Name | Description | Type | Package | Framework |
AdductFormula | Class defining an adduct object in a MolecularFormula. | Class | org.openscience.cdk.silent | CDK |
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AminoAcid | A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom. | Class | org.openscience.cdk.silent | CDK |
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Atom | Represents the idea of an chemical atom. | Class | org.openscience.cdk.silent | CDK |
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AtomContainer | Base class for all chemical objects that maintain a list of Atoms and ElectronContainers. | Class | org.openscience.cdk.silent | CDK |
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AtomContainerSet | A set of AtomContainers. | Class | org.openscience.cdk.silent | CDK |
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AtomParity | Represents the concept of an atom parity identifying the stereochemistry around an atom, given four neighbouring atoms. | Class | org.openscience.cdk.silent | CDK |
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AtomType | The base class for atom types. | Class | org.openscience.cdk.silent | CDK |
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BioPolymer | A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers. | Class | org.openscience.cdk.silent | CDK |
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Bond | considered to be a number of electrons connecting two or more of atoms. | Class | org.openscience.cdk.silent | CDK |
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ChemFile | A Object containing a number of ChemSequences. | Class | org.openscience.cdk.silent | CDK |
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ChemModel | An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, | Class | org.openscience.cdk.silent | CDK |
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ChemObject | The base class for all chemical objects in this cdk. | Class | org.openscience.cdk.silent | CDK |
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ChemSequence | A sequence of ChemModels, which can, for example, be used to store the course of a reaction. | Class | org.openscience.cdk.silent | CDK |
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Crystal | Class representing a molecular crystal. | Class | org.openscience.cdk.silent | CDK |
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ElectronContainer | Base class for entities containing electrons, like bonds, orbitals, lone-pairs. | Class | org.openscience.cdk.silent | CDK |
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Element | Use the IsotopeFactory to get a ready-to-use elements by symbol or atomic number: | Class | org.openscience.cdk.silent | CDK |
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FragmentAtom | Class to represent an IPseudoAtom which embeds an IAtomContainer. | Class | org.openscience.cdk.silent | CDK |
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Isotope | Used to store and retrieve data of a particular isotope. | Class | org.openscience.cdk.silent | CDK |
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LonePair | A LonePair is an orbital primarily located with one Atom, containingSee Also:Serialized FormKeywords:orbital, lone-pair | Class | org.openscience.cdk.silent | CDK |
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Mapping | A Mapping is an relation between two ChemObjects in a non-chemical entity. | Class | org.openscience.cdk.silent | CDK |
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MolecularFormula | Class defining a molecular formula object. | Class | org.openscience.cdk.silent | CDK |
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MolecularFormulaSet | Class defining an set object of MolecularFormulas. | Class | org.openscience.cdk.silent | CDK |
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Molecule | Represents the concept of a chemical molecule, an object composed of atoms connected by bonds. | Class | org.openscience.cdk.silent | CDK |
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MoleculeSet | A set of molecules, for example those taking part in a reaction. | Class | org.openscience.cdk.silent | CDK |
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Monomer | A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms. | Class | org.openscience.cdk.silent | CDK |
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PDBAtom | Represents the idea of an atom as used in PDB files. | Class | org.openscience.cdk.silent | CDK |
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PDBMonomer | Represents the idea of an monomer as used in PDB files. | Class | org.openscience.cdk.silent | CDK |
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PDBPolymer | An entry in the PDB database. | Class | org.openscience.cdk.silent | CDK |
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PDBStructure | Holder for secundary protein structure elements. | Class | org.openscience.cdk.silent | CDK |
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Polymer | Subclass of Molecule to store Polymer specific attributes that a Polymer has. | Class | org.openscience.cdk.silent | CDK |
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PseudoAtom | Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc. | Class | org.openscience.cdk.silent | CDK |
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Reaction | Represents the idea of a chemical reaction. | Class | org.openscience.cdk.silent | CDK |
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ReactionScheme | Classes that extends the definition of reaction to a scheme. | Class | org.openscience.cdk.silent | CDK |
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ReactionSet | A set of reactions, for example those taking part in a reaction. | Class | org.openscience.cdk.silent | CDK |
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Ring | Class representing a ring structure in a molecule. | Class | org.openscience.cdk.silent | CDK |
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RingSet | Maintains a set of Ring objects. | Class | org.openscience.cdk.silent | CDK |
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SilentChemObjectBuilder | | Class | org.openscience.cdk.silent | CDK |
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SingleElectron | A Single Electron is an orbital which is occupied by only one electron. | Class | org.openscience.cdk.silent | CDK |
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Strand | A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms. | Class | org.openscience.cdk.silent | CDK |