Uses of Class
org.openscience.cdk.isomorphism.matchers.QueryChemObject

Packages that use QueryChemObject

Package	Description
org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.isomorphism.matchers.smarts
org.openscience.cdk.pharmacophore

Uses of QueryChemObject in org.openscience.cdk.isomorphism.matchers

Subclasses of QueryChemObject in org.openscience.cdk.isomorphism.matchers

Modifier and Type	Class and Description
class	CTFileQueryBond Captures query bond types defined in the CTFile.
class	InverseSymbolSetQueryAtom A QueryAtom that matches all symbols but those in this container.
class	OrderQueryBond
class	OrderQueryBondOrderOnly IQueryBond that matches IBond object only based on bond order, and disregarding any aromaticity flag.
class	QueryAtom
class	QueryAtomContainer
class	QueryBond Implements the concept of a "query bond" between two or more atoms.
class	RGroupQuery Represents information contained in a Symyx RGfile (R-group query file). It contains a root structure (the scaffold if you like), a map with R-group definitions (each of which can contain multiple substitutes) and a map with attachment points.
class	SymbolAndChargeQueryAtom
class	SymbolChargeIDQueryAtom
class	SymbolQueryAtom
class	SymbolSetQueryAtom A QueryAtom that matches all symbols in this container.

Uses of QueryChemObject in org.openscience.cdk.isomorphism.matchers.smarts

Subclasses of QueryChemObject in org.openscience.cdk.isomorphism.matchers.smarts

Modifier and Type	Class and Description
class	AliphaticAtom This matcher any non-aromatic atom.
class	AliphaticSymbolAtom This smarts atom matches aliphatic atom with element symbol specified.
class	AnyAtom This matcher any Atom including explicit hydrogens.
class	AnyOrderQueryBond This matches a bond of any order.
class	AromaticAtom This matcher any aromatic atom.
class	AromaticOrSingleQueryBond This matches an aromatic or a single bond, used when no bond is specified between an atom.
class	AromaticQueryBond This matches an aromatic bond.
class	AromaticSymbolAtom This class matches aromatic atom with element symbol specified.
class	AtomicNumberAtom This matches an atom using the atomic number.
class	ChiralityAtom This matches an atom with chirality property.
class	ExplicitConnectionAtom Match an atom with the defined degree.
class	FormalChargeAtom This matcher checks the formal charge of the Atom.
class	HybridizationNumberAtom This matcher checks the hybridization state of an atom.
class	HydrogenAtom This matches Hydrogen atoms.
class	ImplicitHCountAtom This matcher checks the number of implicit hydrogens of the Atom.
class	LogicalOperatorAtom This class matches a logical operator that connects two query atoms.
class	LogicalOperatorBond This class matches a logical operator that connects two query bonds.
class	MassAtom This class matches an atom based on the atomic mass.
class	NonCHHeavyAtom This matcher any heavy atom that is not C or H.
class	PeriodicGroupNumberAtom This matcher checks the periodic group number of an atom.
class	ReactionRoleQueryAtom Matches atoms with a particular role in a reaction.
class	RecursiveSmartsAtom This matches recursive smarts atoms.
class	RingBond This smarts bond matches any bond that is in a ring.
class	RingIdentifierAtom This encapsulates an atom with a ring identifier, with an optional ring bond specified.
class	RingMembershipAtom This query is found in a specified number of ring.
class	SmallestRingAtom Match an atom in a specific size ring.
class	SMARTSAtom Abstract smarts atom.
class	SMARTSBond Abstract smarts bond.
class	StereoBond This query bond indicates a particular geometric stereo configuration.
class	TotalConnectionAtom This matches an atom using total number of connections - referred to in SMARTS as the connectivity.
class	TotalHCountAtom SMARTS query atom for matching the total hydrogen count.
class	TotalRingConnectionAtom This matcher checks the number of ring connections of the checked Atom with other Atom's.
class	TotalValencyAtom This matcher checks the valence of the Atom.

Uses of QueryChemObject in org.openscience.cdk.pharmacophore

Subclasses of QueryChemObject in org.openscience.cdk.pharmacophore

Modifier and Type	Class and Description
class	PharmacophoreQuery Represents a colleciton of pharmacophore groups and constraints.