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Public Member Functions

org::openscience::cdk::interfaces::IPDBPolymer Interface Reference

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List of all members.

Public Member Functions

void add (IAtomContainer atomContainer)
void addAtom (IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand)
void addAtom (IAtom oAtom, IMonomer oMonomer)
void addAtom (IAtom oAtom)
void addAtom (IPDBAtom oAtom)
void addAtom (IAtom oAtom, IStrand oStrand)
void addAtom (IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
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 (int atomID)
void addLonePair (ILonePair lonePair)
void addSingleElectron (ISingleElectron singleElectron)
void addSingleElectron (int atomID)
void addStructure (IPDBStructure structure)
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 monName, String strandName)
IMonomer getMonomer (String cName)
int getMonomerCount ()
Collection< String > getMonomerNames ()
boolean getNotification ()
Map< Object, Object > getProperties ()
Object getProperty (Object description)
ISingleElectron getSingleElectron (int number)
int getSingleElectronCount ()
int getSingleElectronNumber (ISingleElectron singleElectron)
IStrand getStrand (String cName)
int getStrandCount ()
Collection< String > getStrandNames ()
Map< String, IStrandgetStrands ()
Collection< IPDBStructuregetStructures ()
Iterable< ILonePairlonePairs ()
void notifyChanged ()
void notifyChanged (IChemObjectChangeEvent evt)
void remove (IAtomContainer atomContainer)
void removeAllBonds ()
void removeAllElectronContainers ()
void removeAllElements ()
void removeAtom (int position)
void removeAtom (IAtom atom)
void removeAtomAndConnectedElectronContainers (IAtom atom)
IBond removeBond (int position)
IBond removeBond (IAtom atom1, IAtom atom2)
void removeBond (IBond bond)
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 removeStrand (String name)
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

A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.

.module interfaces .githash

Author:
Miguel Rojas <miguel.rojas@uni-koeln.de> .created 2006-11-20

.keyword polymer .keyword biopolymer .keyword pdbpolymer

Definition at line 47 of file IPDBPolymer.java.


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

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