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org::openscience::cdk::libio::md::MDMolecule Class Reference

Inheritance diagram for org::openscience::cdk::libio::md::MDMolecule:

org::openscience::cdk::Molecule org::openscience::cdk::AtomContainer org::openscience::cdk::interfaces::IMolecule org::openscience::cdk::ChemObject org::openscience::cdk::interfaces::IAtomContainer org::openscience::cdk::interfaces::IChemObjectListener org::openscience::cdk::interfaces::IAtomContainer org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObjectListener org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObjectListener

List of all members.


Detailed Description

.module libiomd

Definition at line 36 of file MDMolecule.java.


Public Member Functions

void add (IAtomContainer atomContainer)
void addAtom (IAtom atom)
void addAtomParity (IAtomParity parity)
void addBond (int atom1, int atom2, double order)
void addBond (int atom1, int atom2, double order, int stereo)
void addBond (IBond bond)
void addChargeGroup (ChargeGroup chargeGroup)
void addElectronContainer (IElectronContainer electronContainer)
void addListener (IChemObjectListener col)
void addLonePair (int atomID)
void addLonePair (ILonePair lonePair)
void addResidue (Residue residue)
void addSingleElectron (int atomID)
void addSingleElectron (ISingleElectron singleElectron)
java.util.Iterator atoms ()
java.util.Iterator bonds ()
Object clone () throws CloneNotSupportedException
boolean compare (Object object)
boolean contains (IElectronContainer electronContainer)
boolean contains (ISingleElectron singleElectron)
boolean contains (ILonePair lonePair)
boolean contains (IBond bond)
boolean contains (IAtom atom)
Iterator electronContainers ()
IAtom getAtom (int number)
int getAtomCount ()
int getAtomNumber (IAtom atom)
IAtomParity getAtomParity (IAtom atom)
IBond getBond (IAtom atom1, IAtom atom2)
IBond getBond (int number)
int getBondCount ()
int getBondNumber (IBond bond)
int getBondNumber (IAtom atom1, IAtom atom2)
double getBondOrderSum (IAtom atom)
IChemObjectBuilder getBuilder ()
List getChargeGroups ()
int getConnectedAtomsCount (IAtom atom)
List getConnectedAtomsList (IAtom atom)
int getConnectedBondsCount (int atomNumber)
int getConnectedBondsCount (IAtom atom)
List getConnectedBondsList (IAtom atom)
List getConnectedElectronContainersList (IAtom atom)
int getConnectedLonePairsCount (IAtom atom)
List getConnectedLonePairsList (IAtom atom)
int getConnectedSingleElectronsCount (IAtom atom)
List getConnectedSingleElectronsList (IAtom atom)
IElectronContainer getElectronContainer (int number)
int getElectronContainerCount ()
IAtom getFirstAtom ()
boolean getFlag (int flag_type)
boolean[] getFlags ()
String getID ()
IAtom getLastAtom ()
int getListenerCount ()
ILonePair getLonePair (int number)
int getLonePairCount ()
int getLonePairNumber (ILonePair lonePair)
double getMaximumBondOrder (IAtom atom)
double getMinimumBondOrder (IAtom atom)
boolean getNotification ()
Hashtable getProperties ()
Object getProperty (Object description)
List getResidues ()
ISingleElectron getSingleElectron (int number)
int getSingleElectronCount ()
int getSingleElectronNumber (ISingleElectron singleElectron)
Iterator lonePairs ()
 MDMolecule (IAtomContainer container)
void notifyChanged (IChemObjectChangeEvent evt)
void notifyChanged ()
void remove (IAtomContainer atomContainer)
void removeAllBonds ()
void removeAllElectronContainers ()
void removeAllElements ()
void removeAtom (IAtom atom)
void removeAtom (int position)
void removeAtomAndConnectedElectronContainers (IAtom atom)
void removeBond (IBond bond)
IBond removeBond (IAtom atom1, IAtom atom2)
IBond removeBond (int position)
void removeElectronContainer (IElectronContainer electronContainer)
IElectronContainer removeElectronContainer (int number)
void removeListener (IChemObjectListener col)
void removeLonePair (ILonePair lonePair)
ILonePair removeLonePair (int position)
void removeProperty (Object description)
void removeSingleElectron (ISingleElectron singleElectron)
ISingleElectron removeSingleElectron (int position)
void setAtom (int number, IAtom atom)
void setAtoms (IAtom[] atoms)
void setBonds (IBond[] bonds)
void setChargeGroups (List chargeGroups)
void setFlag (int flag_type, boolean flag_value)
void setFlags (boolean[] flagsNew)
void setID (String identifier)
void setNotification (boolean bool)
void setProperties (Hashtable properties)
void setProperty (Object description, Object property)
void setResidues (List residues)
Object shallowCopy ()
Iterator singleElectrons ()
void stateChanged (IChemObjectChangeEvent event)
String toString ()

Protected Member Functions

void growAtomArray ()
void growBondArray ()
void growLonePairArray ()
void growSingleElectronArray ()

Protected Attributes

int atomCount
Hashtable atomParities
IAtom[] atoms
int bondCount
IBond[] bonds
int growArraySize = 10
int lonePairCount
ILonePair[] lonePairs
int singleElectronCount
ISingleElectron[] singleElectrons

Private Attributes

List chargeGroups
List residues

Static Private Attributes

static final long serialVersionUID = -3129626782945020908L

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

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