@TestClass(value="org.openscience.cdk.tools.manipulator.AtomContainerSetManipulatorTest") public class AtomContainerSetManipulator extends Object
ChemModelManipulator
Constructor and Description |
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AtomContainerSetManipulator() |
Modifier and Type | Method and Description |
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static boolean |
containsByID(IAtomContainerSet atomContainerSet,
String id)
Tells if an AtomContainerSet contains at least one AtomContainer with the
same ID as atomContainer.
|
static List<IAtomContainer> |
getAllAtomContainers(IAtomContainerSet set)
Returns all the AtomContainer's of a MoleculeSet.
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static List<IChemObject> |
getAllChemObjects(IAtomContainerSet set)
Does not recursively return the contents of the AtomContainer.
|
static List<String> |
getAllIDs(IAtomContainerSet set) |
static int |
getAtomCount(IAtomContainerSet set) |
static int |
getBondCount(IAtomContainerSet set) |
static IAtomContainer |
getRelevantAtomContainer(IAtomContainerSet containerSet,
IAtom atom) |
static IAtomContainer |
getRelevantAtomContainer(IAtomContainerSet containerSet,
IBond bond) |
static double |
getTotalCharge(IAtomContainerSet set) |
static double |
getTotalFormalCharge(IAtomContainerSet set) |
static int |
getTotalHydrogenCount(IAtomContainerSet set) |
static void |
removeAtomAndConnectedElectronContainers(IAtomContainerSet set,
IAtom atom) |
static void |
removeElectronContainer(IAtomContainerSet set,
IElectronContainer electrons) |
static void |
setAtomProperties(IAtomContainerSet set,
Object propKey,
Object propVal) |
static void |
sort(IAtomContainerSet atomContainerSet)
Sorts the IAtomContainers in the given IAtomContainerSet by the following
criteria with decreasing priority:
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@TestMethod(value="testGetAtomCount_IAtomContainerSet") public static int getAtomCount(IAtomContainerSet set)
@TestMethod(value="testGetBondCount_IAtomContainerSet") public static int getBondCount(IAtomContainerSet set)
@TestMethod(value="testRemoveAtomAndConnectedElectronContainers_IAtomContainerSet_IAtom") public static void removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom)
@TestMethod(value="testRemoveElectronContainer_IAtomContainerSet_IElectronContainer") public static void removeElectronContainer(IAtomContainerSet set, IElectronContainer electrons)
@TestMethod(value="testGetAllAtomContainers_IAtomContainerSet") public static List<IAtomContainer> getAllAtomContainers(IAtomContainerSet set)
set
- The collection of IAtomContainer objects@TestMethod(value="testGetTotalCharge_IAtomContainerSet") public static double getTotalCharge(IAtomContainerSet set)
set
- The collection of IAtomContainer objects@TestMethod(value="testGetTotalFormalCharge_IAtomContainerSet") public static double getTotalFormalCharge(IAtomContainerSet set)
set
- The collection of IAtomContainer objects@TestMethod(value="testGetTotalHydrogenCount_IAtomContainerSet") public static int getTotalHydrogenCount(IAtomContainerSet set)
set
- The collection of IAtomContainer objects@TestMethod(value="testGetAllIDs_IAtomContainerSet") public static List<String> getAllIDs(IAtomContainerSet set)
@TestMethod(value="testSetAtomProperties_IAtomContainerSet_Object_Object") public static void setAtomProperties(IAtomContainerSet set, Object propKey, Object propVal)
@TestMethod(value="testGetRelevantAtomContainer_IAtomContainerSet_IAtom") public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet containerSet, IAtom atom)
@TestMethod(value="testGetRelevantAtomContainer_IAtomContainerSet_IBond") public static IAtomContainer getRelevantAtomContainer(IAtomContainerSet containerSet, IBond bond)
@TestMethod(value="testGetAllChemObjects_IAtomContainerSet") public static List<IChemObject> getAllChemObjects(IAtomContainerSet set)
set
- The collection of IAtomContainer objects@TestMethod(value="testSort_IAtomContainerSet") public static void sort(IAtomContainerSet atomContainerSet)
Sorts the IAtomContainers in the given IAtomContainerSet by the following criteria with decreasing priority:
If no difference can be found with the above criteria, the IAtomContainers are considered equal.
atomContainerSet
- The collection of IAtomContainer objects@TestMethod(value="testContainsByID_IAtomContainerSet_IAtomContainer") public static boolean containsByID(IAtomContainerSet atomContainerSet, String id)
id
- The IAtomContainer to look foratomContainerSet
- The collection of IAtomContainer objects