Modifier and Type | Field and Description |
---|---|
static IBond.Order |
CDKConstants.BONDORDER_DOUBLE
A bond of degree 2.0.
|
static IBond.Order |
CDKConstants.BONDORDER_QUADRUPLE |
static IBond.Order |
CDKConstants.BONDORDER_SINGLE
A bond of degree 1.0.
|
static IBond.Order |
CDKConstants.BONDORDER_TRIPLE
A bond of degree 3.0.
|
Modifier and Type | Method and Description |
---|---|
IBond.Order |
AtomType.getMaxBondOrder()
Gets the MaxBondOrder attribute of the AtomType object.
|
IBond.Order |
AtomContainer.getMaximumBondOrder(IAtom atom)
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
|
IBond.Order |
AtomContainer.getMinimumBondOrder(IAtom atom)
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
|
IBond.Order |
Bond.getOrder()
Returns the bond order of this bond.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.addBond(int atom1,
int atom2,
IBond.Order order)
Adds a bond to this container.
|
void |
AtomContainer.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo)
Adds a bond to this container.
|
void |
AtomType.setMaxBondOrder(IBond.Order maxBondOrder)
Sets the MaxBondOrder attribute of the AtomType object.
|
void |
Bond.setOrder(IBond.Order order)
Sets the bond order of this bond.
|
Constructor and Description |
---|
Bond(IAtom[] atoms,
IBond.Order order)
Constructs a multi-center bond, with a specified order and no stereo information.
|
Bond(IAtom atom1,
IAtom atom2,
IBond.Order order)
Constructs a bond with a given order.
|
Bond(IAtom atom1,
IAtom atom2,
IBond.Order order,
IBond.Stereo stereo)
Constructs a bond with a given order and stereo orientation from an array
of atoms.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugStrand.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugRing.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugPolymer.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugMonomer.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugMolecule.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugCrystal.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugBioPolymer.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugAtomContainer.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugAminoAcid.addBond(int atom1,
int atom2,
IBond.Order order) |
void |
DebugStrand.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugRing.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugPolymer.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugMonomer.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugMolecule.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugCrystal.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugBioPolymer.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugAtomContainer.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugAminoAcid.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo) |
void |
DebugPseudoAtom.setMaxBondOrder(IBond.Order maxBondOrder) |
void |
DebugFragmentAtom.setMaxBondOrder(IBond.Order maxBondOrder) |
void |
DebugAtomType.setMaxBondOrder(IBond.Order maxBondOrder) |
void |
DebugAtom.setMaxBondOrder(IBond.Order maxBondOrder) |
void |
DebugBond.setOrder(IBond.Order order) |
Constructor and Description |
---|
DebugBond(IAtom[] atoms,
IBond.Order order) |
DebugBond(IAtom atom1,
IAtom atom2,
IBond.Order order) |
DebugBond(IAtom atom1,
IAtom atom2,
IBond.Order order,
IBond.Stereo stereo) |
Modifier and Type | Method and Description |
---|---|
IBond.Order |
IAtomType.getMaxBondOrder()
Gets the MaxBondOrder attribute of the AtomType object.
|
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.Order |
IBond.getOrder()
Returns the bond order of this bond.
|
static IBond.Order |
IBond.Order.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static IBond.Order[] |
IBond.Order.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
void |
IAtomContainer.addBond(int atom1,
int atom2,
IBond.Order order)
Adds a bond to this container.
|
void |
IAtomContainer.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo)
Adds a bond to this container.
|
void |
IAtomType.setMaxBondOrder(IBond.Order maxBondOrder)
Sets the MaxBondOrder attribute of the AtomType object.
|
void |
IBond.setOrder(IBond.Order order)
Sets the bond order of this bond.
|
Constructor and Description |
---|
OrderQueryBond(IQueryAtom atom1,
IQueryAtom atom2,
IBond.Order order) |
OrderQueryBondOrderOnly(IQueryAtom atom1,
IQueryAtom atom2,
IBond.Order order) |
Constructor and Description |
---|
AnyOrderQueryBond(IQueryAtom atom1,
IQueryAtom atom2,
IBond.Order order)
Creates a new instance
|
AromaticOrSingleQueryBond(IQueryAtom atom1,
IQueryAtom atom2,
IBond.Order order)
Creates a new instance
|
AromaticQueryBond(IQueryAtom atom1,
IQueryAtom atom2,
IBond.Order order)
Creates a new instance
|
OrderQueryBond(IBond.Order order)
Creates a new instance
|
SMARTSBond(IQueryAtom atom1,
IQueryAtom atom2,
IBond.Order order) |
Modifier and Type | Method and Description |
---|---|
static IBond.Order |
Convertor.resource2Order(com.hp.hpl.jena.rdf.model.Resource rdfOrder)
Converts a
Resource object into the matching IBond.Order . |
Modifier and Type | Method and Description |
---|---|
static com.hp.hpl.jena.rdf.model.Resource |
Convertor.order2Resource(IBond.Order order)
Create the
Resource matching the given IBond.Order . |
Constructor and Description |
---|
NNBond(IAtom[] atoms,
IBond.Order order)
Deprecated.
|
NNBond(IAtom atom1,
IAtom atom2,
IBond.Order order)
Deprecated.
|
NNBond(IAtom atom1,
IAtom atom2,
IBond.Order order,
IBond.Stereo stereo)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
IRenderingElement |
BasicBondGenerator.generateBondElement(IBond bond,
IBond.Order type,
RendererModel model)
Generate a LineElement or an ElementGroup of LineElements for this bond.
|
Modifier and Type | Method and Description |
---|---|
IBond.Order |
AtomType.getMaxBondOrder()
Gets the MaxBondOrder attribute of the AtomType object.
|
IBond.Order |
AtomContainer.getMaximumBondOrder(IAtom atom)
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
|
IBond.Order |
AtomContainer.getMinimumBondOrder(IAtom atom)
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
|
IBond.Order |
Bond.getOrder()
Returns the bond order of this bond.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.addBond(int atom1,
int atom2,
IBond.Order order)
Adds a bond to this container.
|
void |
AtomContainer.addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo)
Adds a bond to this container.
|
void |
AtomType.setMaxBondOrder(IBond.Order maxBondOrder)
Sets the MaxBondOrder attribute of the AtomType object.
|
void |
Bond.setOrder(IBond.Order order)
Sets the bond order of this bond.
|
Constructor and Description |
---|
Bond(IAtom[] atoms,
IBond.Order order)
Constructs a multi-center bond, with a specified order and no stereo information.
|
Bond(IAtom atom1,
IAtom atom2,
IBond.Order order)
Constructs a bond with a given order.
|
Bond(IAtom atom1,
IAtom atom2,
IBond.Order order,
IBond.Stereo stereo)
Constructs a bond with a given order and stereo orientation from an array
of atoms.
|
Modifier and Type | Method and Description |
---|---|
static IBond.Order |
ChemicalFilters.convertOrder(double srcOrder)
Get bond order value as
IBond.Order . |
Modifier and Type | Method and Description |
---|---|
IBond.Order |
BondEnergy.getBondOrder()
Returns the bond order for this bond type energy.
|
Constructor and Description |
---|
BondEnergy(String symbol1,
String symbol2,
IBond.Order order,
int energy)
Creates a new bond energy for the given elements and
bond order.
|
Modifier and Type | Method and Description |
---|---|
int |
BondEnergies.getEnergies(IAtom sourceAtom,
IAtom targetAtom,
IBond.Order bondOrder)
Returns bond energy for a bond type, given atoms and bond type
|
int |
BondEnergies.getEnergies(String sourceAtom,
String targetAtom,
IBond.Order bondOrder)
Returns bond energy for a bond type, given atoms and bond type
|
Modifier and Type | Method and Description |
---|---|
int |
SmilesValencyChecker.calculateNumberOfImplicitHydrogens(IAtom atom,
double bondOrderSum,
IBond.Order maxBondOrder,
int neighbourCount)
Calculates the number of hydrogens that can be added to the given atom to fullfil
the atom's valency.
|
boolean |
SmilesValencyChecker.couldMatchAtomType(IAtom atom,
double bondOrderSum,
IBond.Order maxBondOrder,
IAtomType type)
Determines if the atom can be of type AtomType.
|
Modifier and Type | Method and Description |
---|---|
static IDifference |
BondOrderDifference.construct(String name,
IBond.Order first,
IBond.Order second) |
Modifier and Type | Method and Description |
---|---|
static IBond.Order |
BondManipulator.createBondOrder(double bondOrder)
Convenience method to convert a double into an IBond.Order.
|
static IBond.Order |
BondManipulator.decreaseBondOrder(IBond.Order oldOrder)
Returns the IBond.Order one lower.
|
static IBond.Order |
AtomContainerManipulator.getMaximumBondOrder(IAtomContainer container) |
static IBond.Order |
BondManipulator.getMaximumBondOrder(Iterator<IBond> bonds)
Returns the maximum bond order for a List of bonds, given an iterator to the list.
|
static IBond.Order |
BondManipulator.getMaximumBondOrder(List<IBond> bonds)
Returns the maximum bond order for a List of bonds.
|
static IBond.Order |
BondManipulator.getMinimumBondOrder(Iterator<IBond> bonds)
Returns the minimum bond order for a List of bonds, given an iterator
to the list.
|
static IBond.Order |
BondManipulator.getMinimumBondOrder(List<IBond> bonds)
Returns the minimum bond order for a List of bonds.
|
static IBond.Order |
BondManipulator.increaseBondOrder(IBond.Order oldOrder)
Returns the IBond.Order one higher.
|
Modifier and Type | Method and Description |
---|---|
static IBond.Order |
BondManipulator.decreaseBondOrder(IBond.Order oldOrder)
Returns the IBond.Order one lower.
|
static double |
BondManipulator.destroyBondOrder(IBond.Order bondOrder)
Convert a
IBond.Order to a numeric value. |
static IBond.Order |
BondManipulator.increaseBondOrder(IBond.Order oldOrder)
Returns the IBond.Order one higher.
|
static boolean |
BondManipulator.isHigherOrder(IBond.Order first,
IBond.Order second)
Returns true if the first bond has a higher bond order than the second bond.
|
static boolean |
BondManipulator.isLowerOrder(IBond.Order first,
IBond.Order second)
Returns true if the first bond has a lower bond order than the second bond.
|