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The Octet Molecular Representation Framework v0.8.2 | |||||||||
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AbstractMoleculeBuilder intended for use in building partial
or complete Molecule representations.RepresentationBuilder interface.Molecule.AllCyclesMoleculeQuery that uses
a HanserCycleTraverser for cycle perception.
AllCyclesMoleculequery that delegates
cycle perception to traverser.
Sequence interface backed by an
array.ArraySequence that will return
null for getObjectClass().
ArraySequence from the elements of
collection by enforcing the constraint that all of its
members are of type objectClass.
ArraySequence from the elements of
array by enforcing the constraint that all of its
members are of type objectClass.
AtomCollection represents an immutable
group of Atoms.AtomGraph represents the graph theoretical construct of a graph as applied to
a set of Atoms.AtomGraphCollection is an immutable
group of AtomGraphs.AtomGraph.graph.
AtomGraphCollection.BasicAtomGraph functionality.AtomCollection.Atoms.AtomPair represents a pair of Atoms.AtomPairCollection represents an immutable
group of AtomPairs.AtomPairIterator provides a mechanism to iterate over an
AtomPairCollection.BasicAtomPair.Atom.Atom queries.AtomicSymbols.AtomicSymbolCollection.AtomicSystem functionality.AtomProxy representing an Atom containing
the specified IsotopicDistribution.
AtomProxy representing the specified AtomQuery.
AtomProxy for an Atom represented by the specified one- or two-
letter atomic symbol.
BondingSystem and adds it to the current representation.
atom.
orbital with one electron of spin spinUp.
GammaSequence beginning at start and adds
it to the representation under construction.
configuration
and the specified neighboring atom neighbor.
sequence.
hydrogenCount the number of virtual hydrogen atoms
associated with atom.
Orbital localized on atom.
atom using builder.
pair has just been completed.
atom has just been completed.
AtomCollection interface
backed by an ArraySequence.BasicAtomCollection.
BasicAtomCollection from the elements contained
in atoms.
BasicAtomCollection from the elements contained
in atoms.
AtomGraph interface that is suitable for
representing Molecule subgraphs.BasicAtomGraph.
BasicAtomGraph from the specified AtomPairCollection.
BasicAtomGraph from atoms and pairs.
AtomGraphCollection interface
backed by an ArraySequence.SubgraphCollection.
BasicAtomGraphCollection from the elements contained
in graphs.
BasicAtomGraphCollection from the elements contained
in graphs.
AtomMap interface backed by a
HashMap.BasicAtomMap using the specified Map
for the mapping relationships.
AtomPair interface.BasicAtomPair from source and
target.
AtomPairCollection interface
backed by an ArraySequence.BasicAtomPairCollection.
BasicAtomPairCollection from the elements contained
in pairs.
BasicAtomPairCollection from the elements contained
in pairs.
AtomicSymbolCollection interface backed
by an ArraySequence.BasicAtomicSymbolCollection.
BasicAtomicSymbolCollection from the elements contained
in symbols.
BasicAtomicSymbolCollection from the elements contained
in symbols.
AtomicSystem interface.BondingSystem interface.BondingSystemCollection interface
backed by an ArraySequence.BasicBondingSystemCollection.
BasicBondingSystemCollection from the elements contained
in systems.
BasicBondingSystemCollection from the elements contained
in systems.
BreadthTraverser interface.BasicBreadthTraverser.
Configuration interface.BasicConfiguration from the contents of wheels.
ConfigurationComparator interface.Conformation interface.BasicConformation from wheels and sequences.
ConformationComparator interface.CycleSystemTraverser interface.DepthTraverser interface.BasicDepthTraverser.
Electron interface.BasicElectron with spin spin.
ElectronCollection interface backed
by an ArraySequence.BasicElectronCollection.
BasicElectronCollection from the elements contained
in electrons.
BasicElectronCollection from the elements contained
in electrons.
FlexMolHandler interface.FlexMolWriter interface.BasicGammaSequence interface.BasicGammaSequence from axis and
pairs.
GammaSequenceCollection interface
backed by an ArraySequence.BasicGammaSequenceCollection.
HalfPlane interface.BasicHalfPlane from atoms and positions.
HalfPlaneCollection interface backed
by an ArraySequenceBasicHalfPlaneCollection
BasicHalfPlaneCollection from the elements contained
in planes.
BasicHalfPlaneCollection from the elements contained
in planes.
Measurement interface.BasicMeasurement from
value, uncertainty, and units.
BasicMeasurement from
value, uncertainty, and units.
MoleculeBuilder interface.MoleculeConvertor interface.MoleculeQueryBuilder interface.BasicMoleculeQueryBuilder that uses the specified
MoleculeQueryStrategy.
NonbondingShell interface.BasicNonbondingShell.
BasicNonbondingShell from
orbitals.
NucleusCollection interface backed by
a ArraySequence.BasicNucleusCollection.
BasicNucleusCollection from the elements contained
in nuclei.
BasicNucleusCollection from the elements contained
in nuclei.
Orbital interface.BasicOrbital.
BasicOrbital from the specified
Collection containing Electrons.
BasicOrbital from the specified
array containing Electrons.
OrbitalCollection interface
backed by an ArraySequence.BasicOrbitalCollection.
BasicOrbitalCollection from the elements
contained in orbitals.
BasicOrbitalCollection from the elements
contained in orbitals.
PaddleWheel interface.BasicPaddleWheel from planes and axis.
PaddleWheelCollection interface backed
by an ArraySequenceBasicPaddleWheelCollection.
BasicPaddleWheelCollection from the elements contained
in wheels.
BasicPaddleWheelCollection from the elements contained
in wheels.
PaddleWheelComparator interface.TraversalHandler interface with
empty method implementations.BasicTraversalHandler.
MoleculeQueryStrategy consistent with exact structure matching.BilateralQueryStrategy.
BilateralQueryStrategy that
delegates traversal operations to traverser.
BondingSystem reflects a conceptually general model
of chemical bonding.BondingSystemCollection represents an immutable
group of BondingSystems.BondingSystemIterator provides a mechanism to iterate over a
BondingSystemCollection.BondingSystem.AtomGraph in breadth first order starting
from a client-defined root Atom.TraversalHandler interface that includes methods
specific to BreadthTraverser traversal.BreadthTraverser functionality.RepresentationBuilders.branch.
branch.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder.
BondingSystem comprised of five atoms and six electrons.
AtomProxy array after building an aromatic benzene
representation.
RepresentationBuilder.
builder to construct bicyclo[2.2.2]octane using
the specified RepresentationBuilder.
builder to build biphenyl.
AtomProxy array after building a chain of
length carbons.
AtomProxy array after building a carbocyclic
ring of size members.
RepresentationBuilder
with a charge-separated S-O group.
RepresentationBuilder.
RepresentationBuilder.
builder to build cubane.
builder to build cyclohexane.
builder to build cyclohexene.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder.
builder to build 1,4-diisopropylbenzene.
RepresentationBuilder
with a double-bonded S=0 group.
RepresentationBuilder.
builder to build hexane.
RepresentationBuilder.
builder to build isopentane.
RepresentationBuilder.
RepresentationBuilder.
builder to build Kekule-toluene.
builder to build Kekule-naphthalene.
AtomProxy array after building an aromatic naphthalene
representation.
RepresentationBuilder.
builder to build quinoline with aromatic bonding.
RepresentationBuilder.
RepresentationBuilder,
but with an inverted conformation about the biaryl axis compared to the result obtained
with buildRBinaphthyl.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder.
RepresentaitonBuilder.
RepresentationBuilder.
RepresentationBuilder.
AtomProxy array after building a chain
of length carbons.
AtomProxy array after building a ring
of length carbons.
builder to build serotonin with Kekule aromatic bonding.
builder to build t-butylcyclohexane.
RepresentationBuilder.
RepresentationBuilder.
RepresentationBuilder
MoleculeQuery interface that enables
query results to be cached to improve performance.CachedMoleculeQuery that forwards
requests to query.
net.sf.octet.collection package.net.sf.octet.collection package.Atoms about a central Atom.Configuration.Configuration.Configuration and ConfigurationComparator functionality.Conformations.Molecule conformation.AtomGraph.CycleSystemTraverser events.CycleSystemTraverser functionality.AtomGraph.TraversalHandler interface that includes methods
specific to CycleTraverser traversal.CycleTraverser functionality.input with model using map to
correlate Atoms between the two.
input to model, using the specified AtomMap
to correlate Atoms between the two.
input to model using the specified AtomMap
to correlate Atoms between the two.
AtomProxies in a planar arrangement about an
axis defined by a left and right AtomProxy.
AtomProxies in a tetrahedral arrangement about a central
AtomProxy using Builder.
source with target within the
BondingSystem denoted by system.
atom to sequence.