Package org.openscience.cdk

package org.openscience.cdk
  • Class
    A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.
    Base class for storing interactions like hydrogen bonds and ionic interactions.
    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.
    An atom ref, references a CDK IAtom indirectly.
    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 bond ref, references a CDK IBond indirectly.
    Helper class to provide general information about this CDK library.
    An interface providing predefined values for a number of constants used throughout the CDK.
    A Object containing 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.
    A memory-efficient data structure to store conformers for a single molecule.
    Class representing a molecular crystal.
    A factory class to provide implementation independent ICDKObjects.
    A factory class for constructing ICDKObject and IChemObject implementations.
    A simple creator that helps in creating an anonymous classes for a creator.
    A class which encapsulates the information about an interface (of this implementation) and the parameter types of the constructor.
    An interface that allows posterior modification of an instance after it has been created.
    An interface that wraps object creation via the DynamicFactory.Creator.create(Object[]) method.
    A default interface provider implementation that simply returns the classes from Class.getInterfaces().
    An interface that can provide which interfaces the given class implements.
    Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
    Implements the idea of an element in the periodic table.
    Atom that represents part of an residue in an enzyme, like Arg255.
    Class to represent an IPseudoAtom which embeds an IAtomContainer.
    Interface that is used to describe the specification of a certain implementation of an algorithm.
    Used to store and retrieve data of a particular isotope.
    A LonePair is an orbital primarily located with one Atom, containing two electrons.
    A Mapping is an relation between two ChemObjects in a non-chemical entity.
    A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.
    An class providing predefined properties of physical constants.
    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.
    Classes that extends the definition of reaction to 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.
    A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.
    An implementation of the ISubstance interface.
    A molecular vibration composed of a set of atom vectors.