Uses of Interface
org.openscience.cdk.interfaces.IBond
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Uses of IBond in org.openscience.cdk
Classes in org.openscience.cdk that implement IBond Modifier and Type Class Description class
Bond
Implements the concept of a covalent bond between two or more atoms.class
BondRef
A bond ref, references a CDKIBond
indirectly.Fields in org.openscience.cdk declared as IBond Modifier and Type Field Description protected IBond[]
AtomContainer. bonds
Internal array of bonds.Methods in org.openscience.cdk that return IBond Modifier and Type Method Description IBond
Bond. clone()
Clones this bond object, including clones of the atoms between which the bond is defined.IBond
BondRef. clone()
Returns a deep clone of this IChemObject.IBond
BondRef. deref()
Dereference the bond pointer once providing access to the base bond.static IBond
BondRef. deref(IBond bond)
Utility method to dereference an bond pointer.IBond
Atom. getBond(IAtom atom)
Returns the bond connecting 'this' atom to the provided atom.IBond
AtomContainer. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
AtomContainer. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
AtomRef. getBond(IAtom atom)
Returns the bond connecting 'this' atom to the provided atom.IBond
Ring. getNextBond(IBond bond, IAtom atom)
Returns the next bond in order, relative to a given bond and atom.IBond
DefaultChemObjectBuilder. newBond()
Create a new bond using the default constructor.IBond
AtomContainer. removeBond(int position)
Removes the bond at the given position from the AtomContainer.IBond
AtomContainer. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.Methods in org.openscience.cdk that return types with arguments of type IBond Modifier and Type Method Description Iterable<IBond>
Atom. bonds()
Returns the bonds connected to this atom.Iterable<IBond>
AtomContainer. bonds()
Returns an Iterable for looping over all bonds in this container.Iterable<IBond>
AtomRef. bonds()
List<IBond>
AtomContainer. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.Methods in org.openscience.cdk with parameters of type IBond Modifier and Type Method Description void
AtomContainer. addBond(IBond bond)
Adds a Bond to this AtomContainer.boolean
AtomContainer. contains(IBond bond)
True, if the AtomContainer contains the given bond object.static IBond
BondRef. deref(IBond bond)
Utility method to dereference an bond pointer.int
AtomContainer. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.IBond
Ring. getNextBond(IBond bond, IAtom atom)
Returns the next bond in order, relative to a given bond and atom.IRingSet
RingSet. getRings(IBond bond)
Returns a vector of all rings that this bond is part of.int
AtomContainer. indexOf(IBond bond)
Access the storage index of a bond.boolean
Bond. isConnectedTo(IBond bond)
Checks whether a bond is connected to another one.boolean
BondRef. isConnectedTo(IBond bond)
Checks whether a bond is connected to another one.void
AtomContainer. removeBond(IBond bond)
Removes the bond from this container.void
AtomContainer. setBonds(IBond[] newBonds)
Sets the array of bonds of this AtomContainer.Constructors in org.openscience.cdk with parameters of type IBond Constructor Description BondRef(IBond bond)
Create a pointer for the provided bond. -
Uses of IBond in org.openscience.cdk.aromaticity
Methods in org.openscience.cdk.aromaticity that return types with arguments of type IBond Modifier and Type Method Description Set<IBond>
Aromaticity. findBonds(IAtomContainer molecule)
Find the bonds of amolecule
which this model determined were aromatic. -
Uses of IBond in org.openscience.cdk.charges
Methods in org.openscience.cdk.charges with parameters of type IBond Modifier and Type Method Description double
Polarizability. calculateBondPolarizability(IAtomContainer atomContainer, IBond bond)
calculate bond polarizability. -
Uses of IBond in org.openscience.cdk.debug
Classes in org.openscience.cdk.debug that implement IBond Modifier and Type Class Description class
DebugBond
Debugging data class.Methods in org.openscience.cdk.debug that return IBond Modifier and Type Method Description IBond
DebugBond. clone()
Clones this bond object, including clones of the atoms between which the bond is defined.IBond
DebugAminoAcid. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
DebugAminoAcid. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
DebugAtomContainer. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
DebugAtomContainer. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
DebugBioPolymer. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
DebugBioPolymer. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
DebugCrystal. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
DebugCrystal. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
DebugMonomer. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
DebugMonomer. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
DebugPolymer. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
DebugPolymer. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
DebugRing. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
DebugRing. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
DebugStrand. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
DebugStrand. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
DebugRing. getNextBond(IBond bond, IAtom atom)
Returns the next bond in order, relative to a given bond and atom.IBond
DebugChemObjectBuilder. newBond()
Create a new bond using the default constructor.IBond
DebugAminoAcid. removeBond(int pos)
Removes the bond at the given position from the AtomContainer.IBond
DebugAminoAcid. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.IBond
DebugAtomContainer. removeBond(int pos)
Removes the bond at the given position from the AtomContainer.IBond
DebugAtomContainer. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.IBond
DebugBioPolymer. removeBond(int pos)
Removes the bond at the given position from the AtomContainer.IBond
DebugBioPolymer. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.IBond
DebugCrystal. removeBond(int pos)
Removes the bond at the given position from the AtomContainer.IBond
DebugCrystal. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.IBond
DebugMonomer. removeBond(int pos)
Removes the bond at the given position from the AtomContainer.IBond
DebugMonomer. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.IBond
DebugPolymer. removeBond(int pos)
Removes the bond at the given position from the AtomContainer.IBond
DebugPolymer. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.IBond
DebugRing. removeBond(int pos)
Removes the bond at the given position from the AtomContainer.IBond
DebugRing. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.IBond
DebugStrand. removeBond(int pos)
Removes the bond at the given position from the AtomContainer.IBond
DebugStrand. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.Methods in org.openscience.cdk.debug that return types with arguments of type IBond Modifier and Type Method Description Iterable<IBond>
DebugAminoAcid. bonds()
Returns an Iterable for looping over all bonds in this container.Iterable<IBond>
DebugAtom. bonds()
Returns the bonds connected to this atom.Iterable<IBond>
DebugAtomContainer. bonds()
Returns an Iterable for looping over all bonds in this container.Iterable<IBond>
DebugBioPolymer. bonds()
Returns an Iterable for looping over all bonds in this container.Iterable<IBond>
DebugCrystal. bonds()
Returns an Iterable for looping over all bonds in this container.Iterable<IBond>
DebugMonomer. bonds()
Returns an Iterable for looping over all bonds in this container.Iterable<IBond>
DebugPolymer. bonds()
Returns an Iterable for looping over all bonds in this container.Iterable<IBond>
DebugRing. bonds()
Returns an Iterable for looping over all bonds in this container.Iterable<IBond>
DebugStrand. bonds()
Returns an Iterable for looping over all bonds in this container.List<IBond>
DebugAminoAcid. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.List<IBond>
DebugAtomContainer. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.List<IBond>
DebugBioPolymer. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.List<IBond>
DebugCrystal. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.List<IBond>
DebugMonomer. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.List<IBond>
DebugPolymer. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.List<IBond>
DebugRing. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.List<IBond>
DebugStrand. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.Methods in org.openscience.cdk.debug with parameters of type IBond Modifier and Type Method Description void
DebugAminoAcid. addBond(IBond bond)
Adds a Bond to this AtomContainer.void
DebugAtomContainer. addBond(IBond bond)
Adds a Bond to this AtomContainer.void
DebugBioPolymer. addBond(IBond bond)
Adds a Bond to this AtomContainer.void
DebugCrystal. addBond(IBond bond)
Adds a Bond to this AtomContainer.void
DebugMonomer. addBond(IBond bond)
Adds a Bond to this AtomContainer.void
DebugPolymer. addBond(IBond bond)
Adds a Bond to this AtomContainer.void
DebugRing. addBond(IBond bond)
Adds a Bond to this AtomContainer.void
DebugStrand. addBond(IBond bond)
Adds a Bond to this AtomContainer.boolean
DebugAminoAcid. contains(IBond bond)
True, if the AtomContainer contains the given bond object.boolean
DebugAtomContainer. contains(IBond bond)
True, if the AtomContainer contains the given bond object.boolean
DebugBioPolymer. contains(IBond bond)
True, if the AtomContainer contains the given bond object.boolean
DebugCrystal. contains(IBond bond)
True, if the AtomContainer contains the given bond object.boolean
DebugMonomer. contains(IBond bond)
True, if the AtomContainer contains the given bond object.boolean
DebugPolymer. contains(IBond bond)
True, if the AtomContainer contains the given bond object.boolean
DebugRing. contains(IBond bond)
True, if the AtomContainer contains the given bond object.boolean
DebugStrand. contains(IBond bond)
True, if the AtomContainer contains the given bond object.int
DebugAminoAcid. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.int
DebugBioPolymer. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.int
DebugCrystal. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.int
DebugMonomer. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.int
DebugPolymer. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.int
DebugRing. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.int
DebugStrand. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.IBond
DebugRing. getNextBond(IBond bond, IAtom atom)
Returns the next bond in order, relative to a given bond and atom.IRingSet
DebugRingSet. getRings(IBond bond)
Returns a vector of all rings that this bond is part of.int
DebugAtomContainer. indexOf(IBond bond)
Access the storage index of a bond.boolean
DebugBond. isConnectedTo(IBond bond)
Checks whether a bond is connected to another one.void
DebugAminoAcid. removeBond(IBond bond)
Removes the bond from this container.void
DebugAtomContainer. removeBond(IBond bond)
Removes the bond from this container.void
DebugBioPolymer. removeBond(IBond bond)
Removes the bond from this container.void
DebugCrystal. removeBond(IBond bond)
Removes the bond from this container.void
DebugMonomer. removeBond(IBond bond)
Removes the bond from this container.void
DebugPolymer. removeBond(IBond bond)
Removes the bond from this container.void
DebugRing. removeBond(IBond bond)
Removes the bond from this container.void
DebugStrand. removeBond(IBond bond)
Removes the bond from this container. -
Uses of IBond in org.openscience.cdk.fingerprint
Methods in org.openscience.cdk.fingerprint with parameters of type IBond Modifier and Type Method Description protected String
Fingerprinter. getBondSymbol(IBond bond)
Gets the bondSymbol attribute of the Fingerprinter classprotected String
GraphOnlyFingerprinter. getBondSymbol(IBond bond)
Gets the bondSymbol attribute of the Fingerprinter class.protected String
HybridizationFingerprinter. getBondSymbol(IBond bond)
Gets the bond Symbol attribute of the Fingerprinter class. -
Uses of IBond in org.openscience.cdk.fragment
Methods in org.openscience.cdk.fragment that return types with arguments of type IBond Modifier and Type Method Description protected static List<IBond>
FragmentUtils. traverse(IAtomContainer atomContainer, IAtom atom, List<IBond> bondList)
Methods in org.openscience.cdk.fragment with parameters of type IBond Modifier and Type Method Description protected static List<IAtomContainer>
FragmentUtils. splitMolecule(IAtomContainer atomContainer, IBond bond)
Non destructively split a molecule into two parts at the specified bond.Method parameters in org.openscience.cdk.fragment with type arguments of type IBond Modifier and Type Method Description protected static IAtomContainer
FragmentUtils. makeAtomContainer(IAtom atom, List<IBond> parts, IAtom excludedAtom)
protected static List<IBond>
FragmentUtils. traverse(IAtomContainer atomContainer, IAtom atom, List<IBond> bondList)
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Uses of IBond in org.openscience.cdk.geometry
Methods in org.openscience.cdk.geometry that return IBond Modifier and Type Method Description static IBond
GeometryTools. getClosestBond(double xPosition, double yPosition, IAtomContainer atomCon)
Deprecated.Returns the bond of the given molecule that is closest to the given coordinates.static IBond
GeometryTools. getClosestBond(int xPosition, int yPosition, IAtomContainer atomCon)
Deprecated.Returns the bond of the given molecule that is closest to the given coordinates.static IBond
GeometryUtil. getClosestBond(double xPosition, double yPosition, IAtomContainer atomCon)
Returns the bond of the given molecule that is closest to the given coordinates.static IBond
GeometryUtil. getClosestBond(int xPosition, int yPosition, IAtomContainer atomCon)
Returns the bond of the given molecule that is closest to the given coordinates.Methods in org.openscience.cdk.geometry that return types with arguments of type IBond Modifier and Type Method Description static Comparator<IBond>
GeometryUtil. polarBondComparator(IAtom central)
Sort the bonds using polar/radial coords around a central atom in 2D.Methods in org.openscience.cdk.geometry with parameters of type IBond Modifier and Type Method Description static int[]
GeometryTools. getBondCoordinates(IBond bond)
Deprecated.Writes the coordinates of the atoms participating the given bond into an array.static int[]
GeometryUtil. getBondCoordinates(IBond bond)
Writes the coordinates of the atoms participating the given bond into an array.static double
GeometryTools. getLength2D(IBond bond)
Deprecated.Returns the geometric length of this bond in 2D space.static double
GeometryUtil. getLength2D(IBond bond)
Returns the geometric length of this bond in 2D space.static boolean
GeometryTools. has2DCoordinates(IBond bond)
Deprecated.Determines if this Bond contains 2D coordinates.static boolean
GeometryUtil. has2DCoordinates(IBond bond)
Determines if this Bond contains 2D coordinates.static boolean
BondTools. isValidDoubleBondConfiguration(IAtomContainer container, IBond bond)
Tells if a certain bond is center of a valid double bond configuration.static void
GeometryUtil. reflect(Collection<IAtom> atoms, IBond bond)
Reflect a collection of atoms in the line formed by the specified bond.Method parameters in org.openscience.cdk.geometry with type arguments of type IBond Modifier and Type Method Description static double
GeometryUtil. getBondLengthMedian(Iterable<IBond> bonds, int cap)
Calculate the median bond length of some bonds. -
Uses of IBond in org.openscience.cdk.graph
Methods in org.openscience.cdk.graph that return IBond Modifier and Type Method Description IBond
GraphUtil.EdgeToBondMap. get(int v, int w)
Access the bond store at the end points v and w.Methods in org.openscience.cdk.graph with parameters of type IBond Modifier and Type Method Description static int
Cycles. smallRingSize(IBond bond)
Determine the smallest ring size an bond belongs to.static int
Cycles. smallRingSize(IBond bond, int max)
Determine the smallest ring size an bond belongs to.Method parameters in org.openscience.cdk.graph with type arguments of type IBond Modifier and Type Method Description static int[][]
GraphUtil. toAdjListSubgraph(IAtomContainer container, Set<IBond> include)
Create an adjacent list representation of the container that only includes bonds that are in the set provided as an argument. -
Uses of IBond in org.openscience.cdk.interfaces
Methods in org.openscience.cdk.interfaces that return IBond Modifier and Type Method Description IBond
IBond. clone()
Returns a deep clone of this IChemObject.IBond
IAtom. getBond(IAtom atom)
Returns the bond connecting 'this' atom to the provided atom.IBond
IAtomContainer. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
IAtomContainer. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond[]
IDoubleBondStereochemistry. getBonds()
Returns an array of ligand bonds around the double bond.IBond
IRing. getNextBond(IBond bond, IAtom atom)
Returns the next bond in order, relative to a given bond and atom.IBond
IDoubleBondStereochemistry. getStereoBond()
IBond
that is the stereo center.IBond
IChemObjectBuilder. newBond()
Create a new bond using the default constructor.IBond
IAtomContainer. removeBond(int position)
Removes the bond at the given position from the AtomContainer.IBond
IAtomContainer. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.Methods in org.openscience.cdk.interfaces that return types with arguments of type IBond Modifier and Type Method Description Iterable<IBond>
IAtom. bonds()
Returns the bonds connected to this atom.Iterable<IBond>
IAtomContainer. bonds()
Returns an Iterable for looping over all bonds in this container.List<IBond>
IAtomContainer. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.Methods in org.openscience.cdk.interfaces with parameters of type IBond Modifier and Type Method Description void
IAtomContainer. addBond(IBond bond)
Adds a Bond to this AtomContainer.boolean
IAtomContainer. contains(IBond bond)
True, if the AtomContainer contains the given bond object.int
IAtomContainer. getBondNumber(IBond bond)
Deprecated.IBond
IRing. getNextBond(IBond bond, IAtom atom)
Returns the next bond in order, relative to a given bond and atom.IRingSet
IRingSet. getRings(IBond bond)
Returns a vector of all rings that this bond is part of.int
IAtomContainer. indexOf(IBond bond)
Access the storage index of a bond.boolean
IBond. isConnectedTo(IBond bond)
Checks whether a bond is connected to another one.void
IAtomContainer. removeBond(IBond bond)
Removes the bond from this container.void
IAtomContainer. setBonds(IBond[] bonds)
Sets the array of bonds of this AtomContainer. -
Uses of IBond in org.openscience.cdk.io.cml
Fields in org.openscience.cdk.io.cml declared as IBond Modifier and Type Field Description protected IBond
CMLCoreModule. currentBond
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Uses of IBond in org.openscience.cdk.isomorphism
Methods in org.openscience.cdk.isomorphism that return types with arguments of type IBond Modifier and Type Method Description Iterable<Map<IBond,IBond>>
Mappings. toBondMap()
Convert the permutations to a bond-bond map.Iterable<Map<IBond,IBond>>
Mappings. toBondMap()
Convert the permutations to a bond-bond map.Methods in org.openscience.cdk.isomorphism with parameters of type IBond Modifier and Type Method Description abstract boolean
BondMatcher. matches(IBond bond1, IBond bond2)
Determines ifbond1
is compatible withbond2
. -
Uses of IBond in org.openscience.cdk.isomorphism.matchers
Subinterfaces of IBond in org.openscience.cdk.isomorphism.matchers Modifier and Type Interface Description interface
IQueryBond
Defines the abililty to be matched against IBond's.Classes in org.openscience.cdk.isomorphism.matchers that implement IBond Modifier and Type Class Description class
CTFileQueryBond
Deprecated.UseExpr.Type.SINGLE_OR_AROMATIC
etc.class
OrderQueryBond
Deprecated.class
OrderQueryBondOrderOnly
Deprecated.Usenew QueryBond(beg, end, ORDER, bord)
class
QueryBond
Implements the concept of a "query bond" between two or more atoms.Fields in org.openscience.cdk.isomorphism.matchers declared as IBond Modifier and Type Field Description protected IBond[]
QueryAtomContainer. bonds
Internal array of bonds.Methods in org.openscience.cdk.isomorphism.matchers that return IBond Modifier and Type Method Description IBond
QueryAtom. getBond(IAtom atom)
Returns the bond connecting 'this' atom to the provided atom.IBond
QueryAtomContainer. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
QueryAtomContainer. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
QueryAtomContainer. removeBond(int position)
Removes the bond at the given position from the AtomContainer.IBond
QueryAtomContainer. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.Methods in org.openscience.cdk.isomorphism.matchers that return types with arguments of type IBond Modifier and Type Method Description Iterable<IBond>
QueryAtom. bonds()
Returns the bonds connected to this atom.Iterable<IBond>
QueryAtomContainer. bonds()
Returns an Iterable for looping over all bonds in this container.List<IBond>
QueryAtomContainer. getConnectedBondsList(IAtom atom)
Returns an ArrayList of all Bonds connected to the given atom.Map<IAtom,Map<Integer,IBond>>
IRGroupQuery. getRootAttachmentPoints()
Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.Map<IAtom,Map<Integer,IBond>>
RGroupQuery. getRootAttachmentPoints()
Methods in org.openscience.cdk.isomorphism.matchers with parameters of type IBond Modifier and Type Method Description void
QueryAtomContainer. addBond(IBond bond)
Adds a Bond to this AtomContainer.boolean
QueryAtomContainer. contains(IBond bond)
True, if the AtomContainer contains the given bond object.int
QueryAtomContainer. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.int
QueryAtomContainer. indexOf(IBond bond)
boolean
QueryBond. isConnectedTo(IBond bond)
Checks whether a query bond is connected to another one.boolean
CTFileQueryBond. matches(IBond bond)
Deprecated.boolean
Expr. matches(IBond bond)
boolean
Expr. matches(IBond bond, int stereo)
boolean
IQueryBond. matches(IBond bond)
Returns true of the givenbond
matches this IQueryBond.boolean
OrderQueryBond. matches(IBond bond)
Deprecated.boolean
OrderQueryBondOrderOnly. matches(IBond bond)
Deprecated.boolean
QueryBond. matches(IBond bond)
Returns true of the givenbond
matches this IQueryBond.static CTFileQueryBond
CTFileQueryBond. ofType(IBond bond, int type)
Deprecated.Create a CTFileQueryBond of the specified type (from the MDL spec).void
QueryAtomContainer. removeBond(IBond bond)
Removes the bond from this container.void
QueryAtomContainer. setBonds(IBond[] bonds)
Sets the array of bonds of this AtomContainer.Method parameters in org.openscience.cdk.isomorphism.matchers with type arguments of type IBond Modifier and Type Method Description void
IRGroupQuery. setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints)
Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.void
RGroupQuery. setRootAttachmentPoints(Map<IAtom,Map<Integer,IBond>> rootAttachmentPoints)
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Uses of IBond in org.openscience.cdk.isomorphism.matchers.smarts
Classes in org.openscience.cdk.isomorphism.matchers.smarts that implement IBond Modifier and Type Class Description class
AnyOrderQueryBond
Deprecated.class
AromaticOrSingleQueryBond
Deprecated.class
AromaticQueryBond
Deprecated.class
LogicalOperatorBond
Deprecated.class
OrderQueryBond
Deprecated.class
RingBond
Deprecated.class
SMARTSBond
Deprecated.class
StereoBond
Deprecated.Methods in org.openscience.cdk.isomorphism.matchers.smarts with parameters of type IBond Modifier and Type Method Description boolean
AnyOrderQueryBond. matches(IBond bond)
Deprecated.boolean
AromaticOrSingleQueryBond. matches(IBond bond)
Deprecated.boolean
AromaticQueryBond. matches(IBond bond)
Deprecated.boolean
LogicalOperatorBond. matches(IBond bond)
Deprecated.boolean
OrderQueryBond. matches(IBond bond)
Deprecated.boolean
RingBond. matches(IBond bond)
Deprecated.boolean
SMARTSBond. matches(IBond bond)
Deprecated.boolean
StereoBond. matches(IBond bond)
Deprecated. -
Uses of IBond in org.openscience.cdk.layout
Methods in org.openscience.cdk.layout with parameters of type IBond Modifier and Type Method Description boolean
OverlapResolver. areIntersected(IBond bond1, IBond bond2)
Deprecated.Checks if two bonds cross each other.IAtom
StructureDiagramGenerator. getOtherBondAtom(IAtom atom, IBond bond)
Returns the other atom of the bond. -
Uses of IBond in org.openscience.cdk.libio.cml
Methods in org.openscience.cdk.libio.cml with parameters of type IBond Modifier and Type Method Description org.xmlcml.cml.element.CMLBond
Convertor. cdkBondToCMLBond(IBond cdkBond)
void
ICMLCustomizer. customize(IBond bond, Object nodeToAdd)
Customized the nodeToAdd for the given IBond.void
MDMoleculeCustomizer. customize(IBond bond, Object nodeToAdd)
No customization for bonds.void
PDBAtomCustomizer. customize(IBond bond, Object nodeToAdd)
void
QSARCustomizer. customize(IBond bond, Object nodeToAdd)
-
Uses of IBond in org.openscience.cdk.modeling.builder3d
Methods in org.openscience.cdk.modeling.builder3d with parameters of type IBond Modifier and Type Method Description int
AtomTetrahedralLigandPlacer3D. makeStereocenter(javax.vecmath.Point3d atomA, IBond ax, javax.vecmath.Point3d atomB, javax.vecmath.Point3d atomC, javax.vecmath.Point3d[] branchPoints)
set Atoms in respect to stereoinformation. -
Uses of IBond in org.openscience.cdk.pharmacophore
Classes in org.openscience.cdk.pharmacophore that implement IBond Modifier and Type Class Description class
PharmacophoreAngleBond
Represents an angle relationship between three pharmacophore groups.class
PharmacophoreBond
Represents a distance relationship between two pharmacophore groups.class
PharmacophoreQueryAngleBond
Represents a pharmacophore query angle constraint.class
PharmacophoreQueryBond
Represents a pharmacophore query distance constraint.Methods in org.openscience.cdk.pharmacophore that return types with arguments of type IBond Modifier and Type Method Description List<List<IBond>>
PharmacophoreMatcher. getMatchingPharmacophoreBonds()
Get the matching pharmacophore constraints.List<HashMap<IBond,IBond>>
PharmacophoreMatcher. getTargetQueryBondMappings()
Return a list of HashMap's that allows one to get the query constraint for a given pharmacophore bond.List<HashMap<IBond,IBond>>
PharmacophoreMatcher. getTargetQueryBondMappings()
Return a list of HashMap's that allows one to get the query constraint for a given pharmacophore bond.Methods in org.openscience.cdk.pharmacophore with parameters of type IBond Modifier and Type Method Description static PharmacophoreBond
PharmacophoreBond. get(IBond bond)
boolean
PharmacophoreQueryAngleBond. matches(IBond bond)
Checks whether the query angle constraint matches a target distance.boolean
PharmacophoreQueryBond. matches(IBond bond)
Checks whether the query distance constraint matches a target distance. -
Uses of IBond in org.openscience.cdk.qsar
Methods in org.openscience.cdk.qsar with parameters of type IBond Modifier and Type Method Description void
AbstractBondDescriptor. cacheDescriptorValue(IBond bond, IAtomContainer container, IDescriptorResult doubleResult)
Caches a DescriptorValue for a given IBond.DescriptorValue
IBondDescriptor. calculate(IBond bond, IAtomContainer atomContainer)
Calculates the descriptor value for the given IBond.IDescriptorResult
AbstractBondDescriptor. getCachedDescriptorValue(IBond bond)
Returns the cached DescriptorValue for the given IBond. -
Uses of IBond in org.openscience.cdk.qsar.descriptors.bond
Methods in org.openscience.cdk.qsar.descriptors.bond with parameters of type IBond Modifier and Type Method Description DescriptorValue
AtomicNumberDifferenceDescriptor. calculate(IBond bond, IAtomContainer ac)
DescriptorValue
BondPartialPiChargeDescriptor. calculate(IBond bond, IAtomContainer ac)
The method calculates the bond-pi Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
BondPartialSigmaChargeDescriptor. calculate(IBond bond, IAtomContainer ac)
The method calculates the bond-sigma Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
BondPartialTChargeDescriptor. calculate(IBond bond, IAtomContainer ac)
The method calculates the bond total Partial charge of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
BondSigmaElectronegativityDescriptor. calculate(IBond aBond, IAtomContainer atomContainer)
The method calculates the sigma electronegativity of a given bond It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.DescriptorValue
IPBondLearningDescriptor. calculate(IBond bond, IAtomContainer atomContainer)
Deprecated.This method calculates the ionization potential of a bond. -
Uses of IBond in org.openscience.cdk.renderer
Methods in org.openscience.cdk.renderer that return IBond Modifier and Type Method Description IBond
RendererModel. getHighlightedBond()
Returns the Bond currently highlighted.Methods in org.openscience.cdk.renderer with parameters of type IBond Modifier and Type Method Description void
RendererModel. setHighlightedBond(IBond highlightedBond)
Sets the Bond currently highlighted.Method parameters in org.openscience.cdk.renderer with type arguments of type IBond Modifier and Type Method Description abstract boolean
SymbolVisibility. visible(IAtom atom, List<IBond> neighbors, RendererModel model)
Determine if an atom with the specified bonds is visible. -
Uses of IBond in org.openscience.cdk.renderer.elements
Methods in org.openscience.cdk.renderer.elements with parameters of type IBond Modifier and Type Method Description static MarkedElement
MarkedElement. markupBond(IRenderingElement elem, IBond bond)
Markup a bond with the class 'bond' and optionally the ids/classes from it's properties. -
Uses of IBond in org.openscience.cdk.renderer.generators
Methods in org.openscience.cdk.renderer.generators with parameters of type IBond Modifier and Type Method Description protected boolean
BasicBondGenerator. bindsHydrogen(IBond bond)
Check to see if any of the atoms in this bond are hydrogen atoms.IRenderingElement
BasicBondGenerator. generate(IBond currentBond, RendererModel model)
Generate rendering element(s) for the current bond, including ring elements if this bond is part of a ring.IRenderingElement
BasicBondGenerator. generateBond(IBond bond, RendererModel model)
Generate stereo or bond elements for this bond.IRenderingElement
BasicBondGenerator. generateBondElement(IBond bond, IBond.Order type, RendererModel model)
Generate a LineElement or an ElementGroup of LineElements for this bond.IRenderingElement
BasicBondGenerator. generateBondElement(IBond bond, RendererModel model)
Generate rendering elements for a bond, without ring elements but considering the type of the bond (single, double, triple).LineElement
BasicBondGenerator. generateInnerElement(IBond bond, IRing ring, RendererModel model)
Make the inner ring bond, which is slightly shorter than the outer bond.IRenderingElement
BasicBondGenerator. generateRingElements(IBond bond, IRing ring, RendererModel model)
Generate ring elements, such as inner-ring bonds or ring stereo elements.IRenderingElement
RingGenerator. generateRingElements(IBond bond, IRing ring, RendererModel model)
Generate ring elements, such as inner-ring bonds or ring stereo elements.Color
BasicBondGenerator. getColorForBond(IBond bond, RendererModel model)
Determine the color of a bond, returning either the default color, the override color or whatever is in the color hash for that bond.double
BasicBondGenerator. getWidthForBond(IBond bond, RendererModel model)
Determine the width of a bond, returning either the width defined in the model, or the override width. -
Uses of IBond in org.openscience.cdk.renderer.generators.standard
Method parameters in org.openscience.cdk.renderer.generators.standard with type arguments of type IBond Modifier and Type Method Description boolean
SelectionVisibility. visible(IAtom atom, List<IBond> neighbors, RendererModel model)
Determine if an atom with the specified bonds is visible. -
Uses of IBond in org.openscience.cdk.ringsearch
Methods in org.openscience.cdk.ringsearch with parameters of type IBond Modifier and Type Method Description boolean
RingSearch. cyclic(IBond bond)
Determine whether the bond is cyclic. -
Uses of IBond in org.openscience.cdk.sgroup
Methods in org.openscience.cdk.sgroup that return types with arguments of type IBond Modifier and Type Method Description Set<IBond>
Sgroup. getBonds()
Access the bonds that belong to this substructure group.Methods in org.openscience.cdk.sgroup with parameters of type IBond Modifier and Type Method Description void
Sgroup. addBond(IBond bond)
Add a bond to this Sgroup.void
Sgroup. removeBond(IBond bond)
Remove a bond from this Sgroup. -
Uses of IBond in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement IBond Modifier and Type Class Description class
Bond
Implements the concept of a covalent bond between two or more atoms.Fields in org.openscience.cdk.silent declared as IBond Modifier and Type Field Description protected IBond[]
AtomContainer. bonds
Internal array of bonds.Methods in org.openscience.cdk.silent that return IBond Modifier and Type Method Description IBond
Bond. clone()
Clones this bond object, including clones of the atoms between which the bond is defined.IBond
Atom. getBond(IAtom atom)
Returns the bond connecting 'this' atom to the provided atom.IBond
AtomContainer. getBond(int idx)
Get the bond at the specified idx, the index should be in the range 0 ≤ idx <IAtomContainer.getBondCount()
.IBond
AtomContainer. getBond(IAtom atom1, IAtom atom2)
Returns the bond that connects the two given atoms.IBond
Ring. getNextBond(IBond bond, IAtom atom)
Returns the next bond in order, relative to a given bond and atom.IBond
SilentChemObjectBuilder. newBond()
Create a new bond using the default constructor.IBond
AtomContainer. removeBond(int position)
Removes the bond at the given position from the AtomContainer.IBond
AtomContainer. removeBond(IAtom atom1, IAtom atom2)
Removes the bond that connects the two given atoms.Methods in org.openscience.cdk.silent that return types with arguments of type IBond Modifier and Type Method Description Iterable<IBond>
Atom. bonds()
Returns the bonds connected to this atom.Iterable<IBond>
AtomContainer. bonds()
Returns an Iterable for looping over all bonds in this container.List<IBond>
AtomContainer. getConnectedBondsList(IAtom atom)
Returns the bonds connected connected to the specified atom.Methods in org.openscience.cdk.silent with parameters of type IBond Modifier and Type Method Description void
AtomContainer. addBond(IBond bond)
Adds a Bond to this AtomContainer.boolean
AtomContainer. contains(IBond bond)
True, if the AtomContainer contains the given bond object.int
AtomContainer. getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.IBond
Ring. getNextBond(IBond bond, IAtom atom)
Returns the next bond in order, relative to a given bond and atom.IRingSet
RingSet. getRings(IBond bond)
Returns a vector of all rings that this bond is part of.int
AtomContainer. indexOf(IBond bond)
Access the storage index of a bond.boolean
Bond. isConnectedTo(IBond bond)
Checks whether a bond is connected to another one.void
AtomContainer. removeBond(IBond bond)
Removes the bond from this container.void
AtomContainer. setBonds(IBond[] newBonds)
Sets the array of bonds of this AtomContainer. -
Uses of IBond in org.openscience.cdk.smsd
Methods in org.openscience.cdk.smsd that return types with arguments of type IBond Modifier and Type Method Description List<Map<IBond,IBond>>
Isomorphism. getAllBondMaps()
Deprecated.List<Map<IBond,IBond>>
Isomorphism. getAllBondMaps()
Deprecated.Map<IBond,IBond>
Isomorphism. getFirstBondMap()
Deprecated.Map<IBond,IBond>
Isomorphism. getFirstBondMap()
Deprecated.static Map<IBond,IBond>
Isomorphism. makeBondMapOfAtomMap(IAtomContainer ac1, IAtomContainer ac2, Map<IAtom,IAtom> mapping)
Deprecated.Returns bond map between source and target molecules based on the atomsstatic Map<IBond,IBond>
Isomorphism. makeBondMapOfAtomMap(IAtomContainer ac1, IAtomContainer ac2, Map<IAtom,IAtom> mapping)
Deprecated.Returns bond map between source and target molecules based on the atomsstatic List<Map<IBond,IBond>>
Isomorphism. makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2, List<Map<IAtom,IAtom>> mappings)
Deprecated.Returns bond maps between source and target molecules based on the atomsstatic List<Map<IBond,IBond>>
Isomorphism. makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContainer ac2, List<Map<IAtom,IAtom>> mappings)
Deprecated.Returns bond maps between source and target molecules based on the atoms -
Uses of IBond in org.openscience.cdk.smsd.algorithm.matchers
Methods in org.openscience.cdk.smsd.algorithm.matchers with parameters of type IBond Modifier and Type Method Description static boolean
DefaultMatcher. isAtomMatch(AtomMatcher atomMatcher1, AtomMatcher atomMatcher2, IAtomContainer ac2, IBond bondA2, boolean shouldMatchBonds)
Deprecated.static boolean
DefaultMatcher. isBondMatch(BondMatcher bondMatcher, IAtomContainer ac2, IBond bondA2, boolean shouldMatchBonds)
Deprecated.boolean
BondMatcher. matches(IAtomContainer container, IBond atom)
Deprecated.boolean
DefaultBondMatcher. matches(IAtomContainer targetContainer, IBond targetBond)
Deprecated.boolean
DefaultVFBondMatcher. matches(TargetProperties targetConatiner, IBond targetBond)
Deprecated.boolean
VFBondMatcher. matches(TargetProperties container, IBond atom)
Deprecated.Constructors in org.openscience.cdk.smsd.algorithm.matchers with parameters of type IBond Constructor Description DefaultBondMatcher(IAtomContainer queryMol, IBond queryBond, boolean shouldMatchBonds)
Deprecated.ConstructorDefaultVFBondMatcher(IAtomContainer queryMol, IBond queryBond, boolean shouldMatchBonds)
Deprecated.Constructor -
Uses of IBond in org.openscience.cdk.smsd.algorithm.mcgregor
Methods in org.openscience.cdk.smsd.algorithm.mcgregor with parameters of type IBond Modifier and Type Method Description protected static boolean
McGregorChecks. isMatchFeasible(IAtomContainer ac1, IBond bondA1, IAtomContainer ac2, IBond bondA2, boolean shouldMatchBonds)
Deprecated. -
Uses of IBond in org.openscience.cdk.smsd.algorithm.vflib.builder
Methods in org.openscience.cdk.smsd.algorithm.vflib.builder that return IBond Modifier and Type Method Description IBond
TargetProperties. getBond(IAtom atom1, IAtom atom2)
Deprecated. -
Uses of IBond in org.openscience.cdk.smsd.filters
Methods in org.openscience.cdk.smsd.filters with parameters of type IBond Modifier and Type Method Description static int
ChemicalFilters. convertBondOrder(IBond bond)
Deprecated.Get bond order value asint
value.static int
ChemicalFilters. convertBondStereo(IBond bond)
Deprecated.Get stereo value as integer -
Uses of IBond in org.openscience.cdk.smsd.helper
Methods in org.openscience.cdk.smsd.helper with parameters of type IBond Modifier and Type Method Description boolean
BondEnergy. matches(IBond bond)
Deprecated. -
Uses of IBond in org.openscience.cdk.smsd.tools
Methods in org.openscience.cdk.smsd.tools with parameters of type IBond Modifier and Type Method Description int
BondEnergies. getEnergies(IBond bond)
Deprecated.Returns bond energy for a bond type, given atoms and bond type -
Uses of IBond in org.openscience.cdk.stereo
Methods in org.openscience.cdk.stereo that return IBond Modifier and Type Method Description static IBond
ExtendedCisTrans. findCentralBond(IAtomContainer mol, IAtom atom)
Locate the central double-bond in a chain of cumulated double bonds.IBond[]
DoubleBondStereochemistry. getBonds()
Returns an array of ligand bonds around the double bond.IBond
DoubleBondStereochemistry. getStereoBond()
IBond
that is the stereo center.Methods in org.openscience.cdk.stereo that return types with arguments of type IBond Modifier and Type Method Description protected IStereoElement<IBond,IAtom>
Atropisomeric. create(IBond focus, List<IAtom> carriers, int cfg)
protected IStereoElement<IBond,IBond>
DoubleBondStereochemistry. create(IBond focus, List<IBond> carriers, int cfg)
protected IStereoElement<IBond,IBond>
DoubleBondStereochemistry. create(IBond focus, List<IBond> carriers, int cfg)
protected IStereoElement<IBond,IBond>
ExtendedCisTrans. create(IBond focus, List<IBond> carriers, int cfg)
protected IStereoElement<IBond,IBond>
ExtendedCisTrans. create(IBond focus, List<IBond> carriers, int cfg)
Methods in org.openscience.cdk.stereo with parameters of type IBond Modifier and Type Method Description protected IStereoElement<IBond,IAtom>
Atropisomeric. create(IBond focus, List<IAtom> carriers, int cfg)
protected IStereoElement<IBond,IBond>
DoubleBondStereochemistry. create(IBond focus, List<IBond> carriers, int cfg)
protected IStereoElement<IBond,IBond>
ExtendedCisTrans. create(IBond focus, List<IBond> carriers, int cfg)
static IAtom[]
ExtendedCisTrans. findTerminalAtoms(IAtomContainer container, IBond focus)
Helper method to locate two terminal atoms in a container for this extended Cis/Trans element.Method parameters in org.openscience.cdk.stereo with type arguments of type IBond Modifier and Type Method Description protected IStereoElement<IBond,IBond>
DoubleBondStereochemistry. create(IBond focus, List<IBond> carriers, int cfg)
protected IStereoElement<IBond,IBond>
ExtendedCisTrans. create(IBond focus, List<IBond> carriers, int cfg)
Constructors in org.openscience.cdk.stereo with parameters of type IBond Constructor Description Atropisomeric(IBond focus, IAtom[] carriers, int value)
Define a new atropisomer using the focus bond and the carrier atoms.DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, int config)
DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, IDoubleBondStereochemistry.Conformation stereo)
Creates a new double bond stereo chemistry.ExtendedCisTrans(IBond focus, IBond[] peripherals, int config)
-
Uses of IBond in org.openscience.cdk.tools
Methods in org.openscience.cdk.tools with parameters of type IBond Modifier and Type Method Description boolean
AtomTypeAwareSaturationChecker. bondOrderCanBeIncreased(IBond bond, IAtomContainer atomContainer)
Check if the bond order can be increased.IAtomContainer
StructureResonanceGenerator. getContainer(IAtomContainer molecule, IBond bond)
Get the container which the bond is found on resonance from aIAtomContainer
.static double[]
IonizationPotentialTool. getQSARs(IAtomContainer container, IBond bond)
Deprecated.Get the results of 7 qsar descriptors been applied.boolean
SaturationChecker. isSaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is saturated.boolean
SmilesValencyChecker. isSaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is saturated.boolean
SaturationChecker. isUnsaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is unsaturated.boolean
SmilesValencyChecker. isUnsaturated(IBond bond, IAtomContainer atomContainer)
Returns whether a bond is unsaturated.boolean
SaturationChecker. newSaturate(IBond[] bonds, IAtomContainer atomContainer)
Saturates a set of Bonds in an AtomContainer.boolean
SaturationChecker. newSaturate(IBond bond, IAtomContainer atomContainer)
Saturate atom by adjusting its bond orders.static double
IonizationPotentialTool. predictIP(IAtomContainer container, IBond bond)
Deprecated.Method which is predict the Ionization Potential from given atom.boolean
SmilesValencyChecker. saturate(IBond[] bonds, IAtomContainer atomContainer)
Saturates a set of Bonds in an AtomContainer.boolean
SmilesValencyChecker. saturateByIncreasingBondOrder(IBond bond, IAtomContainer atomContainer)
Tries to saturate a bond by increasing its bond orders by 1.0.boolean
SmilesValencyChecker. unsaturateByDecreasingBondOrder(IBond bond)
Method parameters in org.openscience.cdk.tools with type arguments of type IBond Modifier and Type Method Description int
SaturationChecker. calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, double singleElectronSum, List<IBond> connectedBonds, boolean throwExceptionForUnknowAtom)
Calculate the number of missing hydrogens by subtracting the number of bonds for the atom from the expected number of bonds. -
Uses of IBond in org.openscience.cdk.tools.manipulator
Methods in org.openscience.cdk.tools.manipulator that return IBond Modifier and Type Method Description static IBond[]
AtomContainerManipulator. getBondArray(List<IBond> list)
Constructs an array of Atom objects from a List of Atom objects.static IBond[]
AtomContainerManipulator. getBondArray(IAtomContainer container)
Constructs an array of Bond objects from an AtomContainer.Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IBond Modifier and Type Method Description static Set<IBond>
ReactionManipulator. findMappedBonds(IReaction reaction)
Collect the set of bonds that mapped in both a reactant and a product.Methods in org.openscience.cdk.tools.manipulator with parameters of type IBond Modifier and Type Method Description static void
BondManipulator. decreaseBondOrder(IBond bond)
Decrease the order of a bond.static IAtom[]
BondManipulator. getAtomArray(IBond container)
Constructs an array of Atom objects from Bond.static IRing
RingSetManipulator. getHeaviestRing(IRingSet ringSet, IBond bond)
We define the heaviest ring as the one with the highest number of double bonds.static IBond.Order
BondManipulator. getMaximumBondOrder(IBond firstBond, IBond secondBond)
Returns the maximum bond order for the two bonds.static IAtomContainer
AtomContainerSetManipulator. getRelevantAtomContainer(IAtomContainerSet containerSet, IBond bond)
static IAtomContainer
ChemModelManipulator. getRelevantAtomContainer(IChemModel chemModel, IBond bond)
Retrieves the first IAtomContainer containing a given IBond from an IChemModel.static IAtomContainer
MoleculeSetManipulator. getRelevantAtomContainer(IAtomContainerSet moleculeSet, IBond bond)
static IAtomContainer
ReactionManipulator. getRelevantAtomContainer(IReaction reaction, IBond bond)
static IAtomContainer
ReactionSetManipulator. getRelevantAtomContainer(IReactionSet set, IBond bond)
static IReaction
ReactionSetManipulator. getRelevantReaction(IReactionSet set, IBond bond)
static void
BondManipulator. increaseBondOrder(IBond bond)
Increment the bond order of this bond.Method parameters in org.openscience.cdk.tools.manipulator with type arguments of type IBond Modifier and Type Method Description static IBond[]
AtomContainerManipulator. getBondArray(List<IBond> list)
Constructs an array of Atom objects from a List of Atom objects.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 int
BondManipulator. getSingleBondEquivalentSum(Iterator<IBond> bonds)
Get the single bond equivalent (SBE) of a list of bonds, given an iterator to the list.static int
BondManipulator. getSingleBondEquivalentSum(List<IBond> bonds)
Get the single bond equivalent (SBE) of a list of bonds. -
Uses of IBond in org.openscience.cdk.validate
Methods in org.openscience.cdk.validate with parameters of type IBond Modifier and Type Method Description ValidationReport
AbstractValidator. validateBond(IBond subject)
ValidationReport
BasicValidator. validateBond(IBond subject)
ValidationReport
Geometry3DValidator. validateBond(IBond subject)
ValidationReport
IValidator. validateBond(IBond subject)
ValidationReport
ValidatorEngine. validateBond(IBond subject)
-