Package org.openscience.cdk.debug
Class DebugPDBPolymer
- java.lang.Object
-
- org.openscience.cdk.ChemObject
-
- org.openscience.cdk.AtomContainer
-
- org.openscience.cdk.Polymer
-
- org.openscience.cdk.BioPolymer
-
- org.openscience.cdk.protein.data.PDBPolymer
-
- org.openscience.cdk.debug.DebugPDBPolymer
-
- All Implemented Interfaces:
Serializable
,Cloneable
,IAtomContainer
,IBioPolymer
,ICDKObject
,IChemObject
,IChemObjectListener
,IPDBPolymer
,IPolymer
public class DebugPDBPolymer extends PDBPolymer implements IBioPolymer
Debugging data class.- Author:
- Miguel Rojas
- See Also:
- Serialized Form
- Source code:
- main
- Belongs to CDK module:
- datadebug
-
-
Field Summary
-
Fields inherited from interface org.openscience.cdk.interfaces.IChemObject
ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED
-
-
Constructor Summary
Constructors Constructor Description DebugPDBPolymer()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addStructure(IPDBStructure structure)
Adds the PDBStructure structure a this PDBPolymer.Collection<IPDBStructure>
getStructures()
Returns a Collection containing the PDBStructure in the PDBPolymer.-
Methods inherited from class org.openscience.cdk.protein.data.PDBPolymer
addAtom, addAtom, addAtom, clone, getMonomerNamesInSequentialOrder, toString
-
Methods inherited from class org.openscience.cdk.BioPolymer
addAtom, addAtom, getMonomer, getMonomerCount, getMonomerNames, getStrand, getStrandCount, getStrandNames, getStrands, removeStrand
-
Methods inherited from class org.openscience.cdk.Polymer
addAtom, getMonomer, removeMonomer
-
Methods inherited from class org.openscience.cdk.AtomContainer
add, addAtom, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, newAtom, newAtom, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, shallowCopy, singleElectrons, stateChanged, stereoElements
-
Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty
-
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
-
Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer
add, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, newAtom, newAtom, newAtom, newAtom, newBond, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stereoElements
-
Methods inherited from interface org.openscience.cdk.interfaces.IBioPolymer
addAtom, addAtom, addAtom, getMonomer, getMonomerCount, getMonomerNames, getStrand, getStrandCount, getStrandNames, getStrands, removeStrand
-
Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
-
Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString
-
Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener
stateChanged
-
Methods inherited from interface org.openscience.cdk.interfaces.IPolymer
addAtom, getMonomer, removeMonomer
-
-
-
-
Method Detail
-
getStructures
public Collection<IPDBStructure> getStructures()
Returns a Collection containing the PDBStructure in the PDBPolymer.- Specified by:
getStructures
in interfaceIPDBPolymer
- Overrides:
getStructures
in classPDBPolymer
- Returns:
- Collection containing the PDBStructure in the PDBPolymer
-
addStructure
public void addStructure(IPDBStructure structure)
Adds the PDBStructure structure a this PDBPolymer.- Specified by:
addStructure
in interfaceIPDBPolymer
- Overrides:
addStructure
in classPDBPolymer
- Parameters:
structure
- The PDBStructure to add
-
-