemtoolkit.AbstractMolecule

getIBondCount() - Method in class org.helm.chemtoolkit.IAtomBase

getId() - Method in class org.helm.chemtoolkit.Attachment

getIdFromLabel(String) - Static method in class org.helm.chemtoolkit.AbstractMolecule

getLabel() - Method in class org.helm.chemtoolkit.Attachment

getMolAtom() - Method in class org.helm.chemtoolkit.IAtomBase

getMolecularFormula() - Method in class org.helm.chemtoolkit.MoleculeInfo

getMolecularWeight() - Method in class org.helm.chemtoolkit.MoleculeInfo

getMolecule(String, AttachmentList) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

returns a molecule i)nstance of AbstractMolecule

getMolecule() - Method in class org.helm.chemtoolkit.AbstractMolecule

getMoleculeInfo(AbstractMolecule) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

returns molecule info like molecular formula,exact mass and molecular weight

getName() - Method in class org.helm.chemtoolkit.Attachment

getNeighborAtom(IAtomBase) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

getRgroup() - Method in class org.helm.chemtoolkit.IAtomBase

getRGroupAtom(int, boolean) - Method in class org.helm.chemtoolkit.AbstractMolecule

getRgroups() - Method in class org.helm.chemtoolkit.AbstractMolecule

getRGroupsFromExtendedSmiles(String) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

getSmiles() - Method in class org.helm.chemtoolkit.Attachment

getStereoElement() - Method in interface org.helm.chemtoolkit.IBondBase

getStereoElement() - Method in interface org.helm.chemtoolkit.IStereoElementBase

getStereoInformation(AbstractMolecule, IAtomBase, IAtomBase, IAtomBase) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

getType() - Method in interface org.helm.chemtoolkit.IBondBase

I

IAtomBase - Class in org.helm.chemtoolkit

IAtomBase() - Constructor for class org.helm.chemtoolkit.IAtomBase

IBondBase - Interface in org.helm.chemtoolkit

IChemObjectBase - Interface in org.helm.chemtoolkit

isSingleStereo(IAtomBase) - Method in class org.helm.chemtoolkit.AbstractMolecule

check a given atom connections

IStereoElementBase - Interface in org.helm.chemtoolkit

IStereoElement The container for a stereo element in the molecule.

M

ManipulatorFactory - Class in org.helm.chemtoolkit

ManipulatorFactory TODO comment me

ManipulatorFactory() - Constructor for class org.helm.chemtoolkit.ManipulatorFactory

merge(AbstractMolecule, IAtomBase, AbstractMolecule, IAtomBase) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

merges second molecule to first using given rGroups

mergeAttachments(AbstractMolecule, AbstractMolecule) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

MoleculeInfo - Class in org.helm.chemtoolkit

MoleculeInfo() - Constructor for class org.helm.chemtoolkit.MoleculeInfo

MoleculeInfo(double, String, double) - Constructor for class org.helm.chemtoolkit.MoleculeInfo

O

org.helm.chemtoolkit - package org.helm.chemtoolkit

R

removeAttachment(IAtomBase) - Method in class org.helm.chemtoolkit.AbstractMolecule

removes a given attachment from molecule

removeIBase(IChemObjectBase) - Method in class org.helm.chemtoolkit.AbstractMolecule

removeINode(IAtomBase) - Method in class org.helm.chemtoolkit.AbstractMolecule

renderMol(String, AbstractChemistryManipulator.OutputType, int, int, int) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

renders a image of given molecule

renderSequence(String, AbstractChemistryManipulator.OutputType, int, int, int) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

renders a image of molecule

S

setAttachments(AttachmentList) - Method in class org.helm.chemtoolkit.AbstractMolecule

setExactMass(double) - Method in class org.helm.chemtoolkit.MoleculeInfo

setFlag(AbstractMolecule.Flag) - Method in class org.helm.chemtoolkit.IAtomBase

setId(String) - Method in class org.helm.chemtoolkit.Attachment

setLabel(String) - Method in class org.helm.chemtoolkit.Attachment

setMolecularFormula(String) - Method in class org.helm.chemtoolkit.MoleculeInfo

setMolecularWeight(double) - Method in class org.helm.chemtoolkit.MoleculeInfo

setName(String) - Method in class org.helm.chemtoolkit.Attachment

setRgroup(int) - Method in class org.helm.chemtoolkit.IAtomBase

setSmiles(String) - Method in class org.helm.chemtoolkit.Attachment

setStereoInformation(AbstractMolecule, IAtomBase, AbstractMolecule, IAtomBase, IAtomBase, IAtomBase) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

recycles and set stereo information on firstContaner

SMILES_EXTENSION_SEPARATOR_REGEX - Static variable in class org.helm.chemtoolkit.AbstractChemistryManipulator

T

toString() - Method in enum org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType

V

validateSMILES(String) - Method in class org.helm.chemtoolkit.AbstractChemistryManipulator

valueOf(String) - Static method in enum org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.helm.chemtoolkit.AbstractChemistryManipulator.StType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.helm.chemtoolkit.AbstractMolecule.Flag

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.helm.chemtoolkit.AbstractChemistryManipulator.OutputType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.helm.chemtoolkit.AbstractChemistryManipulator.StType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.helm.chemtoolkit.AbstractMolecule.Flag

Returns an array containing the constants of this enum type, in the order they are declared.

A B C D F G I M O R S T V