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 |
AtomRef
An atom ref, references a CDK
IAtom indirectly. |
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 |
BondRef
A bond ref, references a CDK
IBond indirectly. |
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 |
ChemObject
The base class for all chemical objects in this cdk.
|
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 |
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.
|
class |
Substance
An implementation of the
ISubstance interface. |
Modifier and Type | Method and Description |
---|---|
IChemObject |
Mapping.getChemObject(int pos)
Retrieves the first or second of the related IChemObjects.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IChemObject> |
Mapping.relatedChemObjects()
Returns an Iterable to the two IChemObjects.
|
Constructor and Description |
---|
ChemObject(IChemObject chemObject)
Constructs a new IChemObject by copying the flags, and the
identifier.
|
Mapping(IChemObject objectOne,
IChemObject objectTwo)
Constructs an unconnected lone pair.
|
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 |
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.
|
class |
DebugSubstance
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IChemObject |
DebugMapping.getChemObject(int pos)
Retrieves the first or second of the related IChemObjects.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IChemObject> |
DebugMapping.relatedChemObjects()
Returns an Iterable to the two IChemObjects.
|
Constructor and Description |
---|
DebugChemObject(IChemObject object) |
DebugMapping(IChemObject objectOne,
IChemObject objectTwo) |
Modifier and Type | Method and Description |
---|---|
DepictionGenerator |
DepictionGenerator.withHighlight(Iterable<? extends IChemObject> chemObjs,
Color color)
Highlight the provided set of atoms and bonds in the depiction in the
specified color.
|
Modifier and Type | Method and Description |
---|---|
static void |
CDKDictionaryReferences.makeReferencesExplicit(IChemObject object) |
Modifier and Type | Interface and Description |
---|---|
interface |
IStereoElement<F extends IChemObject,C extends IChemObject>
Representation of stereochemical configuration.
|
interface |
IStereoElement<F extends IChemObject,C extends IChemObject>
Representation of stereochemical configuration.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IAminoAcid
A AminoAcid is Monomer which stores additional amino acid specific
informations, like the N-terminus atom.
|
interface |
IAtom
Represents the idea of an chemical atom.
|
interface |
IAtomContainer
Base class for all chemical objects that maintain a list of Atoms and
ElectronContainers.
|
interface |
IAtomContainerSet
A set of AtomContainers.
|
interface |
IAtomType
The base class for atom types.
|
interface |
IBioPolymer
A BioPolymer is a subclass of a Polymer which is supposed to store
additional informations about the Polymer which are connected to BioPolymers.
|
interface |
IBond
Implements the concept of a covalent bond between two or more atoms.
|
interface |
IChemFile
An
IChemObject containing a number of ChemSequences. |
interface |
IChemModel
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
|
interface |
IChemSequence
A sequence of ChemModels, which can, for example, be used to
store the course of a reaction.
|
interface |
ICrystal
Class representing a molecular crystal.
|
interface |
IElectronContainer
Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
|
interface |
IElement
Implements the idea of an element in the periodic table.
|
interface |
IFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
interface |
IIsotope
Used to store and retrieve data of a particular isotope.
|
interface |
ILonePair
A LonePair is an orbital primarily located with one Atom, containing
two electrons.
|
interface |
IMapping
Represents a mapping of two atoms.
|
interface |
IMonomer
A Monomer is an AtomContainer which stores additional monomer specific
informations for a group of Atoms.
|
interface |
IPDBAtom
A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
|
interface |
IPDBMonomer
Represents the idea of an protein monomer as found in PDB files.
|
interface |
IPDBPolymer
A PDBPolymer is a subclass of a BioPolymer which is supposed to store
additional informations about the BioPolymer which are connected to BioPolymers.
|
interface |
IPolymer
Subclass of Molecule to store Polymer specific attributes that a Polymer has.
|
interface |
IPseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
|
interface |
IReaction
Represents the idea of a chemical reaction.
|
interface |
IReactionScheme
Classes that implement this interface of a scheme.
|
interface |
IReactionSet
A set of reactions, for example those taking part in a reaction.
|
interface |
IRing
Class representing a ring structure in a molecule.
|
interface |
IRingSet
Maintains a set of Ring objects.
|
interface |
ISingleElectron
A Single Electron is an orbital which is occupied by only one electron.
|
interface |
IStrand
A Strand is an AtomContainer which stores additional strand specific
informations for a group of Atoms.
|
interface |
ISubstance
A chemical substance that consists of one or more chemical structures.
|
Modifier and Type | Method and Description |
---|---|
IChemObject |
IMapping.getChemObject(int pos)
Retrieve the first or second of the related IChemObjects.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IChemObject> |
IMapping.relatedChemObjects()
Returns an
Iterable to the two IChemObjects. |
Modifier and Type | Method and Description |
---|---|
IStereoElement<F,C> |
IStereoElement.map(Map<IChemObject,IChemObject> chemobjs) |
IStereoElement<F,C> |
IStereoElement.map(Map<IChemObject,IChemObject> chemobjs) |
Modifier and Type | Method and Description |
---|---|
<T extends IChemObject> |
MoSSOutputReader.read(T object)
Read a
IAtomContainerSet from the input source. |
<T extends IChemObject> |
SMILESReader.read(T object)
Reads the content from a XYZ input.
|
<T extends IChemObject> |
PDBReader.read(T oObj)
Takes an object which subclasses IChemObject, e.g.
|
<T extends IChemObject> |
PCSubstanceXMLReader.read(T object) |
<T extends IChemObject> |
XYZReader.read(T object)
reads the content from a XYZ input.
|
<T extends IChemObject> |
CMLReader.read(T object)
Read a IChemObject from input.
|
<T extends IChemObject> |
PCCompoundASNReader.read(T object) |
<T extends IChemObject> |
GhemicalMMReader.read(T object) |
<T extends IChemObject> |
PCCompoundXMLReader.read(T object) |
<T extends IChemObject> |
ShelXReader.read(T object)
Read a ChemFile from input.
|
<T extends IChemObject> |
CIFReader.read(T object)
Read a ChemFile from input.
|
<T extends IChemObject> |
PMPReader.read(T object)
reads the content from a PMP input.
|
<T extends IChemObject> |
HINReader.read(T object)
Reads the content from a HIN input.
|
<T extends IChemObject> |
Gaussian03Reader.read(T object) |
<T extends IChemObject> |
CTXReader.read(T object) |
<T extends IChemObject> |
Gaussian98Reader.read(T object) |
<T extends IChemObject> |
Mol2Reader.read(T object) |
<T extends IChemObject> |
Mopac7Reader.read(T object) |
<T extends IChemObject> |
MDLV2000Reader.read(T object)
Takes an object which subclasses IChemObject, e.g.
|
<T extends IChemObject> |
MDLRXNReader.read(T object)
Deprecated.
Takes an object which subclasses IChemObject, e.g.Molecule, and will read
this (from file, database, internet etc).
|
<T extends IChemObject> |
MDLV3000Reader.read(T object) |
<T extends IChemObject> |
MDLRXNV3000Reader.read(T object) |
<T extends IChemObject> |
MDLRXNV2000Reader.read(T object)
Takes an object which subclasses IChemObject, e.g.Molecule, and will read
this (from file, database, internet etc).
|
<T extends IChemObject> |
RGroupQueryReader.read(T object)
Check input IChemObject and proceed to parse.
|
<T extends IChemObject> |
MDLReader.read(T object)
Deprecated.
Takes an object which subclasses IChemObject, e.g.
|
<T extends IChemObject> |
CrystClustReader.read(T object) |
<T extends IChemObject> |
ZMatrixReader.read(T object)
Returns a IChemObject of type object bye reading from
the input.
|
<T extends IChemObject> |
INChIPlainTextReader.read(T object)
Reads a IChemObject of type object from input.
|
<T extends IChemObject> |
VASPReader.read(T object) |
<T extends IChemObject> |
INChIReader.read(T object)
Reads a IChemObject of type object from input.
|
<T extends IChemObject> |
GamessReader.read(T object) |
<T extends IChemObject> |
ISimpleChemObjectReader.read(T object)
Reads an IChemObject of type "object" from input.
|
Modifier and Type | Method and Description |
---|---|
boolean |
Mol2Reader.accepts(IChemObject object) |
boolean |
MDLRXNReader.accepts(IChemObject object)
Deprecated.
|
boolean |
MDLRXNV3000Reader.accepts(IChemObject object) |
boolean |
MDLRXNV2000Reader.accepts(IChemObject object) |
void |
SMILESWriter.write(IChemObject object)
Writes the content from object to output.
|
void |
PDBWriter.write(IChemObject object) |
void |
CMLWriter.write(IChemObject object)
Serializes the IChemObject to CML and redirects it to the output Writer.
|
void |
RssWriter.write(IChemObject object)
Writes a IChemObject to the MDL molfile formated output.
|
void |
Mol2Writer.write(IChemObject object) |
void |
HINWriter.write(IChemObject object) |
void |
CDKSourceCodeWriter.write(IChemObject object) |
void |
XYZWriter.write(IChemObject object) |
void |
RGroupQueryWriter.write(IChemObject object)
The actual writing of the output.
|
void |
MDLV3000Writer.write(IChemObject object)
Writes a molecule to the V3000 format.
|
void |
MDLRXNWriter.write(IChemObject object)
Writes a IChemObject to the MDL RXN file formated output.
|
void |
SDFWriter.write(IChemObject object)
Writes a IChemObject to the MDL SD file formated output.
|
void |
MDLV2000Writer.write(IChemObject object)
Writes a
IChemObject to the MDL molfile formated output. |
void |
ShelXWriter.write(IChemObject object)
Serializes the IChemObject to ShelX and redirects it to the output Writer.
|
void |
CrystClustWriter.write(IChemObject object)
Serializes the IChemObject to CrystClust format and redirects it to the output Writer.
|
void |
IChemObjectWriter.write(IChemObject object)
Writes the content of "object" to output.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SMILESWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
MoSSOutputReader.accepts(Class<? extends IChemObject> testClass)
Returns whether the given
IChemObject can be read or written. |
boolean |
SMILESReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
PDBWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
PDBReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
CMLWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
RssWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
PCSubstanceXMLReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
XYZReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
CMLReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
PCCompoundASNReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
Mol2Writer.accepts(Class<? extends IChemObject> classObject) |
boolean |
HINWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
GhemicalMMReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
PCCompoundXMLReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
ShelXReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
CIFReader.accepts(Class<? extends IChemObject> testClass) |
boolean |
PMPReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
CDKSourceCodeWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
HINReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
Gaussian03Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
CTXReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
Gaussian98Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
Mol2Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
Mopac7Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
XYZWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
MDLV2000Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
MDLRXNReader.accepts(Class<? extends IChemObject> classObject)
Deprecated.
|
boolean |
MDLV3000Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
RGroupQueryWriter.accepts(Class<? extends IChemObject> classObject)
Returns true for accepted input types.
|
boolean |
MDLRXNV3000Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
MDLRXNV2000Reader.accepts(Class<? extends IChemObject> classObject) |
boolean |
RGroupQueryReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
MDLV3000Writer.accepts(Class<? extends IChemObject> c)
Returns whether the given
IChemObject can be read or written. |
boolean |
MDLRXNWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
SDFWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
MDLReader.accepts(Class<? extends IChemObject> classObject)
Deprecated.
|
boolean |
MDLV2000Writer.accepts(Class<? extends IChemObject> classObject) |
boolean |
CrystClustReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
ZMatrixReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
INChIPlainTextReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
ShelXWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
INChIReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
CrystClustWriter.accepts(Class<? extends IChemObject> classObject) |
boolean |
GamessReader.accepts(Class<? extends IChemObject> classObject) |
boolean |
IChemObjectIO.accepts(Class<? extends IChemObject> classObject)
Returns whether the given
IChemObject can be read or written. |
Modifier and Type | Class and Description |
---|---|
class |
DefaultIteratingChemObjectReader<T extends IChemObject>
Abstract class that IteratingChemObjectReader's can implement to have it
take care of basic stuff, like managing the ReaderListeners.
|
interface |
IIteratingChemObjectReader<T extends IChemObject>
Interface for an iterating molecule reader.
|
Modifier and Type | Method and Description |
---|---|
boolean |
DefaultIteratingChemObjectReader.accepts(Class<? extends IChemObject> objectClass) |
Modifier and Type | Method and Description |
---|---|
boolean |
DefaultEventChemObjectReader.accepts(IChemObject object) |
Modifier and Type | Method and Description |
---|---|
boolean |
DefaultEventChemObjectReader.accepts(Class<? extends IChemObject> objectClass) |
Modifier and Type | Method and Description |
---|---|
void |
Mopac7Writer.write(IChemObject arg0)
Writes the content of "object" to output.
|
void |
GaussianInputWriter.write(IChemObject object) |
Modifier and Type | Method and Description |
---|---|
boolean |
Mopac7Writer.accepts(Class<? extends IChemObject> classObject) |
boolean |
GaussianInputWriter.accepts(Class<? extends IChemObject> classObject) |
Modifier and Type | Method and Description |
---|---|
IChemObject |
RandomAccessReader.first() |
IChemObject |
RandomAccessReader.last() |
IChemObject |
RandomAccessReader.next() |
IChemObject |
RandomAccessReader.previous() |
protected IChemObject |
RandomAccessSDFReader.processContent() |
protected IChemObject |
RandomAccessReader.processContent()
The reader is already set to read the record buffer.
|
IChemObject |
RandomAccessReader.readRecord(int record)
Returns the object at given record No.
|
Modifier and Type | Method and Description |
---|---|
void |
RandomAccessReader.add(IChemObject arg0) |
void |
RandomAccessReader.set(IChemObject arg0) |
Modifier and Type | Method and Description |
---|---|
boolean |
RandomAccessSDFReader.accepts(Class<? extends IChemObject> classObject) |
Modifier and Type | Method and Description |
---|---|
<T extends IChemObject> |
CDKOWLReader.read(T object)
Reads an IChemObject of type "object" from input.
|
Modifier and Type | Method and Description |
---|---|
void |
CDKOWLWriter.write(IChemObject object)
Writes the content of "object" to output.
|
Modifier and Type | Method and Description |
---|---|
boolean |
CDKOWLWriter.accepts(Class<? extends IChemObject> classObject)
Returns whether the given
IChemObject can be read or written. |
boolean |
CDKOWLReader.accepts(Class<? extends IChemObject> classObject)
Returns whether the given
IChemObject can be read or written. |
Modifier and Type | Method and Description |
---|---|
Iterable<Map<IChemObject,IChemObject>> |
Mappings.toAtomBondMap()
Convert the permutations to an atom-atom bond-bond map.
|
Iterable<Map<IChemObject,IChemObject>> |
Mappings.toAtomBondMap()
Convert the permutations to an atom-atom bond-bond map.
|
Iterable<IChemObject> |
Mappings.toChemObjects()
Obtain the chem objects (atoms and bonds) that have 'hit' in the target molecule.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryAtom
Defines the ability to be matched against
IAtom 's. |
interface |
IQueryAtomContainer
General concept of a IAtomContainer aimed at doing molecular subgraph
queries using the UniversalIsomorphismTester.
|
interface |
IQueryBond
Defines the abililty to be matched against IBond's.
|
interface |
IRGroupQuery
Interface definition for Rgroup query classes.
|
Modifier and Type | Class and Description |
---|---|
class |
CTFileQueryBond
Deprecated.
Use
Expr.Type.SINGLE_OR_AROMATIC etc. |
class |
InverseSymbolSetQueryAtom
Deprecated.
@deprecated Use
new Expr(Element, 6).and(new Expr(Element, 8)).negate() etc |
class |
OrderQueryBond
Deprecated.
|
class |
OrderQueryBondOrderOnly
Deprecated.
Use
new QueryBond(beg, end, ORDER, bord) |
class |
QueryAtom |
class |
QueryAtomContainer |
class |
QueryBond
Implements the concept of a "query bond" between two or more atoms.
|
class |
QueryChemObject |
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
Deprecated.
|
class |
SymbolChargeIDQueryAtom |
class |
SymbolQueryAtom
Deprecated.
|
class |
SymbolSetQueryAtom
Deprecated.
Use
new Expr(Element, 6).and(new Expr(Element, 8)) etc |
Modifier and Type | Class and Description |
---|---|
class |
AliphaticAtom
Deprecated.
|
class |
AliphaticSymbolAtom
Deprecated.
|
class |
AnyAtom
Deprecated.
|
class |
AnyOrderQueryBond
Deprecated.
|
class |
AromaticAtom
Deprecated.
|
class |
AromaticOrSingleQueryBond
Deprecated.
|
class |
AromaticQueryBond
Deprecated.
|
class |
AromaticSymbolAtom
Deprecated.
|
class |
AtomicNumberAtom
Deprecated.
|
class |
ChiralityAtom
Deprecated.
|
class |
ExplicitConnectionAtom
Deprecated.
|
class |
FormalChargeAtom
Deprecated.
|
class |
HybridizationNumberAtom
Deprecated.
|
class |
HydrogenAtom
Deprecated.
|
class |
ImplicitHCountAtom
Deprecated.
|
class |
LogicalOperatorAtom
Deprecated.
|
class |
LogicalOperatorBond
Deprecated.
|
class |
MassAtom
Deprecated.
|
class |
NonCHHeavyAtom
Deprecated.
|
class |
PeriodicGroupNumberAtom
Deprecated.
|
class |
ReactionRoleQueryAtom
Deprecated.
|
class |
RecursiveSmartsAtom
Deprecated.
|
class |
RingBond
Deprecated.
|
class |
RingIdentifierAtom
Deprecated.
|
class |
RingMembershipAtom
Deprecated.
|
class |
SmallestRingAtom
Deprecated.
|
class |
SMARTSAtom
Deprecated.
|
class |
SMARTSBond
Deprecated.
|
class |
StereoBond
Deprecated.
|
class |
TotalConnectionAtom
Deprecated.
|
class |
TotalHCountAtom
Deprecated.
|
class |
TotalRingConnectionAtom
Deprecated.
|
class |
TotalValencyAtom
Deprecated.
|
Constructor and Description |
---|
OverlapPair(IChemObject co1,
IChemObject co2)
Constructor for the OverlapPair object.
|
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 |
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.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractRenderer<T extends IChemObject>
The base class for all renderers, handling the core aspects of rendering
such as the location of the model in 'model space' and the location on
the screen to draw the model.
|
interface |
IRenderer<T extends IChemObject>
Interface that all 2D renderers implement.
|
Modifier and Type | Method and Description |
---|---|
Map<IChemObject,Color> |
RendererModel.ColorHash.getDefault()
Gets the default value for this parameter.
|
Modifier and Type | Method and Description |
---|---|
void |
RendererModel.registerParameters(IGenerator<? extends IChemObject> generator)
Registers rendering parameters from
IGenerator s
with this model. |
Modifier and Type | Interface and Description |
---|---|
interface |
IGenerator<T extends IChemObject>
An
IGenerator converts chemical entities into parts of the
chemical drawing expressed as IRenderingElement s. |
Modifier and Type | Method and Description |
---|---|
<E extends IChemObject> |
IChemObjectSelection.elements(Class<E> clazz)
Returns a
Collection of all selected IChemObject s of the
given type. |
Modifier and Type | Method and Description |
---|---|
protected void |
AbstractSelection.addToAtomContainer(IAtomContainer ac,
IChemObject item)
Utility method to add an
IChemObject to an IAtomContainer . |
boolean |
IChemObjectSelection.contains(IChemObject obj)
Determines if the
IChemObject is part of the current selection. |
Modifier and Type | Method and Description |
---|---|
IChemObject |
Mapping.getChemObject(int pos)
Retrieves the first or second of the related IChemObjects.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IChemObject> |
Mapping.relatedChemObjects()
Returns an Iterable to the two IChemObjects.
|
Constructor and Description |
---|
ChemObject(IChemObject chemObject)
Constructs a new IChemObject by copying the flags, and the
identifier.
|
Mapping(IChemObject objectOne,
IChemObject objectTwo)
Constructs an unconnected lone pair.
|
Modifier and Type | Method and Description |
---|---|
ITetrahedralChirality |
TetrahedralChirality.map(Map<IChemObject,IChemObject> chemobjs) |
ITetrahedralChirality |
TetrahedralChirality.map(Map<IChemObject,IChemObject> chemobjs) |
Modifier and Type | Method and Description |
---|---|
static void |
IDCreator.createIDs(IChemObject chemObject)
Labels the Atom's and Bond's in the AtomContainer using the a1, a2, b1, b2
scheme often used in CML.
|
Modifier and Type | Method and Description |
---|---|
static String |
IsotopeDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
LonePairDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
AtomDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
BondDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
ElectronContainerDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
ElementDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
SingleElectronDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
AtomContainerDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
AtomTypeDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static String |
ChemObjectDiff.diff(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as a String . |
static IDifference |
IsotopeDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
LonePairDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
AtomDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
BondDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
ElectronContainerDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
ElementDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
SingleElectronDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
AtomContainerDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
AtomTypeDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
static IDifference |
ChemObjectDiff.difference(IChemObject first,
IChemObject second)
Compare two
IChemObject classes and return the difference as an IDifference . |
Modifier and Type | Method and Description |
---|---|
static IChemObject |
ReactionManipulator.getMappedChemObject(IReaction reaction,
IChemObject chemObject)
get the IAtom which is mapped
|
Modifier and Type | Method and Description |
---|---|
static List<IChemObject> |
MoleculeSetManipulator.getAllChemObjects(IAtomContainerSet set) |
static List<IChemObject> |
AtomContainerSetManipulator.getAllChemObjects(IAtomContainerSet set)
Does not recursively return the contents of the AtomContainer.
|
static List<IChemObject> |
ChemFileManipulator.getAllChemObjects(IChemFile file)
Returns a List of all IChemObject inside a ChemFile.
|
static List<IChemObject> |
ChemModelManipulator.getAllChemObjects(IChemModel chemModel)
Retrieve a List of all ChemObject objects within an IChemModel.
|
static List<IChemObject> |
ChemSequenceManipulator.getAllChemObjects(IChemSequence sequence)
Returns a List of all IChemObject inside a ChemSequence.
|
static List<IChemObject> |
ReactionManipulator.getAllChemObjects(IReaction reaction) |
static List<IChemObject> |
ReactionSetManipulator.getAllChemObjects(IReactionSet set) |
Modifier and Type | Method and Description |
---|---|
static IChemObject |
ReactionManipulator.getMappedChemObject(IReaction reaction,
IChemObject chemObject)
get the IAtom which is mapped
|
Modifier and Type | Method and Description |
---|---|
static List<Sgroup> |
SgroupManipulator.copy(Collection<Sgroup> sgroups,
Map<? extends IChemObject,? extends IChemObject> replace)
|
static List<Sgroup> |
SgroupManipulator.copy(Collection<Sgroup> sgroups,
Map<? extends IChemObject,? extends IChemObject> replace)
|
Modifier and Type | Method and Description |
---|---|
IChemObject |
ValidationTest.getChemObject() |
Modifier and Type | Method and Description |
---|---|
static void |
ProblemMarker.markWithError(IChemObject object) |
static void |
ProblemMarker.markWithWarning(IChemObject object) |
static void |
ProblemMarker.unmark(IChemObject object) |
static void |
ProblemMarker.unmarkWithError(IChemObject object) |
static void |
ProblemMarker.unmarkWithWarning(IChemObject object) |
ValidationReport |
AbstractValidator.validateChemObject(IChemObject subject) |
ValidationReport |
IValidator.validateChemObject(IChemObject object) |
ValidationReport |
DictionaryValidator.validateChemObject(IChemObject subject) |
ValidationReport |
ValidatorEngine.validateChemObject(IChemObject subject) |
Constructor and Description |
---|
ValidationTest(IChemObject object,
String error) |
ValidationTest(IChemObject object,
String error,
String details) |
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