Modifier and Type | Class and Description |
---|---|
class |
Atom
Represents the idea of an chemical atom.
|
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 |
PseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugAtom
Debugging data class.
|
class |
DebugAtomType
Debugging data class.
|
class |
DebugFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
class |
DebugPDBAtom
Debugging data class.
|
class |
DebugPseudoAtom
Debugging data class.
|
Modifier and Type | Class and Description |
---|---|
class |
InverseSymbolSetQueryAtom
A QueryAtom that matches all symbols but those in this container.
|
class |
SymbolAndChargeQueryAtom |
class |
SymbolChargeIDQueryAtom |
class |
SymbolQueryAtom |
class |
SymbolSetQueryAtom
A QueryAtom that matches all symbols in this container.
|
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.
|
class |
AromaticAtom
This matcher any aromatic atom.
|
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 |
ConnectionCountAtom
This matcher checks the total valency of the Atom.
|
class |
DegreeAtom
This matcher checks the number of connections of the checked Atom
with other Atom's.
|
class |
ExplicitConnectionAtom
This smarts atom matches any atom with a certain number of explicit
connections.
|
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 |
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 |
RecursiveSmartsAtom
This matches recursive smarts atoms.
|
class |
RingAtom
This matches an atom in a specific size ring.
|
class |
RingIdentifierAtom
This encapsulates an atom with a ring identifier, with an optional ring
bond specified.
|
class |
RingMembershipAtom
This query atom matches any atom with a certain number of SSSR.
|
class |
SmallestRingAtom
This smarts atom matches any atom with the smallest SSSR size being a
certain value.
|
class |
SMARTSAtom
Abstract smarts atom.
|
class |
TotalConnectionAtom
This matches an atom using total number of connections.
|
class |
TotalHCountAtom
This matcher checks the formal charge of the Atom.
|
class |
TotalRingConnectionAtom
This matcher checks the number of ring connections of the checked Atom with
other Atom's.
|
class |
TotalValencyAtom
This matcher checks the total valency of the Atom.
|
Modifier and Type | Class and Description |
---|---|
class |
NNAtom
Deprecated.
Use the
Atom instead. |
class |
NNAtomType
Deprecated.
Use the
AtomType instead. |
class |
NNFragmentAtom
Deprecated.
Use the
FragmentAtom instead. |
class |
NNPDBAtom
Deprecated.
Use the
PDBAtom instead. |
class |
NNPseudoAtom
Deprecated.
Use the
PseudoAtom instead. |
Modifier and Type | Class and Description |
---|---|
class |
PharmacophoreAtom
A representation of a pharmacophore group.
|
class |
PharmacophoreQueryAtom
Represents a query pharmacophore group.
|
Modifier and Type | Class and Description |
---|---|
class |
PDBAtom
Represents the idea of an atom as used in PDB files.
|