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Public Member Functions

org::openscience::cdk::interfaces::IAtomContainer Interface Reference

Inheritance diagram for org::openscience::cdk::interfaces::IAtomContainer:
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Collaboration diagram for org::openscience::cdk::interfaces::IAtomContainer:
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List of all members.

Public Member Functions

void add (IAtomContainer atomContainer)
void addAtom (IAtom atom)
void addAtomParity (IAtomParity parity)
void addBond (int atom1, int atom2, IBond.Order order, int stereo)
void addBond (int atom1, int atom2, IBond.Order order)
void addBond (IBond bond)
void addElectronContainer (IElectronContainer electronContainer)
void addListener (IChemObjectListener col)
void addLonePair (int atomID)
void addLonePair (ILonePair lonePair)
void addSingleElectron (int atomID)
void addSingleElectron (ISingleElectron singleElectron)
Iterable< IAtomatoms ()
Iterable< IBondbonds ()
Object clone () throws CloneNotSupportedException
boolean contains (IAtom atom)
boolean contains (IBond bond)
boolean contains (ILonePair lonePair)
boolean contains (ISingleElectron singleElectron)
boolean contains (IElectronContainer electronContainer)
Iterable< IElectronContainerelectronContainers ()
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 (IAtom atom1, IAtom atom2)
int getBondNumber (IBond bond)
double getBondOrderSum (IAtom atom)
IChemObjectBuilder getBuilder ()
int getConnectedAtomsCount (IAtom atom)
List< IAtomgetConnectedAtomsList (IAtom atom)
int getConnectedBondsCount (IAtom atom)
int getConnectedBondsCount (int atomnumber)
List< IBondgetConnectedBondsList (IAtom atom)
List< IElectronContainergetConnectedElectronContainersList (IAtom atom)
int getConnectedLonePairsCount (IAtom atom)
List< ILonePairgetConnectedLonePairsList (IAtom atom)
int getConnectedSingleElectronsCount (IAtom atom)
List< ISingleElectrongetConnectedSingleElectronsList (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)
Order getMaximumBondOrder (IAtom atom)
Order getMinimumBondOrder (IAtom atom)
boolean getNotification ()
Map< Object, Object > getProperties ()
Object getProperty (Object description)
ISingleElectron getSingleElectron (int number)
int getSingleElectronCount ()
int getSingleElectronNumber (ISingleElectron singleElectron)
Iterable< ILonePairlonePairs ()
void notifyChanged (IChemObjectChangeEvent evt)
void notifyChanged ()
void remove (IAtomContainer atomContainer)
void removeAllBonds ()
void removeAllElectronContainers ()
void removeAllElements ()
void removeAtom (int position)
void removeAtom (IAtom atom)
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 position)
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 setFlag (int flag_type, boolean flag_value)
void setFlags (boolean[] flagsNew)
void setID (String identifier)
void setNotification (boolean bool)
void setProperties (Map< Object, Object > properties)
void setProperty (Object description, Object property)
Iterable< ISingleElectronsingleElectrons ()
void stateChanged (IChemObjectChangeEvent event)
String toString ()

Detailed Description

Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.

Looping over all IBonds in the IAtomContainer is typically done like:

  for (IBond bond : atomContainer.bonds()) {
    // do something
  }
  

If you do need an explicit Iterator then use

 Iterator<IBond> bondIter = atomContainer.bonds().iterator();
 

.module interfaces .githash

Author:
steinbeck .created 2000-10-02

Definition at line 49 of file IAtomContainer.java.


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

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