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Static Public Member Functions | Static Private Member Functions

org::openscience::cdk::tools::manipulator::AtomContainerManipulator Class Reference

List of all members.

Static Public Member Functions

static void clearAtomConfigurations (IAtomContainer container)
static void convertImplicitToExplicitHydrogens (IAtomContainer atomContainer)
static int countExplicitHydrogens (IAtomContainer atomContainer, IAtom atom)
static int countHydrogens (IAtomContainer atomContainer, IAtom atom)
static IAtomContainer createAllCarbonAllSingleNonAromaticBondAtomContainer (IAtomContainer atomContainer) throws CloneNotSupportedException
static List< String > getAllIDs (IAtomContainer mol)
static IAtom[] getAtomArray (IAtomContainer container)
static IAtom[] getAtomArray (java.util.List< IAtom > list)
static IAtom getAtomById (IAtomContainer ac, String id) throws CDKException
static IBond[] getBondArray (IAtomContainer container)
static IBond[] getBondArray (java.util.List< IBond > list)
static double getBondOrderSum (IAtomContainer container, IAtom atom)
static IElectronContainer[] getElectronContainerArray (IAtomContainer container)
static IElectronContainer[] getElectronContainerArray (java.util.List< IElectronContainer > list)
static List< IAtomgetHeavyAtoms (IAtomContainer container)
static IAtomContainer getIntersection (IAtomContainer container1, IAtomContainer container2)
static IBond.Order getMaximumBondOrder (IAtomContainer container)
static double getNaturalExactMass (IAtomContainer atomContainer)
static int getSingleBondEquivalentSum (IAtomContainer container)
static double getTotalCharge (IAtomContainer atomContainer)
static double getTotalExactMass (IAtomContainer atomContainer)
static int getTotalFormalCharge (IAtomContainer atomContainer)
static int getTotalHydrogenCount (IAtomContainer atomContainer)
static double getTotalNaturalAbundance (IAtomContainer atomContainer)
static int getTotalNegativeFormalCharge (IAtomContainer atomContainer)
static int getTotalPositiveFormalCharge (IAtomContainer atomContainer)
static void percieveAtomTypesAndConfigureAtoms (IAtomContainer container) throws CDKException
static void percieveAtomTypesAndConfigureUnsetProperties (IAtomContainer container) throws CDKException
static IAtomContainer removeHydrogens (IAtomContainer atomContainer)
static IAtomContainer removeHydrogensPreserveMultiplyBonded (IAtomContainer ac)
static boolean replaceAtomByAtom (IAtomContainer container, IAtom atom, IAtom newAtom)
static void setAtomProperties (IAtomContainer container, Object propKey, Object propVal)
static void unregisterAtomListeners (IAtomContainer container)
static void unregisterElectronContainerListeners (IAtomContainer container)

Static Private Member Functions

static IAtomContainer removeHydrogens (IAtomContainer ac, List< IAtom > preserve)

Detailed Description

Class with convenience methods that provide methods to manipulate AtomContainer's. For example:

 AtomContainerManipulator.replaceAtomByAtom(container, atom1, atom2);

will replace the Atom in the AtomContainer, but in all the ElectronContainer's it participates too.

.module standard .githash

Egon Willighagen .created 2003-08-07

Definition at line 61 of file AtomContainerManipulator.java.

The documentation for this class was generated from the following file:

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