Package org.openscience.cdk.libio.md
Class MDMolecule
- java.lang.Object
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- org.openscience.cdk.ChemObject
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- org.openscience.cdk.AtomContainer
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- org.openscience.cdk.libio.md.MDMolecule
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- All Implemented Interfaces:
Serializable
,Cloneable
,IAtomContainer
,ICDKObject
,IChemObject
,IChemObjectListener
public class MDMolecule extends AtomContainer
- See Also:
- Serialized Form
- Source code:
- main
- Belongs to CDK module:
- libiomd
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description MDMolecule()
MDMolecule(IAtomContainer container)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addChargeGroup(ChargeGroup chargeGroup)
Add a ChargeGroup to the MDMolecule if not already present.void
addResidue(Residue residue)
Add a Residue to the MDMolecule if not already present.List<ChargeGroup>
getChargeGroups()
List<Residue>
getResidues()
void
setChargeGroups(List<ChargeGroup> chargeGroups)
void
setResidues(List<Residue> residues)
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Methods inherited from class org.openscience.cdk.AtomContainer
add, addAtom, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, clone, 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, toString
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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
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer
newAtom, newAtom, newBond
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Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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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
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Constructor Detail
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MDMolecule
public MDMolecule()
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MDMolecule
public MDMolecule(IAtomContainer container)
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Method Detail
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addResidue
public void addResidue(Residue residue)
Add a Residue to the MDMolecule if not already present.- Parameters:
residue
- Residue to add
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getChargeGroups
public List<ChargeGroup> getChargeGroups()
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setChargeGroups
public void setChargeGroups(List<ChargeGroup> chargeGroups)
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addChargeGroup
public void addChargeGroup(ChargeGroup chargeGroup)
Add a ChargeGroup to the MDMolecule if not already present.- Parameters:
chargeGroup
-ChargeGroup
to add
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