| Package | Description |
|---|---|
| org.openscience.cdk.hash | |
| org.openscience.cdk.interfaces | |
| org.openscience.cdk.isomorphism.matchers | |
| org.openscience.cdk.libio.cml |
| Modifier and Type | Method and Description |
|---|---|
int |
AtomEncoder.encode(IAtom atom,
IAtomContainer container)
Encode an invariant attribute of the given atom.
|
| Modifier and Type | Interface and Description |
|---|---|
interface |
IFragmentAtom
Class to represent an IPseudoAtom which embeds an IAtomContainer.
|
interface |
IPDBAtom
A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.
|
interface |
IPseudoAtom
Represents the idea of a non-chemical atom-like entity, like Me,
R, X, Phe, His, etc.
|
| Modifier and Type | Method and Description |
|---|---|
IAtom |
IAtom.clone()
Returns a deep clone of this IChemObject.
|
IAtom |
ISingleElectron.getAtom()
Returns the associated Atom.
|
IAtom |
ILonePair.getAtom()
Returns the associated Atom.
|
IAtom |
IBond.getAtom(int position)
Returns an Atom from this bond.
|
IAtom |
IAtomContainer.getAtom(int idx)
Get the atom at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getAtomCount(). |
IAtom |
IBond.getBegin()
Access the begin (or first) atom of the bond.
|
IAtom |
ITetrahedralChirality.getChiralAtom()
Atom that is the chirality center.
|
IAtom |
IBond.getConnectedAtom(IAtom atom)
Deprecated.
use the method
IBond.getOther(IAtom) |
IAtom[] |
IBond.getConnectedAtoms(IAtom atom)
Returns all the atoms in the bond connected to the given atom.
|
IAtom |
IAminoAcid.getCTerminus()
Retrieves the C-terminus atom.
|
IAtom |
IBond.getEnd()
Access the end (or second) atom of the bond.
|
IAtom |
IAtomContainer.getFirstAtom()
Deprecated.
|
IAtom |
IAtomContainer.getLastAtom()
Deprecated.
|
IAtom[] |
ITetrahedralChirality.getLigands()
Returns an array of ligand atoms around the chiral atom.
|
IAtom |
IAminoAcid.getNTerminus()
Retrieves the N-terminus atom.
|
IAtom |
IBond.getOther(IAtom atom)
Returns the other atom in the bond, the atom is connected to the given atom.This
method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined
and the more correct
IBond.getConnectedAtoms(IAtom) should be used. |
IAtom |
IChemObjectBuilder.newAtom()
Create a new atom using the default constructor.
|
| Modifier and Type | Method and Description |
|---|---|
Iterable<IAtom> |
IBond.atoms()
Returns the Iterable to atoms making up this bond.
|
Iterable<IAtom> |
IAtomContainer.atoms()
Returns an Iterable for looping over all atoms in this container.
|
List<IAtom> |
IAtomContainer.getConnectedAtomsList(IAtom atom)
Returns the atoms connected connected to the specified atom by
a bond.
|
| Modifier and Type | Method and Description |
|---|---|
void |
IStrand.addAtom(IAtom oAtom)
Adds the atom oAtom without specifying a Monomer or a Strand.
|
void |
IPolymer.addAtom(IAtom oAtom)
Adds the atom oAtom without specifying a Monomer.
|
void |
ICrystal.addAtom(IAtom atom)
Adds the atom to the crystal.
|
void |
IBioPolymer.addAtom(IAtom oAtom)
Adds the atom oAtom without specifying a Monomer or a Strand.
|
void |
IAtomContainer.addAtom(IAtom atom)
Adds an atom to this container.
|
void |
IStrand.addAtom(IAtom oAtom,
IMonomer oMonomer)
Adds the atom oAtom to a specific Monomer.
|
void |
IPolymer.addAtom(IAtom oAtom,
IMonomer oMonomer)
Adds the atom oAtom to a specified Monomer.
|
void |
IBioPolymer.addAtom(IAtom oAtom,
IMonomer oMonomer,
IStrand oStrand)
Adds the atom to a specified Strand and a specified Monomer.
|
void |
IBioPolymer.addAtom(IAtom oAtom,
IStrand oStrand)
Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
|
void |
IAminoAcid.addCTerminus(IAtom atom)
Add an Atom and makes it the C-terminus atom.
|
void |
IAminoAcid.addNTerminus(IAtom atom)
Add an Atom and makes it the N-terminus atom.
|
boolean |
IStereoElement.contains(IAtom atom)
Does the stereo element contain the provided atom.
|
boolean |
ISingleElectron.contains(IAtom atom)
Returns true if the given atom participates in this SingleElectron.
|
boolean |
IRingSet.contains(IAtom atom)
True, if at least one of the rings in the ringset contains
the given atom.
|
boolean |
ILonePair.contains(IAtom atom)
Returns true if the given atom participates in this lone pair.
|
boolean |
IBond.contains(IAtom atom)
Returns true if the given atom participates in this bond.
|
boolean |
IAtomContainer.contains(IAtom atom)
True, if the AtomContainer contains the given atom object.
|
int |
IAtomContainer.getAtomNumber(IAtom atom)
Deprecated.
|
IBond |
IAtomContainer.getBond(IAtom atom1,
IAtom atom2)
Returns the bond that connects the two given atoms.
|
int |
IAtomContainer.getBondNumber(IAtom atom1,
IAtom atom2)
Deprecated.
|
double |
IAtomContainer.getBondOrderSum(IAtom atom)
Returns the sum of the bond orders for a given Atom.
|
IAtom |
IBond.getConnectedAtom(IAtom atom)
Deprecated.
use the method
IBond.getOther(IAtom) |
IAtom[] |
IBond.getConnectedAtoms(IAtom atom)
Returns all the atoms in the bond connected to the given atom.
|
int |
IAtomContainer.getConnectedAtomsCount(IAtom atom)
Deprecated.
|
List<IAtom> |
IAtomContainer.getConnectedAtomsList(IAtom atom)
Returns the atoms connected connected to the specified atom by
a bond.
|
int |
IAtomContainer.getConnectedBondsCount(IAtom atom)
Returns the number of connected bonds (explicit degree) to the
specified atom.
|
List<IBond> |
IAtomContainer.getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.
|
List<IElectronContainer> |
IAtomContainer.getConnectedElectronContainersList(IAtom atom)
Returns the electron containers (bonds, radicals, and lone pairs )
connected connected to the specified atom.
|
int |
IAtomContainer.getConnectedLonePairsCount(IAtom atom)
Returns the number of lone pairs connected to the specified atom.
|
List<ILonePair> |
IAtomContainer.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
int |
IAtomContainer.getConnectedSingleElectronsCount(IAtom atom)
Returns the number of single electrons connected to the specified atom.
|
List<ISingleElectron> |
IAtomContainer.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
IBond.Order |
IAtomContainer.getMaximumBondOrder(IAtom atom)
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
|
IBond.Order |
IAtomContainer.getMinimumBondOrder(IAtom atom)
Returns the minimum bond order that this atom currently has
in the context of this AtomContainer.
|
IBond |
IRing.getNextBond(IBond bond,
IAtom atom)
Returns the next bond in order, relative to a given bond and atom.
|
IAtom |
IBond.getOther(IAtom atom)
Returns the other atom in the bond, the atom is connected to the given atom.This
method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined
and the more correct
IBond.getConnectedAtoms(IAtom) should be used. |
IRingSet |
IRingSet.getRings(IAtom atom)
Returns a vector of all rings that this atom is part of.
|
int |
IAtomContainer.indexOf(IAtom atom)
Access the storage index of an atom.
|
void |
IAtomContainer.removeAtom(IAtom atom)
Safely remove an atom from the container.
|
void |
IAtomContainer.removeAtomAndConnectedElectronContainers(IAtom atom)
Deprecated.
Method has be renamed
IAtomContainer.removeAtom(IAtom). |
void |
IAtomContainer.removeAtomOnly(IAtom atom)
Unsafely remove atom.
|
IBond |
IAtomContainer.removeBond(IAtom atom1,
IAtom atom2)
Removes the bond that connects the two given atoms.
|
void |
ISingleElectron.setAtom(IAtom atom)
Sets the associated Atom.
|
void |
ILonePair.setAtom(IAtom atom)
Sets the associated Atom.
|
void |
IBond.setAtom(IAtom atom,
int position)
Sets an Atom in this bond.
|
void |
IAtomContainer.setAtom(int idx,
IAtom atom)
Set the atom at
idx, the index must have an existing atom
and therefore be in the range 0 ≤ idx < mol.getAtomCount(). |
void |
IBond.setAtoms(IAtom[] atoms)
Sets the array of atoms making up this bond.
|
void |
IAtomContainer.setAtoms(IAtom[] atoms)
Sets the array of atoms of this AtomContainer.
|
| Modifier and Type | Method and Description |
|---|---|
ITetrahedralChirality |
ITetrahedralChirality.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
ITetrahedralChirality |
ITetrahedralChirality.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
IStereoElement |
IStereoElement.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
IStereoElement |
IStereoElement.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
IDoubleBondStereochemistry |
IDoubleBondStereochemistry.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
IDoubleBondStereochemistry |
IDoubleBondStereochemistry.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
| Modifier and Type | Interface and Description |
|---|---|
interface |
IQueryAtom
Defines the ability to be matched against
IAtom's. |
| Modifier and Type | Method and Description |
|---|---|
boolean |
IQueryAtom.matches(IAtom atom)
Returns true of the given
atom matches this IQueryAtom. |
| Modifier and Type | Method and Description |
|---|---|
void |
ICMLCustomizer.customize(IAtom atom,
Object nodeToAdd)
Customized the nodeToAdd for the given Atom.
|
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