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Public Member Functions

org::openscience::cdk::interfaces::IStrand Interface Reference

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List of all members.

Public Member Functions

void add (IAtomContainer atomContainer)
void addAtom (IAtom oAtom)
void addAtom (IAtom oAtom, IMonomer oMonomer)
void addAtomParity (IAtomParity parity)
void addBond (IBond bond)
void addBond (int atom1, int atom2, IBond.Order order, int stereo)
void addBond (int atom1, int atom2, IBond.Order order)
void addElectronContainer (IElectronContainer electronContainer)
void addListener (IChemObjectListener col)
void addLonePair (ILonePair lonePair)
void addLonePair (int atomID)
void addSingleElectron (ISingleElectron singleElectron)
void addSingleElectron (int atomID)
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 (int number)
IBond getBond (IAtom atom1, IAtom atom2)
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)
IMonomer getMonomer (String cName)
int getMonomerCount ()
Collection< String > getMonomerNames ()
Map< String, IMonomergetMonomers ()
boolean getNotification ()
Map< Object, Object > getProperties ()
Object getProperty (Object description)
ISingleElectron getSingleElectron (int number)
int getSingleElectronCount ()
int getSingleElectronNumber (ISingleElectron singleElectron)
String getStrandName ()
String getStrandType ()
Iterable< ILonePairlonePairs ()
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)
IBond removeBond (int position)
void removeBond (IBond bond)
IBond removeBond (IAtom atom1, IAtom atom2)
void removeElectronContainer (IElectronContainer electronContainer)
IElectronContainer removeElectronContainer (int position)
void removeListener (IChemObjectListener col)
ILonePair removeLonePair (int position)
void removeLonePair (ILonePair lonePair)
void removeMonomer (String name)
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)
void setStrandName (String cStrandName)
void setStrandType (String cStrandType)
Iterable< ISingleElectronsingleElectrons ()
void stateChanged (IChemObjectChangeEvent event)
String toString ()

Detailed Description

A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.

.module interfaces .githash .created 2004-12-20

Author:
Martin Eklund <martin.eklund@farmbio.uu.se>

Definition at line 42 of file IStrand.java.


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

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