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Public Member Functions

org::openscience::cdk::interfaces::IAminoAcid Interface Reference

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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 (IBond bond)
void addBond (int atom1, int atom2, IBond.Order order, int stereo)
void addBond (int atom1, int atom2, IBond.Order order)
void addCTerminus (IAtom atom)
void addElectronContainer (IElectronContainer electronContainer)
void addListener (IChemObjectListener col)
void addLonePair (ILonePair lonePair)
void addLonePair (int atomID)
void addNTerminus (IAtom atom)
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 (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)
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 lonePair)
Order getMaximumBondOrder (IAtom atom)
Order getMinimumBondOrder (IAtom atom)
String getMonomerName ()
String getMonomerType ()
boolean getNotification ()
IAtom getNTerminus ()
Map< Object, Object > getProperties ()
Object getProperty (Object description)
ISingleElectron getSingleElectron (int number)
int getSingleElectronCount ()
int getSingleElectronNumber (ISingleElectron singleElectron)
Iterable< ILonePairlonePairs ()
void notifyChanged ()
void notifyChanged (IChemObjectChangeEvent evt)
void remove (IAtomContainer atomContainer)
void removeAllBonds ()
void removeAllElectronContainers ()
void removeAllElements ()
void removeAtom (IAtom atom)
void removeAtom (int position)
void removeAtomAndConnectedElectronContainers (IAtom atom)
IBond removeBond (IAtom atom1, IAtom atom2)
void removeBond (IBond bond)
IBond removeBond (int position)
IElectronContainer removeElectronContainer (int position)
void removeElectronContainer (IElectronContainer electronContainer)
void removeListener (IChemObjectListener col)
ILonePair removeLonePair (int position)
void removeLonePair (ILonePair lonePair)
void removeProperty (Object description)
ISingleElectron removeSingleElectron (int position)
void removeSingleElectron (ISingleElectron singleElectron)
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 (Map< Object, Object > properties)
void setProperty (Object description, Object property)
Iterable< ISingleElectronsingleElectrons ()
void stateChanged (IChemObjectChangeEvent event)
String toString ()

Detailed Description

A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.

.module interfaces .githash

Author:
Egon Willighagen <e.willighagen@science.ru.nl> .created 2005-12-05 .keyword amino acid

Definition at line 38 of file IAminoAcid.java.


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

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