- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.AdductFormula
-
Adds all molecularFormulas in the AdductFormula to this chemObject.
- add(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer
- add(IAtomContainerSet) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Adds all atomContainers in the AtomContainerSet to this container.
- add(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Adds an molecularFormula to this MolecularFormula.
- add(IMolecularFormulaSet) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.
- add(IReactionScheme) - Method in class org.openscience.cdk.silent.ReactionScheme
-
Add a Scheme of Reactions.
- add(IRingSet) - Method in class org.openscience.cdk.silent.RingSet
-
Adds all rings of another RingSet if they are not already part of this ring set.
- addAgent(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Adds an agent to this reaction.
- addAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- addAtom(IAtom, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer
-
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
- addAtom(IAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.BioPolymer
-
Adds the atom to a specified Strand and a specified Monomer.
- addAtom(IPDBAtom) - Method in class org.openscience.cdk.silent.PDBPolymer
-
Adds the atom oAtom without specifying a
IMonomer or a Strand.
- addAtom(IPDBAtom, IMonomer) - Method in class org.openscience.cdk.silent.PDBPolymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IPDBAtom, IMonomer, IStrand) - Method in class org.openscience.cdk.silent.PDBPolymer
-
Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Polymer
-
Adds the atom oAtom to a specified Monomer.
- addAtom(IAtom) - Method in class org.openscience.cdk.silent.Strand
-
Adds the atom oAtom without specifying a Monomer or a Strand.
- addAtom(IAtom, IMonomer) - Method in class org.openscience.cdk.silent.Strand
-
Adds the atom oAtom to a specific Monomer.
- addAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Adds an atomContainer to this container.
- addAtomContainer(IAtomContainer, double) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Adds an atomContainer to this container with the given
multiplier.
- addBond(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.silent.AtomContainer
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.silent.AtomContainer
- addChemModel(IChemModel) - Method in class org.openscience.cdk.silent.ChemSequence
-
Adds an chemModel to this container.
- addChemSequence(IChemSequence) - Method in class org.openscience.cdk.silent.ChemFile
-
Adds a ChemSequence to this container.
- addCTerminus(IAtom) - Method in class org.openscience.cdk.silent.AminoAcid
-
Add an Atom and makes it the C-terminus atom.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
- addIsotope(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Adds an Isotope to this MolecularFormula one time.
- addIsotope(IIsotope, int) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Adds an Isotope to this MolecularFormula in a number of occurrences.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.silent.ChemObject
-
Use this to add yourself to this IChemObject as a listener.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
- addLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
- addMapping(IMapping) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a mapping between the reactant and product side to this
Reaction.
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula
-
Adds an molecularFormula to this chemObject.
- addMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Adds an molecularFormula to this chemObject.
- addNTerminus(IAtom) - Method in class org.openscience.cdk.silent.AminoAcid
-
Add an Atom and makes it the N-terminus atom.
- addProduct(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a product to this reaction.
- addProduct(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a product to this reaction.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets the properties of this object.
- addReactant(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a reactant to this reaction.
- addReactant(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Adds a reactant to this reaction with a stoichiometry coefficient.
- addReaction(IReaction) - Method in class org.openscience.cdk.silent.ReactionSet
-
Adds an reaction to this container.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
- addSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.silent.AtomContainer
- addStructure(IPDBStructure) - Method in class org.openscience.cdk.silent.PDBPolymer
-
- AdductFormula - Class in org.openscience.cdk.silent
-
Class defining an adduct object in a MolecularFormula.
- AdductFormula() - Constructor for class org.openscience.cdk.silent.AdductFormula
-
Constructs an empty AdductFormula.
- AdductFormula(IMolecularFormula) - Constructor for class org.openscience.cdk.silent.AdductFormula
-
Constructs an AdductFormula with a copy AdductFormula of another
AdductFormula (A shallow copy, i.e., with the same objects as in
the original AdductFormula).
- agents - Variable in class org.openscience.cdk.silent.Reaction
-
These are the used solvent, catalysts etc that normally appear above
the reaction arrow
- AminoAcid - Class in org.openscience.cdk.silent
-
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
- AminoAcid() - Constructor for class org.openscience.cdk.silent.AminoAcid
-
Constructs a new AminoAcid.
- Atom - Class in org.openscience.cdk.silent
-
Represents the idea of an chemical atom.
- Atom() - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an completely unset Atom.
- Atom(int) - Constructor for class org.openscience.cdk.silent.Atom
-
Create a new atom with of the specified element.
- Atom(int, int) - Constructor for class org.openscience.cdk.silent.Atom
-
Create a new atom with of the specified element and hydrogen count.
- Atom(int, int, int) - Constructor for class org.openscience.cdk.silent.Atom
-
Create a new atom with of the specified element, hydrogen count, and formal charge.
- Atom(String) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an Atom from a string containing an element symbol and optionally
the atomic mass, hydrogen count, and formal charge.
- Atom(String, Point3d) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an Atom from an Element and a Point3d.
- Atom(String, Point2d) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an Atom from an Element and a Point2d.
- Atom(IElement) - Constructor for class org.openscience.cdk.silent.Atom
-
Constructs an isotope by copying the symbol, atomic number,
flags, identifier, exact mass, natural abundance, mass
number, maximum bond order, bond order sum, van der Waals
and covalent radii, formal charge, hybridization, electron
valency, formal neighbour count and atom type name from the
given IAtomType.
- atom - Variable in class org.openscience.cdk.silent.LonePair
-
The atom with which this lone pair is associated.
- atom - Variable in class org.openscience.cdk.silent.SingleElectron
-
The atom with which this single electron is associated.
- AtomContainer - Class in org.openscience.cdk.silent
-
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
- AtomContainer() - Constructor for class org.openscience.cdk.silent.AtomContainer
-
Constructs an empty AtomContainer.
- AtomContainer(IAtomContainer) - Constructor for class org.openscience.cdk.silent.AtomContainer
-
Constructs an AtomContainer with a copy of the atoms and electronContainers
of another AtomContainer (A shallow copy, i.e., with the same objects as in
the original AtomContainer).
- AtomContainer(int, int, int, int) - Constructor for class org.openscience.cdk.silent.AtomContainer
-
Constructs an empty AtomContainer that will contain a certain number of
atoms and electronContainers.
- atomContainerCount - Variable in class org.openscience.cdk.silent.AtomContainerSet
-
Number of AtomContainers contained by this container.
- atomContainers - Variable in class org.openscience.cdk.silent.AtomContainerSet
-
Array of AtomContainers.
- atomContainers() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Get an iterator for this AtomContainerSet.
- AtomContainerSet - Class in org.openscience.cdk.silent
-
A set of AtomContainers.
- AtomContainerSet() - Constructor for class org.openscience.cdk.silent.AtomContainerSet
-
Constructs an empty AtomContainerSet.
- atomCount - Variable in class org.openscience.cdk.silent.AtomContainer
-
Number of atoms contained by this object.
- atomCount - Variable in class org.openscience.cdk.silent.Bond
-
Number of atoms contained by this object.
- atomicNumber - Variable in class org.openscience.cdk.silent.Element
-
The atomic number for this element giving their position in the periodic table.
- atoms - Variable in class org.openscience.cdk.silent.AtomContainer
-
Internal array of atoms.
- atoms() - Method in class org.openscience.cdk.silent.AtomContainer
- atoms - Variable in class org.openscience.cdk.silent.Bond
-
A list of atoms participating in this bond.
- atoms() - Method in class org.openscience.cdk.silent.Bond
-
Returns the Iterator to atoms making up this bond.
- AtomType - Class in org.openscience.cdk.silent
-
The base class for atom types.
- AtomType(String) - Constructor for class org.openscience.cdk.silent.AtomType
-
Constructor for the AtomType object.
- AtomType(String, String) - Constructor for class org.openscience.cdk.silent.AtomType
-
Constructor for the AtomType object.
- AtomType(IElement) - Constructor for class org.openscience.cdk.silent.AtomType
-
Constructs an isotope by copying the symbol, atomic number,
flags, identifier, exact mass, natural abundance and mass
number from the given IIsotope.
- charge - Variable in class org.openscience.cdk.silent.Atom
-
The partial charge of the atom.
- ChemFile - Class in org.openscience.cdk.silent
-
A Object containing a number of ChemSequences.
- ChemFile() - Constructor for class org.openscience.cdk.silent.ChemFile
-
Constructs an empty ChemFile.
- ChemModel - Class in org.openscience.cdk.silent
-
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
- ChemModel() - Constructor for class org.openscience.cdk.silent.ChemModel
-
Constructs an new ChemModel with a null setOfMolecules.
- chemModelCount - Variable in class org.openscience.cdk.silent.ChemSequence
-
Number of ChemModels contained by this container.
- chemModels - Variable in class org.openscience.cdk.silent.ChemSequence
-
Array of ChemModels.
- chemModels() - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns an Iterable to ChemModels in this container.
- ChemObject - Class in org.openscience.cdk.silent
-
The base class for all chemical objects in this cdk.
- ChemObject() - Constructor for class org.openscience.cdk.silent.ChemObject
-
Constructs a new IChemObject.
- ChemObject(IChemObject) - Constructor for class org.openscience.cdk.silent.ChemObject
-
Constructs a new IChemObject by copying the flags, and the
identifier.
- ChemSequence - Class in org.openscience.cdk.silent
-
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
- ChemSequence() - Constructor for class org.openscience.cdk.silent.ChemSequence
-
Constructs an empty ChemSequence.
- chemSequenceCount - Variable in class org.openscience.cdk.silent.ChemFile
-
Number of ChemSequences contained by this container.
- chemSequences - Variable in class org.openscience.cdk.silent.ChemFile
-
Array of ChemSquences.
- chemSequences() - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the Iterable to ChemSequences of this container.
- clone() - Method in class org.openscience.cdk.silent.AdductFormula
-
Clones this AdductFormula object and its content.
- clone() - Method in class org.openscience.cdk.silent.AminoAcid
-
Clones this AminoAcid object.
- clone() - Method in class org.openscience.cdk.silent.Atom
-
Clones this atom object and its content.
- clone() - Method in class org.openscience.cdk.silent.AtomContainer
-
Clones this IChemObject.
- clone() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Clones this AtomContainerSet and its content.
- clone() - Method in class org.openscience.cdk.silent.AtomType
-
- clone() - Method in class org.openscience.cdk.silent.BioPolymer
-
- clone() - Method in class org.openscience.cdk.silent.Bond
-
Clones this bond object, including clones of the atoms between which the
bond is defined.
- clone() - Method in class org.openscience.cdk.silent.ChemFile
-
Allows for getting an clone of this object.
- clone() - Method in class org.openscience.cdk.silent.ChemModel
-
Clones this ChemModel and its content.
- clone() - Method in class org.openscience.cdk.silent.ChemObject
-
Clones this IChemObject.
- clone() - Method in class org.openscience.cdk.silent.ChemSequence
-
- clone() - Method in class org.openscience.cdk.silent.Crystal
-
Makes a clone of this crystal.
- clone() - Method in class org.openscience.cdk.silent.ElectronContainer
-
- clone() - Method in class org.openscience.cdk.silent.Element
-
- clone() - Method in class org.openscience.cdk.silent.FragmentAtom
-
- clone() - Method in class org.openscience.cdk.silent.Isotope
-
- clone() - Method in class org.openscience.cdk.silent.LonePair
-
Clones this LonePair object, including a clone of the atom for which the
lone pair is defined.
- clone() - Method in class org.openscience.cdk.silent.Mapping
-
Clones this Mapping and the mapped IChemObjects.
- clone() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Clones this MolecularFormula object and its content.
- clone() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Clones this MolecularFormulaSet object and its content.
- clone() - Method in class org.openscience.cdk.silent.Monomer
-
Clones this IChemObject.
- clone() - Method in class org.openscience.cdk.silent.PDBMonomer
-
Clones this IChemObject.
- clone() - Method in class org.openscience.cdk.silent.PDBPolymer
-
Clones this IChemObject.
- clone() - Method in class org.openscience.cdk.silent.Polymer
-
- clone() - Method in class org.openscience.cdk.silent.PseudoAtom
-
- clone() - Method in class org.openscience.cdk.silent.Reaction
-
Clones this Reaction and its content.
- clone() - Method in class org.openscience.cdk.silent.ReactionScheme
-
Clones this ReactionScheme object and its content.
- clone() - Method in class org.openscience.cdk.silent.ReactionSet
-
Clones this ReactionSet and the contained Reactions
too.
- clone() - Method in class org.openscience.cdk.silent.Ring
-
Clones this IChemObject.
- clone() - Method in class org.openscience.cdk.silent.RingSet
-
Clones this RingSet including the Rings.
- clone() - Method in class org.openscience.cdk.silent.SingleElectron
-
Clones this SingleElectron object, including a clone of the atom for which the
SingleElectron is defined.
- clone() - Method in class org.openscience.cdk.silent.Strand
-
- compare(Object) - Method in class org.openscience.cdk.silent.Atom
-
Compares a atom with this atom.
- compare(Object) - Method in class org.openscience.cdk.silent.AtomType
-
Compares a atom type with this atom type.
- compare(Object) - Method in class org.openscience.cdk.silent.Bond
-
Compares a bond with this bond.
- compare(Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Compares a IChemObject with this IChemObject.
- compare(Object) - Method in class org.openscience.cdk.silent.Element
-
Compares an Element with this Element.
- compare(Object) - Method in class org.openscience.cdk.silent.Isotope
-
Compares an isotope with this isotope.
- contains(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula
-
True, if the AdductFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula
-
True, if the AdductFormula contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- contains(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
- contains(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
- contains(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
- contains(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
- contains(IAtom) - Method in class org.openscience.cdk.silent.Bond
-
Returns true if the given atom participates in this bond.
- contains(IAtom) - Method in class org.openscience.cdk.silent.LonePair
-
Returns true if the given atom participates in this lone pair.
- contains(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
True, if the MolecularFormula contains the given IIsotope object and not
the instance.
- contains(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
True, if the MolecularFormulaSet contains the given IMolecularFormula object.
- contains(IAtom) - Method in class org.openscience.cdk.silent.RingSet
-
True, if at least one of the rings in the ringset contains
the given atom.
- contains(IAtomContainer) - Method in class org.openscience.cdk.silent.RingSet
-
Checks for presence of a ring in this RingSet.
- contains(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns true if the given atom participates in this SingleElectron.
- crystal - Variable in class org.openscience.cdk.silent.ChemModel
-
A Crystal.
- Crystal - Class in org.openscience.cdk.silent
-
Class representing a molecular crystal.
- Crystal() - Constructor for class org.openscience.cdk.silent.Crystal
-
Constructs a new crystal with zero length cell axis.
- Crystal(IAtomContainer) - Constructor for class org.openscience.cdk.silent.Crystal
-
Constructs a new crystal with zero length cell axis
and adds the atoms in the AtomContainer as cell content.
- get2DCenter() - Method in class org.openscience.cdk.silent.Bond
-
Returns the geometric 2D center of the bond.
- get3DCenter() - Method in class org.openscience.cdk.silent.Bond
-
Returns the geometric 3D center of the bond.
- getA() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the A unit cell axes in Cartesian coordinates
as a three element double array.
- getAgents() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the agents in this reaction.
- getAltLoc() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Alternate location indicator of this atom.
- getAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer
- getAtom(int) - Method in class org.openscience.cdk.silent.Bond
-
Returns an Atom from this bond.
- getAtom() - Method in class org.openscience.cdk.silent.LonePair
-
Returns the associated Atom.
- getAtom() - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns the associated Atom.
- getAtomContainer(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the AtomContainer at position number in the
container.
- getAtomContainerCount() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the number of AtomContainers in this Container.
- getAtomCount() - Method in class org.openscience.cdk.silent.AtomContainer
- getAtomCount() - Method in class org.openscience.cdk.silent.Bond
-
Returns the number of Atoms in this Bond.
- getAtomicNumber() - Method in class org.openscience.cdk.silent.Element
-
Returns the atomic number of this element.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getAtomTypeName() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the id attribute of the AtomType object.
- getAttachPointNum() - Method in class org.openscience.cdk.silent.PseudoAtom
- getB() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the B unit cell axes in Cartesian coordinates
as a three element double array.
- getBegin() - Method in class org.openscience.cdk.silent.Bond
- getBond(int) - Method in class org.openscience.cdk.silent.AtomContainer
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getBondCount() - Method in class org.openscience.cdk.silent.Atom
- getBondCount() - Method in class org.openscience.cdk.silent.AtomContainer
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getBondNumber(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getBondOrderSum() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum() - Method in class org.openscience.cdk.silent.Ring
-
Returns the sum of all bond orders in the ring.
- getBuilder() - Method in class org.openscience.cdk.silent.AdductFormula
-
- getBuilder() - Method in class org.openscience.cdk.silent.ChemObject
-
- getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormula
-
- getBuilder() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
- getC() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the C unit cell axes in Cartesian coordinates
as a three element double array.
- getChainID() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Chain identifier of this atom.
- getChainID() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getCharge() - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the partial charge of this Adduct.
- getCharge() - Method in class org.openscience.cdk.silent.Atom
-
Returns the partial charge of this atom.
- getCharge() - Method in class org.openscience.cdk.silent.MolecularFormula
- getChemModel(int) - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns the ChemModel at position number in the
container.
- getChemModelCount() - Method in class org.openscience.cdk.silent.ChemSequence
-
Returns the number of ChemModels in this Container.
- getChemObject(int) - Method in class org.openscience.cdk.silent.Mapping
-
Retrieves the first or second of the related IChemObjects.
- getChemSequence(int) - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the ChemSequence at position number in the container.
- getChemSequenceCount() - Method in class org.openscience.cdk.silent.ChemFile
-
Returns the number of ChemSequences in this Container.
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.silent.Bond
- getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.silent.Bond
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedBondsCount(int) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedRings(IRing) - Method in class org.openscience.cdk.silent.RingSet
-
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getContainer() - Method in class org.openscience.cdk.silent.Atom
- getContainer() - Method in class org.openscience.cdk.silent.Bond
- getCovalentRadius() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the covalent radius for this AtomType.
- getCrystal() - Method in class org.openscience.cdk.silent.ChemModel
-
Gets the Crystal contained in this ChemModel.
- getCTerminus() - Method in class org.openscience.cdk.silent.AminoAcid
-
Retrieves the C-terminus atom.
- getDirection() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the direction of the reaction.
- getElectronContainer(int) - Method in class org.openscience.cdk.silent.AtomContainer
- getElectronContainerCount() - Method in class org.openscience.cdk.silent.AtomContainer
- getElectronCount() - Method in class org.openscience.cdk.silent.ElectronContainer
-
Returns the number of electrons in this electron container.
- getElectronCount() - Method in class org.openscience.cdk.silent.LonePair
-
Returns the number of electrons in a LonePair.
- getElectronCount() - Method in class org.openscience.cdk.silent.SingleElectron
-
Returns the number of electrons in this SingleElectron.
- getEnd() - Method in class org.openscience.cdk.silent.Bond
- getEndChainID() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending Chain identifier of this structure.
- getEndInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending Code for insertion of residues of this structure.
- getEndSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the ending sequence number of this structure.
- getExactMass() - Method in class org.openscience.cdk.silent.FragmentAtom
-
The exact mass of an FragmentAtom is defined as the sum of exact masses
of the IAtom's in the fragment.
- getExactMass() - Method in class org.openscience.cdk.silent.Isotope
-
Gets the ExactMass attribute of the Isotope object.
- getFirstAtom() - Method in class org.openscience.cdk.silent.AtomContainer
- getFlag(int) - Method in class org.openscience.cdk.silent.ChemObject
- getFlags() - Method in class org.openscience.cdk.silent.ChemObject
- getFlagValue() - Method in class org.openscience.cdk.silent.ChemObject
- getFormalCharge() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the formal charge of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the formal neighbour count of this atom.
- getFractionalPoint3d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getFragment() - Method in class org.openscience.cdk.silent.FragmentAtom
-
- getHetAtom() - Method in class org.openscience.cdk.silent.PDBAtom
-
- getHybridization() - Method in class org.openscience.cdk.silent.AtomType
-
Returns the hybridization of this atom.
- getICode() - Method in class org.openscience.cdk.silent.PDBAtom
-
get Code for insertion of residues of this atom.
- getICode() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getID() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns the identifier (ID) of this object.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.silent.Atom
-
Returns the hydrogen count of this atom.
- getIndex() - Method in class org.openscience.cdk.silent.Atom
- getIndex() - Method in class org.openscience.cdk.silent.Bond
- getInstance() - Static method in class org.openscience.cdk.silent.SilentChemObjectBuilder
-
Access the singleton instance of this SilentChemObjectBuilder.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.AdductFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
adduct formula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.silent.AdductFormula
-
Checks a set of Nodes for the number of different isotopes in the
adduct formula.
- getIsotopeCount(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Checks a set of Nodes for the occurrence of the isotope in the
IMolecularFormula from a particular isotope.
- getIsotopeCount() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Checks a set of Nodes for the number of different isotopes in the
IMolecularFormula.
- getLabel() - Method in class org.openscience.cdk.silent.PseudoAtom
-
Returns the label of this PseudoAtom.
- getLastAtom() - Method in class org.openscience.cdk.silent.AtomContainer
- getListenerCount() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
- getLonePairCount() - Method in class org.openscience.cdk.silent.AtomContainer
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
- getMapping(int) - Method in class org.openscience.cdk.silent.Reaction
-
Retrieves a mapping between the reactant and product side to this
Reaction.
- getMappingCount() - Method in class org.openscience.cdk.silent.Reaction
-
Get the number of mappings between the reactant and product side to this
Reaction.
- getMassNumber() - Method in class org.openscience.cdk.silent.Isotope
-
Returns the atomic mass of this element.
- getMaxBondOrder() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- getMolecularFormula(int) - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the MolecularFormula at position number in the
chemObject.
- getMolecularFormula(int) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Returns the MolecularFormula at position number in the
chemObject.
- getMoleculeSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Returns the MoleculeSet of this ChemModel.
- getMonomer(String, String) - Method in class org.openscience.cdk.silent.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.silent.Polymer
-
Retrieves a Monomer object by specifying its name.
- getMonomer(String) - Method in class org.openscience.cdk.silent.Strand
-
Retrieves a Monomer object by specifying its name.
- getMonomerCount() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns the number of monomers present in BioPolymer.
- getMonomerCount() - Method in class org.openscience.cdk.silent.Polymer
-
Returns the number of monomers present in the Polymer.
- getMonomerCount() - Method in class org.openscience.cdk.silent.Strand
-
Returns the number of monomers present in the Strand.
- getMonomerName() - Method in class org.openscience.cdk.silent.Monomer
-
Retrieves the monomer name.
- getMonomerNames() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns a collection of the names of all Monomers in this
BioPolymer.
- getMonomerNames() - Method in class org.openscience.cdk.silent.Polymer
-
Returns a collection of the names of all Monomers in this
polymer.
- getMonomerNames() - Method in class org.openscience.cdk.silent.Strand
-
Returns a collection of the names of all Monomers in this
polymer.
- getMonomerNamesInSequentialOrder() - Method in class org.openscience.cdk.silent.PDBPolymer
-
Returns the monomer names in the order in which they were added.
- getMonomers() - Method in class org.openscience.cdk.silent.Strand
-
Returns a hashtable containing the monomers in the strand.
- getMonomerType() - Method in class org.openscience.cdk.silent.Monomer
-
Retrieves the monomer type.
- getMultiplier(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the multiplier for the AtomContainer at position number in the
container.
- getMultiplier(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns the multiplier of the given AtomContainer.
- getMultipliers() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getName() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Atom name of this atom.
- getNaturalAbundance() - Method in class org.openscience.cdk.silent.Isotope
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNextBond(IBond, IAtom) - Method in class org.openscience.cdk.silent.Ring
-
Returns the next bond in order, relative to a given bond and atom.
- getNotification() - Method in class org.openscience.cdk.silent.ChemObject
-
- getNTerminus() - Method in class org.openscience.cdk.silent.AminoAcid
-
Retrieves the N-terminus atom.
- getOccupancy() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Occupancy of this atom.
- getOrder() - Method in class org.openscience.cdk.silent.Bond
-
Returns the bond order of this bond.
- getOther(IAtom) - Method in class org.openscience.cdk.silent.Bond
- getOxt() - Method in class org.openscience.cdk.silent.PDBAtom
-
- getPoint2d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint3d() - Method in class org.openscience.cdk.silent.Atom
-
Returns a point specifying the location of this
atom in a 3D space.
- getProductCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Returns the stoichiometry coefficient of the given product.
- getProductCoefficients() - Method in class org.openscience.cdk.silent.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the products.
- getProductCount() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the number of products in this reaction.
- getProducts() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the products of this reaction.
- getProperties() - Method in class org.openscience.cdk.silent.ChemObject
-
Returns a Map with the IChemObject's properties.
- getProperties() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Returns a Map with the IChemObject's properties.I should
integrate into ChemObject.
- getProperty(Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Returns a property for the IChemObject.
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.silent.ChemObject
- getProperty(Object) - Method in class org.openscience.cdk.silent.MolecularFormula
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.silent.MolecularFormula
- getReactantCoefficient(IAtomContainer) - Method in class org.openscience.cdk.silent.Reaction
-
Returns the stoichiometry coefficient of the given reactant.
- getReactantCoefficients() - Method in class org.openscience.cdk.silent.Reaction
-
Returns an array of double with the stoichiometric coefficients
of the reactants.
- getReactantCount() - Method in class org.openscience.cdk.silent.Reaction
-
Returns the number of reactants in this reaction.
- getReactants() - Method in class org.openscience.cdk.silent.Reaction
-
Returns a MoleculeSet containing the reactants in this reaction.
- getReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet
-
Returns the Reaction at position number in the
container.
- getReactionCount() - Method in class org.openscience.cdk.silent.ReactionSet
-
Returns the number of Reactions in this Container.
- getReactionSchemeCount() - Method in class org.openscience.cdk.silent.ReactionScheme
-
Returns the number of ReactionScheme in this Scheme.
- getReactionSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Gets the ReactionSet contained in this ChemModel.
- getRecord() - Method in class org.openscience.cdk.silent.PDBAtom
-
get one entire line from the PDB entry file which describe the IPDBAtom.
- getResName() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Residue name of this atom.
- getResSeq() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Residue sequence number of this atom.
- getResSeq() - Method in class org.openscience.cdk.silent.PDBMonomer
-
- getRings(IBond) - Method in class org.openscience.cdk.silent.RingSet
-
Returns a vector of all rings that this bond is part of.
- getRings(IAtom) - Method in class org.openscience.cdk.silent.RingSet
-
Returns a vector of all rings that this atom is part of.
- getRingSet() - Method in class org.openscience.cdk.silent.ChemModel
-
Returns the RingSet of this ChemModel.
- getRingSize() - Method in class org.openscience.cdk.silent.Ring
-
Returns the number of atoms\edges in this ring.
- getSegID() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Segment identifier, left-justified of this atom.
- getSerial() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Atom serial number of this atom.
- getSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
- getSingleElectronCount() - Method in class org.openscience.cdk.silent.AtomContainer
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
- getSpaceGroup() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the space group of this crystal.
- getStartChainID() - Method in class org.openscience.cdk.silent.PDBStructure
-
get start Chain identifier of this structure.
- getStartInsertionCode() - Method in class org.openscience.cdk.silent.PDBStructure
-
get start Code for insertion of residues of this structure.
- getStartSequenceNumber() - Method in class org.openscience.cdk.silent.PDBStructure
-
get the start sequence number of this structure.
- getStereo() - Method in class org.openscience.cdk.silent.Bond
-
Returns the stereo descriptor for this bond.
- getStereoParity() - Method in class org.openscience.cdk.silent.Atom
-
Returns the stereo parity of this atom.
- getStrand(String) - Method in class org.openscience.cdk.silent.BioPolymer
-
Retrieves a Monomer object by specifying its name.
- getStrandCount() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns the number of strands present in the BioPolymer.
- getStrandName() - Method in class org.openscience.cdk.silent.Strand
-
Retrieves the strand name.
- getStrandNames() - Method in class org.openscience.cdk.silent.BioPolymer
-
Returns a collection of the names of all Strands in this
BioPolymer.
- getStrands() - Method in class org.openscience.cdk.silent.BioPolymer
-
- getStrandType() - Method in class org.openscience.cdk.silent.Strand
-
Retrieves the strand type.
- getStructures() - Method in class org.openscience.cdk.silent.PDBPolymer
-
- getStructureType() - Method in class org.openscience.cdk.silent.PDBStructure
-
get Structure Type of this structure.
- getSymbol() - Method in class org.openscience.cdk.silent.Element
-
Returns the element symbol of this element.
- getTempFactor() - Method in class org.openscience.cdk.silent.PDBAtom
-
get the Temperature factor of this atom.
- getTitle() - Method in class org.openscience.cdk.silent.AtomContainer
- getValency() - Method in class org.openscience.cdk.silent.AtomType
-
Gets the the exact electron valency of the AtomType object.
- getZ() - Method in class org.openscience.cdk.silent.Crystal
-
Gets the number of asymmetric parts in the unit cell.
- growArraySize - Variable in class org.openscience.cdk.silent.AtomContainer
-
Amount by which the bond and atom arrays grow when elements are added and
the arrays are not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.silent.AtomContainerSet
-
Amount by which the AtomContainers array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.silent.ChemFile
-
Amount by which the chemsequence array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.silent.ChemSequence
-
Amount by which the chemModels array grows when elements are added and
the array is not large enough for that.
- growArraySize - Variable in class org.openscience.cdk.silent.Reaction
-
- growAtomContainerArray() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Grows the atomContainer array by a given size.
- growChemModelArray() - Method in class org.openscience.cdk.silent.ChemSequence
-
Grows the chemModel array by a given size.
- growChemSequenceArray() - Method in class org.openscience.cdk.silent.ChemFile
-
Grows the ChemSequence array by a given size.
- reactants - Variable in class org.openscience.cdk.silent.Reaction
-
- Reaction - Class in org.openscience.cdk.silent
-
Represents the idea of a chemical reaction.
- Reaction() - Constructor for class org.openscience.cdk.silent.Reaction
-
Constructs an empty, forward reaction.
- reactions() - Method in class org.openscience.cdk.silent.ReactionSet
-
Get an iterator for this reaction set.
- ReactionScheme - Class in org.openscience.cdk.silent
-
Classes that extends the definition of reaction to a scheme.
- ReactionScheme() - Constructor for class org.openscience.cdk.silent.ReactionScheme
-
Constructs an empty ReactionScheme.
- reactionSchemes() - Method in class org.openscience.cdk.silent.ReactionScheme
-
Returns an Iterable for looping over all IMolecularScheme
in this ReactionScheme.
- ReactionSet - Class in org.openscience.cdk.silent
-
A set of reactions, for example those taking part in a reaction.
- ReactionSet() - Constructor for class org.openscience.cdk.silent.ReactionSet
-
Constructs an empty ReactionSet.
- relatedChemObjects() - Method in class org.openscience.cdk.silent.Mapping
-
Returns an Iterable to the two IChemObjects.
- remove(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainer
- removeAllAtomContainers() - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Removes all AtomContainer from this container.
- removeAllBonds() - Method in class org.openscience.cdk.silent.AtomContainer
- removeAllElectronContainers() - Method in class org.openscience.cdk.silent.AtomContainer
- removeAllElements() - Method in class org.openscience.cdk.silent.AtomContainer
- removeAllIsotopes() - Method in class org.openscience.cdk.silent.MolecularFormula
-
Removes all isotopes of this molecular formula.
- removeAllMolecularFormulas() - Method in class org.openscience.cdk.silent.AdductFormula
-
Removes all IMolecularFormula from this chemObject.
- removeAllMolecularFormulas() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Removes all IMolecularFormula from this chemObject.
- removeAllReactions() - Method in class org.openscience.cdk.silent.ReactionSet
-
Removes all Reactions from this container.
- removeAllReactionSchemes() - Method in class org.openscience.cdk.silent.ReactionScheme
-
Removes all IReactionScheme from this chemObject.
- removeAtom(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- removeAtom(int) - Method in class org.openscience.cdk.silent.AtomContainer
- removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
-
Deprecated.
- removeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Removes an AtomContainer from this container.
- removeAtomContainer(int) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Removes an AtomContainer from this container.
- removeAtomOnly(int) - Method in class org.openscience.cdk.silent.AtomContainer
- removeAtomOnly(IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- removeBond(int) - Method in class org.openscience.cdk.silent.AtomContainer
- removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- removeBond(IBond) - Method in class org.openscience.cdk.silent.AtomContainer
- removeChemModel(int) - Method in class org.openscience.cdk.silent.ChemSequence
-
Remove a ChemModel from this ChemSequence.
- removeChemSequence(int) - Method in class org.openscience.cdk.silent.ChemFile
-
Removes a ChemSequence from this container.
- removeElectronContainer(int) - Method in class org.openscience.cdk.silent.AtomContainer
- removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.silent.AtomContainer
- removeIsotope(IIsotope) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Removes the given isotope from the MolecularFormula.
- removeListener(IChemObjectListener) - Method in class org.openscience.cdk.silent.ChemObject
-
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
- removeLonePair(int) - Method in class org.openscience.cdk.silent.AtomContainer
- removeLonePair(ILonePair) - Method in class org.openscience.cdk.silent.AtomContainer
- removeMapping(int) - Method in class org.openscience.cdk.silent.Reaction
-
Removes a mapping between the reactant and product side to this
Reaction.
- removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.AdductFormula
-
Removes an IMolecularFormula from this chemObject.
- removeMolecularFormula(int) - Method in class org.openscience.cdk.silent.AdductFormula
-
Removes an MolecularFormula from this chemObject.
- removeMolecularFormula(IMolecularFormula) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Removes an IMolecularFormula from this chemObject.
- removeMolecularFormula(int) - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Removes an MolecularFormula from this chemObject.
- removeMonomer(String) - Method in class org.openscience.cdk.silent.Polymer
-
Removes a particular monomer, specified by its name.
- removeMonomer(String) - Method in class org.openscience.cdk.silent.Strand
-
Removes a particular monomer, specified by its name.
- removeProperty(Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Removes a property for a IChemObject.
- removeProperty(Object) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Removes a property for a IChemObject.
- removeReaction(int) - Method in class org.openscience.cdk.silent.ReactionSet
-
Remove a reaction from this set.
- removeReaction(IReaction) - Method in class org.openscience.cdk.silent.ReactionSet
-
- removeReactionScheme(IReactionScheme) - Method in class org.openscience.cdk.silent.ReactionScheme
-
Removes an IReactionScheme from this chemObject.
- removeSingleElectron(int) - Method in class org.openscience.cdk.silent.AtomContainer
- removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.silent.AtomContainer
- removeStrand(String) - Method in class org.openscience.cdk.silent.BioPolymer
-
Removes a particular strand, specified by its name.
- replaceAtomContainer(int, IAtomContainer) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Replace the AtomContainer at a specific position (array has to be large enough).
- Ring - Class in org.openscience.cdk.silent
-
Class representing a ring structure in a molecule.
- Ring() - Constructor for class org.openscience.cdk.silent.Ring
-
Constructs an empty ring.
- Ring(IAtomContainer) - Constructor for class org.openscience.cdk.silent.Ring
-
Constructs a ring from the atoms in an IAtomContainer object.
- Ring(int, String) - Constructor for class org.openscience.cdk.silent.Ring
-
Constructs a ring that will have a certain number of atoms of the given elements.
- Ring(int) - Constructor for class org.openscience.cdk.silent.Ring
-
Constructs an empty ring that will have a certain size.
- ringSet - Variable in class org.openscience.cdk.silent.ChemModel
-
A RingSet.
- RingSet - Class in org.openscience.cdk.silent
-
Maintains a set of Ring objects.
- RingSet() - Constructor for class org.openscience.cdk.silent.RingSet
-
The constructor.
- setA(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the A unit cell axes in Cartesian coordinates in a
Euclidean space.
- setAltLoc(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Alternate location indicator of this atom.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.silent.AtomContainer
- setAtom(IAtom, int) - Method in class org.openscience.cdk.silent.Bond
-
Sets an Atom in this bond.
- setAtom(IAtom) - Method in class org.openscience.cdk.silent.LonePair
-
Sets the associated Atom.
- setAtom(IAtom) - Method in class org.openscience.cdk.silent.SingleElectron
-
Sets the associated Atom.
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.silent.Element
-
Sets the atomic number of this element.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.AtomContainer
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.silent.Bond
-
Sets the array of atoms making up this bond.
- setAtomTypeName(String) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the if attribute of the AtomType object.
- setAttachPointNum(int) - Method in class org.openscience.cdk.silent.PseudoAtom
- setB(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the B unit cell axes in Cartesian coordinates.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBonds(IBond[]) - Method in class org.openscience.cdk.silent.AtomContainer
- setC(Vector3d) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the C unit cell axes in Cartesian coordinates.
- setChainID(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Chain identifier of this atom.
- setChainID(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setCharge(Integer) - Method in class org.openscience.cdk.silent.AdductFormula
-
Deprecated.
- setCharge(Double) - Method in class org.openscience.cdk.silent.Atom
-
Sets the partial charge of this atom.
- setCharge(Integer) - Method in class org.openscience.cdk.silent.MolecularFormula
- setCovalentRadius(Double) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the covalent radius for this AtomType.
- setCrystal(ICrystal) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the Crystal contained in this ChemModel.
- setDirection(IReaction.Direction) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the direction of the reaction.
- setElectronCount(Integer) - Method in class org.openscience.cdk.silent.ElectronContainer
-
Sets the number of electrons in this electron container.
- setEndChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending Chain identifier of this structure.
- setEndInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending Code for insertion of residues of this structure.
- setEndSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the ending sequence number of this structure.
- setExactMass(Double) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setExactMass(Double) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the ExactMass attribute of the Isotope object.
- setExpanded(boolean) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.silent.ChemObject
- setFlags(boolean[]) - Method in class org.openscience.cdk.silent.ChemObject
- setFormalCharge(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the formal charge of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the formal neighbour count of this atom.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setFragment(IAtomContainer) - Method in class org.openscience.cdk.silent.FragmentAtom
-
- setHetAtom(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
-
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the hybridization of this atom.
- setICode(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Code for insertion of residues of this atom.
- setICode(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setID(String) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets the identifier (ID) of this object.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.silent.Atom
-
Sets the number of implicit hydrogen count of this atom.
- setIsAromatic(boolean) - Method in class org.openscience.cdk.silent.Atom
- setIsAromatic(boolean) - Method in class org.openscience.cdk.silent.Bond
- setIsInRing(boolean) - Method in class org.openscience.cdk.silent.Atom
- setIsInRing(boolean) - Method in class org.openscience.cdk.silent.Bond
- setLabel(String) - Method in class org.openscience.cdk.silent.PseudoAtom
-
Sets the label of this PseudoAtom.
- setMassNumber(Integer) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the atomic mass of this element.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the MaxBondOrder attribute of the AtomType object.
- setMoleculeSet(IAtomContainerSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the MoleculeSet of this ChemModel.
- setMonomerName(String) - Method in class org.openscience.cdk.silent.Monomer
-
Sets the name of the Monomer object.
- setMonomerType(String) - Method in class org.openscience.cdk.silent.Monomer
-
Sets the type of the Monomer object.
- setMultiplier(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultiplier(int, Double) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the coefficient of a AtomContainer to a given value.
- setMultipliers(Double[]) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sets the multipliers of the AtomContainers.
- setName(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Atom name of this atom.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.silent.Isotope
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNotification(boolean) - Method in class org.openscience.cdk.silent.ChemObject
-
- setOccupancy(Double) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Occupancy of this atom.
- setOfMolecules - Variable in class org.openscience.cdk.silent.ChemModel
-
A MoleculeSet.
- setOfReactions - Variable in class org.openscience.cdk.silent.ChemModel
-
A ReactionSet.
- setOrder(IBond.Order) - Method in class org.openscience.cdk.silent.Bond
-
Sets the bond order of this bond.
- setOxt(Boolean) - Method in class org.openscience.cdk.silent.PDBAtom
-
- setPoint2d(Point2d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.silent.Atom
-
Sets a point specifying the location of this
atom in 3D space.
- setProductCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of a a product to a given value.
- setProductCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of the products.
- setProducts(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction
-
Assigns a MoleculeSet to the products of this reaction.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.ChemObject
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Sets the properties of this object.
- setProperty(Object, Object) - Method in class org.openscience.cdk.silent.ChemObject
-
Sets a property for a IChemObject.
- setProperty(Object, Object) - Method in class org.openscience.cdk.silent.MolecularFormula
-
Sets a property for a IChemObject.
- setReactantCoefficient(IAtomContainer, Double) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficient of a a reactant to a given value.
- setReactantCoefficients(Double[]) - Method in class org.openscience.cdk.silent.Reaction
-
Sets the coefficients of the reactants.
- setReactants(IAtomContainerSet) - Method in class org.openscience.cdk.silent.Reaction
-
Assigns a MoleculeSet to the reactants in this reaction.
- setReactionSet(IReactionSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the ReactionSet contained in this ChemModel.
- setRecord(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set one entire line from the PDB entry file which describe the IPDBAtom.
- setResName(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Residue name of this atom.
- setResSeq(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Residue sequence number of this atom.
- setResSeq(String) - Method in class org.openscience.cdk.silent.PDBMonomer
-
- setRingSet(IRingSet) - Method in class org.openscience.cdk.silent.ChemModel
-
Sets the RingSet of this ChemModel.
- setSegID(String) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Segment identifier, left-justified of this atom.
- setSerial(Integer) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Atom serial number of this atom.
- setSpaceGroup(String) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the space group of this crystal.
- setStartChainID(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start Chain identifier of this structure.
- setStartInsertionCode(Character) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start Chain identifier of this structure.
- setStartSequenceNumber(Integer) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the start sequence number of this structure.
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.silent.Bond
-
Sets the stereo descriptor for this bond.
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.silent.AtomContainer
- setStereoParity(Integer) - Method in class org.openscience.cdk.silent.Atom
-
Sets the stereo parity for this atom.
- setStereoParity(Integer) - Method in class org.openscience.cdk.silent.PseudoAtom
-
Dummy method: the stereo parity is undefined, final.
- setStrandName(String) - Method in class org.openscience.cdk.silent.Strand
-
Sets the name of the Strand object.
- setStrandType(String) - Method in class org.openscience.cdk.silent.Strand
-
Sets the type of the Strand object.
- setStructureType(String) - Method in class org.openscience.cdk.silent.PDBStructure
-
set the Structure Type of this structure.
- setSymbol(String) - Method in class org.openscience.cdk.silent.Element
-
Sets the element symbol of this element.
- setTempFactor(Double) - Method in class org.openscience.cdk.silent.PDBAtom
-
set the Temperature factor of this atom.
- setTitle(String) - Method in class org.openscience.cdk.silent.AtomContainer
- setValency(Integer) - Method in class org.openscience.cdk.silent.AtomType
-
Sets the the exact electron valency of the AtomType object.
- setZ(Integer) - Method in class org.openscience.cdk.silent.Crystal
-
Sets the number of asymmetric parts in the unit cell.
- shallowCopy() - Method in class org.openscience.cdk.silent.ChemObject
-
Clones this IChemObject, but preserves references to Objects.
- SHEET - Static variable in class org.openscience.cdk.silent.PDBStructure
-
- SilentChemObjectBuilder - Class in org.openscience.cdk.silent
-
A factory class to provide implementation independent
ICDKObjects.
- SingleElectron - Class in org.openscience.cdk.silent
-
A Single Electron is an orbital which is occupied by only one electron.
- SingleElectron(IAtom) - Constructor for class org.openscience.cdk.silent.SingleElectron
-
Constructs an single electron orbital on an Atom.
- SingleElectron() - Constructor for class org.openscience.cdk.silent.SingleElectron
-
Constructs an single electron orbital with an associated Atom.
- singleElectronCount - Variable in class org.openscience.cdk.silent.AtomContainer
-
Number of single electrons contained by this object.
- singleElectrons - Variable in class org.openscience.cdk.silent.AtomContainer
-
Internal array of single electrons.
- singleElectrons() - Method in class org.openscience.cdk.silent.AtomContainer
- size() - Method in class org.openscience.cdk.silent.AdductFormula
-
Returns the number of MolecularFormulas in this AdductFormula.
- size() - Method in class org.openscience.cdk.silent.MolecularFormulaSet
-
Returns the number of MolecularFormulas in this MolecularFormulaSet.
- SMALL_FIRST - Static variable in class org.openscience.cdk.silent.RingSet
-
Flag to denote that the set is order with the smallest ring first?
- sortAtomContainers(Comparator<IAtomContainer>) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Sort the AtomContainers and multipliers using a provided Comparator
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainer
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.AtomContainerSet
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemFile
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemModel
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ChemSequence
-
Called by objects to which this object has
registered as a listener.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.silent.ReactionSet
-
- stereo - Variable in class org.openscience.cdk.silent.Bond
-
A descriptor the stereochemical orientation of this bond.
- stereoElements - Variable in class org.openscience.cdk.silent.AtomContainer
-
Internal list of atom parities.
- stereoElements() - Method in class org.openscience.cdk.silent.AtomContainer
- stereoParity - Variable in class org.openscience.cdk.silent.Atom
-
A stereo parity descriptor for the stereochemistry of this atom.
- Strand - Class in org.openscience.cdk.silent
-
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
- Strand() - Constructor for class org.openscience.cdk.silent.Strand
-
Constructs a new Strand.
- Substance - Class in org.openscience.cdk.silent
-
- Substance() - Constructor for class org.openscience.cdk.silent.Substance
-
- symbol - Variable in class org.openscience.cdk.silent.Element
-
The element symbol for this element as listed in the periodic table.