Uses of Class
org.openscience.cdk.ChemObject
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Packages that use ChemObject Package Description org.openscience.cdk org.openscience.cdk.debug org.openscience.cdk.libio.md org.openscience.cdk.pharmacophore org.openscience.cdk.protein.data org.openscience.cdk.reaction -
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Uses of ChemObject in org.openscience.cdk
Subclasses of ChemObject in org.openscience.cdk Modifier and Type Class Description class
AminoAcid
A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.class
Association
Base class for storing interactions like hydrogen bonds and ionic interactions.class
Atom
Represents the idea of an chemical atom.class
AtomContainer
Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.class
AtomContainerSet
A set of AtomContainers.class
AtomType
The base class for atom types.class
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
Bond
Implements the concept of a covalent bond between two or more atoms.class
ChemFile
A Object containing a number of ChemSequences.class
ChemModel
An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.class
ChemSequence
A sequence of ChemModels, which can, for example, be used to store the course of a reaction.class
Crystal
Class representing a molecular crystal.class
ElectronContainer
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.class
Element
Implements the idea of an element in the periodic table.class
EnzymeResidueLocator
Atom that represents part of an residue in an enzyme, like Arg255.class
FragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
Isotope
Used to store and retrieve data of a particular isotope.class
LonePair
A LonePair is an orbital primarily located with one Atom, containing two electrons.class
Mapping
A Mapping is an relation between two ChemObjects in a non-chemical entity.class
Monomer
A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.class
Polymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.class
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.class
Reaction
Represents the idea of a chemical reaction.class
ReactionScheme
Classes that extends the definition of reaction to a scheme.class
ReactionSet
A set of reactions, for example those taking part in a reaction.class
Ring
Class representing a ring structure in a molecule.class
RingSet
Maintains a set of Ring objects.class
SingleElectron
A Single Electron is an orbital which is occupied by only one electron.class
Strand
A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.class
Substance
An implementation of theISubstance
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Uses of ChemObject in org.openscience.cdk.debug
Subclasses of ChemObject in org.openscience.cdk.debug Modifier and Type Class Description class
DebugAminoAcid
Debugging data class.class
DebugAtom
Debugging data class.class
DebugAtomContainer
Debugging data class.class
DebugAtomContainerSet
Debugging data class.class
DebugAtomType
Debugging data class.class
DebugBioPolymer
Debugging data class.class
DebugBond
Debugging data class.class
DebugChemFile
Debugging data class.class
DebugChemModel
Debugging data class.class
DebugChemObject
Debugging data class.class
DebugChemSequence
Debugging data class.class
DebugCrystal
Debugging data class.class
DebugElectronContainer
Debugging data class.class
DebugElement
Debugging data class.class
DebugFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.class
DebugIsotope
Debugging data class.class
DebugLonePair
Debugging data class.class
DebugMapping
Debugging data class.class
DebugMonomer
Debugging data class.class
DebugPDBAtom
Debugging data class.class
DebugPDBMonomer
Debugging data class.class
DebugPDBPolymer
Debugging data class.class
DebugPDBStructure
Debugging data class.class
DebugPolymer
Debugging data class.class
DebugPseudoAtom
Debugging data class.class
DebugReaction
Debugging data class.class
DebugReactionScheme
Debugging data class.class
DebugReactionSet
Debugging data class.class
DebugRing
Debugging data class.class
DebugRingSet
Debugging data class.class
DebugSingleElectron
Debugging data class.class
DebugStrand
Debugging data class.class
DebugSubstance
Debugging data class. -
Uses of ChemObject in org.openscience.cdk.libio.md
Subclasses of ChemObject in org.openscience.cdk.libio.md Modifier and Type Class Description class
ChargeGroup
A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule.class
MDMolecule
class
Residue
A residue is a named, numbered collection of atoms in an MDMolecule. -
Uses of ChemObject in org.openscience.cdk.pharmacophore
Subclasses of ChemObject in org.openscience.cdk.pharmacophore Modifier and Type Class Description class
PharmacophoreAngleBond
Represents an angle relationship between three pharmacophore groups.class
PharmacophoreAtom
A representation of a pharmacophore group.class
PharmacophoreBond
Represents a distance relationship between two pharmacophore groups.class
PharmacophoreQueryAngleBond
Represents a pharmacophore query angle constraint.class
PharmacophoreQueryAtom
Represents a query pharmacophore group.class
PharmacophoreQueryBond
Represents a pharmacophore query distance constraint. -
Uses of ChemObject in org.openscience.cdk.protein.data
Subclasses of ChemObject in org.openscience.cdk.protein.data Modifier and Type Class Description class
PDBAtom
Represents the idea of an atom as used in PDB files.class
PDBMonomer
Represents the idea of an monomer as used in PDB files.class
PDBPolymer
An entry in the PDB database.class
PDBStrand
An entry in the PDB database.class
PDBStructure
Holder for secundary protein structure elements. -
Uses of ChemObject in org.openscience.cdk.reaction
Subclasses of ChemObject in org.openscience.cdk.reaction Modifier and Type Class Description class
ReactionChain
Classes that extends the definition of reaction to a chain reaction.
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