Modifier and Type | Class and 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 |
Molecule
Represents the concept of a chemical molecule, an object composed of
atoms connected by bonds.
|
class |
MoleculeSet
A set of molecules, for example those taking part in a reaction.
|
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.
|
Modifier and Type | Class and 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 |
DebugMolecule
Debugging data class.
|
class |
DebugMoleculeSet
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.
|
Modifier and Type | Class and Description |
---|---|
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 |
QueryAtomContainer |
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.
|
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 |
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 |
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 |
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 |
RecursiveSmartsAtom
This matches recursive smarts atoms.
|
class |
RingAtom
This matches an atom in a specific size ring.
|
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 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 |
SMARTSBond
Abstract smarts bond.
|
class |
StereoBond
This query bond matches bonds with specific stereo type.
|
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 |
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.
|
Modifier and Type | Class and Description |
---|---|
class |
NNAminoAcid
Deprecated.
Use the
AminoAcid instead. |
class |
NNAtom
Deprecated.
Use the
Atom instead. |
class |
NNAtomContainer
Deprecated.
Use the
AtomContainer instead. |
class |
NNAtomContainerSet
Deprecated.
Use the
AtomContainerSet instead. |
class |
NNAtomType
Deprecated.
Use the
AtomType instead. |
class |
NNBioPolymer
Deprecated.
Use the
BioPolymer instead. |
class |
NNBond
Deprecated.
Use the
Bond instead. |
class |
NNChemFile
Deprecated.
Use the
ChemFile instead. |
class |
NNChemModel
Deprecated.
Use the
ChemModel instead. |
class |
NNChemObject
Deprecated.
Use the
ChemObject instead. |
class |
NNChemSequence
Deprecated.
Use the
ChemSequence instead. |
class |
NNCrystal
Deprecated.
Use the
Crystal instead. |
class |
NNElectronContainer
Deprecated.
Use the
ElectronContainer instead. |
class |
NNElement
Deprecated.
Use the
Element instead. |
class |
NNFragmentAtom
Deprecated.
Use the
FragmentAtom instead. |
class |
NNIsotope
Deprecated.
Use the
Isotope instead. |
class |
NNLonePair
Deprecated.
Use the
LonePair instead. |
class |
NNMapping
Deprecated.
Use the
Mapping instead. |
class |
NNMolecule
Deprecated.
Use the
Molecule instead. |
class |
NNMoleculeSet
Deprecated.
Use the
MoleculeSet instead. |
class |
NNMonomer
Deprecated.
Use the
Monomer instead. |
class |
NNPDBAtom
Deprecated.
Use the
PDBAtom instead. |
class |
NNPDBMonomer
Deprecated.
Use the
PDBMonomer instead. |
class |
NNPDBPolymer
Deprecated.
Use the
PDBPolymer instead. |
class |
NNPDBStructure
Deprecated.
Use the
PDBStructure instead. |
class |
NNPolymer
Deprecated.
Use the
Polymer instead. |
class |
NNPseudoAtom
Deprecated.
Use the
PseudoAtom instead. |
class |
NNReaction
Deprecated.
Use the
Reaction instead. |
class |
NNReactionScheme
Deprecated.
Use the
ReactionScheme instead. |
class |
NNReactionSet
Deprecated.
Use the
ReactionSet instead. |
class |
NNRing
Deprecated.
Use the
Ring instead. |
class |
NNRingSet
Deprecated.
Use the
RingSet instead. |
class |
NNSingleElectron
Deprecated.
Use the
SingleElectron instead. |
class |
NNStrand
Deprecated.
Use the
Strand instead. |
Modifier and Type | Class and 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 |
PharmacophoreQuery
Represents a colleciton of pharmacophore groups and constraints.
|
class |
PharmacophoreQueryAngleBond
Represents a pharmacophore query angle constraint.
|
class |
PharmacophoreQueryAtom
Represents a query pharmacophore group.
|
class |
PharmacophoreQueryBond
Represents a pharmacophore query distance constraint.
|
Modifier and Type | Class and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
ReactionChain
Classes that extends the definition of reaction to a chain reaction.
|