Uses of Package
org.openscience.cdk.interfaces
Packages that use org.openscience.cdk.interfaces
Package
Description
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdkClassDescriptionA AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Represents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for atom types.An enum for the different hybridization states.A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.Implements the concept of a covalent bond between two or more atoms.Bond display style, controlling how bonds appear in a 2D depiction.A list of permissible bond orders.Enumeration of possible stereo types of two-atom bonds.The base class for all data objects in this CDK.An
IChemObjectcontaining a number of ChemSequences.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.A helper class to instantiate aICDKObjectinstance for a specific implementation.Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.A sequence of ChemModels, which can, for example, be used to store the course of a reaction.Class representing a molecular crystal.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Class to represent an IPseudoAtom which embeds an IAtomContainer.Used to store and retrieve data of a particular isotope.A LonePair is an orbital primarily located with one Atom, containing two electrons.Represents a mapping of two atoms.A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.Subclass of Molecule to store Polymer specific attributes that a Polymer has.Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Represents the idea of a chemical reaction.Permissible reaction directions.Classes that implement this interface of a scheme.A set of reactions, for example those taking part in a reaction.Class representing a ring structure in a molecule.Maintains a set of Ring objects.A Single Electron is an orbital which is occupied by only one electron.Representation of stereochemical configuration.A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.A chemical substance that consists of one or more chemical structures. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.aromaticityClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.Class representing a ring structure in a molecule.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.atomtypeClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for atom types.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Maintains a set of Ring objects. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.chargesClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.configClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for atom types.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Implements the idea of an element in the periodic table.Used to store and retrieve data of a particular isotope.Class defining a molecular formula object. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.config.atomtypesClassDescriptionThe base class for atom types.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.config.isotopesClassDescriptionA helper class to instantiate a
ICDKObjectinstance for a specific implementation.Used to store and retrieve data of a particular isotope. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.debugClassDescriptionClass defining an adduct object in a MolecularFormula.A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Represents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for atom types.An enum for the different hybridization states.A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.Implements the concept of a covalent bond between two or more atoms.A list of permissible bond orders.Enumeration of possible stereo types of two-atom bonds.The base class for all data objects in this CDK.An
IChemObjectcontaining a number of ChemSequences.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.A helper class to instantiate aICDKObjectinstance for a specific implementation.Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.A sequence of ChemModels, which can, for example, be used to store the course of a reaction.Class representing a molecular crystal.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Class to represent an IPseudoAtom which embeds an IAtomContainer.Used to store and retrieve data of a particular isotope.A LonePair is an orbital primarily located with one Atom, containing two electrons.Represents a mapping of two atoms.Class defining a molecular formula object.Class defining a molecular formula object.A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.Represents the idea of an protein monomer as found in PDB files.A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.Represents the idea of an chemical structure.Subclass of Molecule to store Polymer specific attributes that a Polymer has.Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Represents the idea of a chemical reaction.Permissible reaction directions.Classes that implement this interface of a scheme.A set of reactions, for example those taking part in a reaction.Class representing a ring structure in a molecule.Maintains a set of Ring objects.A Single Electron is an orbital which is occupied by only one electron.Representation of stereochemical configuration.A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.A chemical substance that consists of one or more chemical structures. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.depictClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for all chemical objects in this cdk.Represents the idea of a chemical reaction.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.dict
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.eventClassDescriptionEvent fired by CDK IChemObject classes to their registered listeners in case something changed within them.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.fingerprintClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Maintains a set of Ring objects. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.fingerprint.modelClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.forcefield.mmffClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.formulaClassDescriptionClass defining an adduct object in a MolecularFormula.The base class for all data objects in this CDK.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Used to store and retrieve data of a particular isotope.Class defining a molecular formula object.Class defining a molecular formula object. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.formula.rules
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.fragmentClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.geometryClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.Class representing a molecular crystal.Represents the idea of a chemical reaction.Maintains a set of Ring objects.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.geometry.alignmentClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.geometry.cipClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Stereochemistry specification for double bond stereochemistry.Stereochemistry specification for quadrivalent atoms.Enumeration that defines the two possible chiralities for this stereochemistry type.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.geometry.surfaceClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.geometry.volumeClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.graphClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.Implements the concept of a covalent bond between two or more atoms.Maintains a set of Ring objects.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.graph.invariantClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.graph.matrixClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.graph.rebondClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.groupClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.hashClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.hash.stereoClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.inchiClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.interfacesClassDescriptionA AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Represents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for atom types.An enum for the different hybridization states.A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.Implements the concept of a covalent bond between two or more atoms.Bond display style, controlling how bonds appear in a 2D depiction.A list of permissible bond orders.Enumeration of possible stereo types of two-atom bonds.The base class for all data objects in this CDK.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.A sequence of ChemModels, which can, for example, be used to store the course of a reaction.Class representing a molecular crystal.Stereochemistry specification for double bond stereochemistry.Enumeration that defines the two possible values for this stereochemistry type.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Used to store and retrieve data of a particular isotope.A LonePair is an orbital primarily located with one Atom, containing two electrons.Represents a mapping of two atoms.Class defining a molecular formula object.Class defining a molecular formula object.A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.Represents the idea of an protein monomer as found in PDB files.A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.Represents the idea of an chemical structure.Subclass of Molecule to store Polymer specific attributes that a Polymer has.Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Represents the idea of a chemical reaction.Permissible reaction directions.Classes that implement this interface of a scheme.A set of reactions, for example those taking part in a reaction.Class representing a ring structure in a molecule.Maintains a set of Ring objects.A Single Electron is an orbital which is occupied by only one electron.Representation of stereochemical configuration.A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.Stereochemistry specification for quadrivalent atoms.Enumeration that defines the two possible chiralities for this stereochemistry type. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.ioClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Class representing a molecular crystal. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.cmlClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.Implements the concept of a covalent bond between two or more atoms.An
IChemObjectcontaining a number of ChemSequences.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.A sequence of ChemModels, which can, for example, be used to store the course of a reaction.A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.Represents the idea of a chemical reaction.A set of reactions, for example those taking part in a reaction.A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.inchiClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.iteratorClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.iterator.eventClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.programClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for all chemical objects in this cdk.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.pubchemxmlClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.randomClassDescriptionThe base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.rdf
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.io.setting
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.isomorphismClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.The base class for all chemical objects in this cdk.Represents the idea of a chemical reaction.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.isomorphism.matchersClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for atom types.An enum for the different hybridization states.Implements the concept of a covalent bond between two or more atoms.Bond display style, controlling how bonds appear in a 2D depiction.A list of permissible bond orders.Enumeration of possible stereo types of two-atom bonds.The base class for all data objects in this CDK.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Used to store and retrieve data of a particular isotope.A LonePair is an orbital primarily located with one Atom, containing two electrons.A Single Electron is an orbital which is occupied by only one electron.Representation of stereochemical configuration. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.isomorphism.matchers.smartsClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for atom types.Implements the concept of a covalent bond between two or more atoms.A list of permissible bond orders.The base class for all data objects in this CDK.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Used to store and retrieve data of a particular isotope. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.iupac.parserClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.layoutClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.Implements the concept of a covalent bond between two or more atoms.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Represents the idea of a chemical reaction.Class representing a ring structure in a molecule.Maintains a set of Ring objects. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.libio.cmlClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.Implements the concept of a covalent bond between two or more atoms.An
IChemObjectcontaining a number of ChemSequences.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.A sequence of ChemModels, which can, for example, be used to store the course of a reaction.Class representing a molecular crystal.A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.Represents the idea of a chemical reaction.Classes that implement this interface of a scheme.A set of reactions, for example those taking part in a reaction. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.libio.jenaClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A list of permissible bond orders.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.libio.mdClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for all data objects in this CDK.The base class for all chemical objects in this cdk.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.math.qm
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.modeling.builder3dClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for atom types.Implements the concept of a covalent bond between two or more atoms.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Maintains a set of Ring objects. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.normalizeClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.pharmacophoreClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for atom types.Implements the concept of a covalent bond between two or more atoms.The base class for all data objects in this CDK.The base class for all chemical objects in this cdk.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Used to store and retrieve data of a particular isotope.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.proteinClassDescriptionA BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.protein.dataClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.The base class for atom types.A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.The base class for all data objects in this CDK.The base class for all chemical objects in this cdk.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.Implements the idea of an element in the periodic table.Used to store and retrieve data of a particular isotope.A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.Represents the idea of an protein monomer as found in PDB files.A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.Represents the idea of an chemical structure.Subclass of Molecule to store Polymer specific attributes that a Polymer has.A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.qsarClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.qsar.descriptors.atomicClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Maintains a set of Ring objects.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.qsar.descriptors.atompairClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.qsar.descriptors.bondClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.qsar.descriptors.molecularClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.qsar.descriptors.proteinClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.qsar.descriptors.substanceClassDescriptionA helper class to instantiate a
ICDKObjectinstance for a specific implementation.A chemical substance that consists of one or more chemical structures. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.reactionClassDescriptionRepresents the idea of an chemical atom.A set of AtomContainers.The base class for all data objects in this CDK.The base class for all chemical objects in this cdk.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.Represents the idea of a chemical reaction.A set of reactions, for example those taking part in a reaction.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.reaction.mechanismClassDescriptionRepresents the idea of an chemical atom.A set of AtomContainers.Represents the idea of a chemical reaction.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.reaction.typeClassDescriptionA set of AtomContainers.A set of reactions, for example those taking part in a reaction.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.rendererClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.Implements the concept of a covalent bond between two or more atoms.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.Represents the idea of a chemical reaction.A set of reactions, for example those taking part in a reaction.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.renderer.color
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.renderer.elementsClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.renderer.generatorsClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.A list of permissible bond orders.The base class for all chemical objects in this cdk.Represents the idea of a chemical reaction.Class representing a ring structure in a molecule.Maintains a set of Ring objects.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.renderer.generators.standardClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.renderer.selectionClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.ringsearchClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.Maintains a set of Ring objects.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.sgroup
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.signatureClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.silentClassDescriptionClass defining an adduct object in a MolecularFormula.A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Represents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for atom types.An enum for the different hybridization states.A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.Implements the concept of a covalent bond between two or more atoms.Bond display style, controlling how bonds appear in a 2D depiction.A list of permissible bond orders.Enumeration of possible stereo types of two-atom bonds.The base class for all data objects in this CDK.An
IChemObjectcontaining a number of ChemSequences.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.A helper class to instantiate aICDKObjectinstance for a specific implementation.Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.A sequence of ChemModels, which can, for example, be used to store the course of a reaction.Class representing a molecular crystal.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Class to represent an IPseudoAtom which embeds an IAtomContainer.Used to store and retrieve data of a particular isotope.A LonePair is an orbital primarily located with one Atom, containing two electrons.Represents a mapping of two atoms.Class defining a molecular formula object.Class defining a molecular formula object.A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.Represents the idea of an protein monomer as found in PDB files.A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.Represents the idea of an chemical structure.Subclass of Molecule to store Polymer specific attributes that a Polymer has.Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.Represents the idea of a chemical reaction.Permissible reaction directions.Classes that implement this interface of a scheme.A set of reactions, for example those taking part in a reaction.Class representing a ring structure in a molecule.Maintains a set of Ring objects.A Single Electron is an orbital which is occupied by only one electron.Representation of stereochemical configuration.A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.A chemical substance that consists of one or more chemical structures. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.similarityClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smartsClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smilesClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Represents the idea of a chemical reaction. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smiles.smartsClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smiles.smarts.parserClassDescriptionA helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsdClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.matchersClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.mcgregorClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.mcsplusClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.rgraphClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.singleClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.vflibClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.vflib.builderClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.vflib.interfacesClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.vflib.mapClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.algorithm.vflib.queryClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.filtersClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.A list of permissible bond orders.Enumeration of possible stereo types of two-atom bonds.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.helperClassDescriptionImplements the concept of a covalent bond between two or more atoms.A list of permissible bond orders.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.interfacesClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.labellingClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.Represents the idea of a chemical reaction.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.ringClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Maintains a set of Ring objects.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.smsd.toolsClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.A list of permissible bond orders.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.stereoClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.Implements the concept of a covalent bond between two or more atoms.The base class for all data objects in this CDK.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Stereochemistry specification for double bond stereochemistry.Enumeration that defines the two possible values for this stereochemistry type.Representation of stereochemical configuration.Stereochemistry specification for quadrivalent atoms.Enumeration that defines the two possible chiralities for this stereochemistry type. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.structgenClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.structgen.maygenClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.structgen.stochasticClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.structgen.stochastic.operatorClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.tautomersClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.templatesClassDescriptionA AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.templates.saturatedhydrocarbonsClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.A helper class to instantiate a
ICDKObjectinstance for a specific implementation. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.toolsClassDescriptionA AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Represents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for atom types.A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.Implements the concept of a covalent bond between two or more atoms.A list of permissible bond orders.The base class for all chemical objects in this cdk.A helper class to instantiate a
ICDKObjectinstance for a specific implementation.Class representing a ring structure in a molecule.Maintains a set of Ring objects.A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.tools.diff
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.tools.diff.treeClassDescriptionAn enum for the different hybridization states.A list of permissible bond orders.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.tools.featuresClassDescriptionBase class for all chemical objects that maintain a list of Atoms and ElectronContainers.
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Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.tools.manipulatorClassDescriptionA AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.Represents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for atom types.Implements the concept of a covalent bond between two or more atoms.A list of permissible bond orders.An
IChemObjectcontaining a number of ChemSequences.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.A helper class to instantiate aICDKObjectinstance for a specific implementation.A sequence of ChemModels, which can, for example, be used to store the course of a reaction.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Used to store and retrieve data of a particular isotope.Class defining a molecular formula object.Class defining a molecular formula object.Represents the idea of a chemical reaction.Classes that implement this interface of a scheme.A set of reactions, for example those taking part in a reaction.Class representing a ring structure in a molecule.Maintains a set of Ring objects. -
Classes in org.openscience.cdk.interfaces used by org.openscience.cdk.validateClassDescriptionRepresents the idea of an chemical atom.Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.A set of AtomContainers.The base class for atom types.Implements the concept of a covalent bond between two or more atoms.An
IChemObjectcontaining a number of ChemSequences.An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.The base class for all chemical objects in this cdk.A sequence of ChemModels, which can, for example, be used to store the course of a reaction.Class representing a molecular crystal.Base class for entities containing electrons, like bonds, orbitals, lone-pairs.Implements the idea of an element in the periodic table.Used to store and retrieve data of a particular isotope.Represents the idea of a chemical reaction.A set of reactions, for example those taking part in a reaction.