MDMolecule (cdk 2.9 API)

java.lang.Object
- org.openscience.cdk.ChemObject
- - org.openscience.cdk.AtomContainer
  - - org.openscience.cdk.libio.md.MDMolecule

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

Field Summary
- Fields inherited from class org.openscience.cdk.AtomContainer
  atomCount, atoms, bondCount, bonds, growArraySize, lonePairCount, lonePairs, singleElectronCount, singleElectrons, stereoElements

Constructor Summary

Constructors
Constructor Description

MDMolecule()

MDMolecule(IAtomContainer container)

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)`

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, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stateChanged, stereoElements, toString

Methods inherited from class org.openscience.cdk.ChemObject
addListener, addProperties, compare, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Constructor Detail

MDMolecule
```
public MDMolecule()
```

MDMolecule

public MDMolecule(IAtomContainer container)

Method Detail

getResidues
```
public List<Residue> getResidues()
```

setResidues

public void setResidues(List<Residue> residues)

addResidue
```
public void addResidue(Residue residue)
```
Add a Residue to the MDMolecule if not already present.

Parameters:

residue - Residue to add

getChargeGroups

public List<ChargeGroup> getChargeGroups()

setChargeGroups

public void setChargeGroups(List<ChargeGroup> chargeGroups)

addChargeGroup
```
public void addChargeGroup(ChargeGroup chargeGroup)
```
Add a ChargeGroup to the MDMolecule if not already present.

Parameters:

chargeGroup - ChargeGroup to add