Package org.openscience.cdk.interfaces
package org.openscience.cdk.interfaces
-
ClassDescriptionClass 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.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.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 simple setting that can be managed by the SettingManager.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.Stereochemistry specification for quadrivalent atoms.Enumeration that defines the two possible chiralities for this stereochemistry type.