Logo Search packages:      
Sourcecode: cdk version File versions  Download package

org::openscience::cdk::debug::DebugAminoAcid Class Reference

Inheritance diagram for org::openscience::cdk::debug::DebugAminoAcid:

org::openscience::cdk::AminoAcid org::openscience::cdk::interfaces::IAminoAcid org::openscience::cdk::Monomer org::openscience::cdk::interfaces::IAminoAcid org::openscience::cdk::interfaces::IMonomer org::openscience::cdk::AtomContainer org::openscience::cdk::interfaces::IMonomer org::openscience::cdk::interfaces::IMonomer org::openscience::cdk::interfaces::IAtomContainer org::openscience::cdk::ChemObject org::openscience::cdk::interfaces::IAtomContainer org::openscience::cdk::interfaces::IChemObjectListener org::openscience::cdk::interfaces::IAtomContainer org::openscience::cdk::interfaces::IAtomContainer org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObjectListener 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 org::openscience::cdk::interfaces::IChemObject org::openscience::cdk::interfaces::IChemObjectListener

List of all members.


Detailed Description

Debugging data class.

Author:
egonw .module datadebug

Definition at line 45 of file DebugAminoAcid.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 addCTerminus (IAtom atom)
void addElectronContainer (IElectronContainer electronContainer)
void addListener (IChemObjectListener col)
void addLonePair (int atomID)
void addLonePair (ILonePair ec)
void addNTerminus (IAtom atom)
void addSingleElectron (int atomID)
void addSingleElectron (ISingleElectron ec)
java.util.Iterator atoms ()
java.util.Iterator bonds ()
Object clone () throws CloneNotSupportedException
boolean compare (Object object)
boolean contains (IElectronContainer electronContainer)
boolean contains (ISingleElectron ec)
boolean contains (ILonePair ec)
boolean contains (IBond bond)
boolean contains (IAtom atom)
java.util.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 ()
int getConnectedAtomsCount (IAtom atom)
List getConnectedAtomsList (IAtom atom)
int getConnectedBondsCount (int atomNumber)
int getConnectedBondsCount (IAtom atom)
List getConnectedBondsList (IAtom atom)
java.util.List getConnectedElectronContainersList (IAtom atom)
int getConnectedLonePairsCount (IAtom atom)
List getConnectedLonePairsList (IAtom atom)
int getConnectedSingleElectronsCount (IAtom atom)
List getConnectedSingleElectronsList (IAtom atom)
IAtom getCTerminus ()
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 bond)
double getMaximumBondOrder (IAtom atom)
double getMinimumBondOrder (IAtom atom)
String getMonomerName ()
String getMonomerType ()
boolean getNotification ()
IAtom getNTerminus ()
Hashtable getProperties ()
Object getProperty (Object description)
ISingleElectron getSingleElectron (int number)
int getSingleElectronCount ()
int getSingleElectronNumber (ISingleElectron bond)
java.util.Iterator lonePairs ()
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 pos)
void removeElectronContainer (IElectronContainer electronContainer)
IElectronContainer removeElectronContainer (int position)
void removeListener (IChemObjectListener col)
void removeLonePair (ILonePair ec)
ILonePair removeLonePair (int pos)
void removeProperty (Object description)
void removeSingleElectron (ISingleElectron ec)
ISingleElectron removeSingleElectron (int pos)
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 setMonomerName (String cMonomerName)
void setMonomerType (String cMonomerType)
void setNotification (boolean bool)
void setProperties (Hashtable properties)
void setProperty (Object description, Object property)
Object shallowCopy ()
java.util.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

Package Attributes

LoggingTool logger = new LoggingTool(DebugAtomContainer.class)

Static Private Attributes

static final long serialVersionUID = 4092864536013855890L

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

Generated by  Doxygen 1.6.0   Back to index