org.openscience.cdk.interfaces

Interface IBioPolymer

All Superinterfaces:

Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IPolymer

All Known Subinterfaces:

IPDBPolymer

All Known Implementing Classes:

BioPolymer, BioPolymer, DebugBioPolymer, DebugPDBPolymer, PDBPolymer, PDBPolymer

public interface IBioPolymer
extends IPolymer

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

Author:

Edgar Luttmann <edgar@uni-paderborn.de>

Source code:

master

Belongs to CDK module:

interfaces

Keywords:

polymer, biopolymer

Created on:

2001-08-06

Method Summary

Modifier and Type	Method and Description
void	addAtom(IAtom oAtom) Adds the atom oAtom without specifying a Monomer or a Strand.
void	addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand) Adds the atom to a specified Strand and a specified Monomer.
void	addAtom(IAtom oAtom, IStrand oStrand) Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.
IBioPolymer	clone() Returns a deep clone of this IChemObject.
IMonomer	getMonomer(String monName, String strandName) Retrieve a Monomer object by specifying its name.
int	getMonomerCount() Return the number of monomers present in BioPolymer.
Collection<String>	getMonomerNames() Returns a collection of the names of all Monomers in this BioPolymer.
IStrand	getStrand(String cName) Retrieve a Monomer object by specifying its name.
int	getStrandCount() Return the number of strands present in the BioPolymer.
Collection<String>	getStrandNames() Returns a collection of the names of all Strands in this BioPolymer.
Map<String,IStrand>	getStrands() Returns a Map containing the strands in the Polymer.
void	removeStrand(String name) Removes a particular strand, specified by its name.

Methods inherited from interface org.openscience.cdk.interfaces.IPolymer

addAtom, getMonomer, removeMonomer

Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer

add, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stereoElements

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener

stateChanged

Method Detail

addAtom

void addAtom(IAtom oAtom)

Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the atom to this AtomContainer, but not to a certain Strand or Monomer (intended e.g. for HETATMs).

Specified by:

addAtom in interface IAtomContainer

Specified by:

addAtom in interface IPolymer

Parameters:

oAtom - The atom to add

addAtom

void addAtom(IAtom oAtom,
             IStrand oStrand)

Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence the atom will be added to a Monomer of type UNKNOWN in the specified Strand.

Parameters:

oAtom - The atom to add

oStrand - The strand the atom belongs to

addAtom

void addAtom(IAtom oAtom,
             IMonomer oMonomer,
             IStrand oStrand)

Adds the atom to a specified Strand and a specified Monomer.

Parameters:

oAtom - The atom to add

oMonomer - The monomer the atom belongs to

oStrand - The strand the atom belongs to

getMonomerCount

int getMonomerCount()

Return the number of monomers present in BioPolymer.

Specified by:

getMonomerCount in interface IPolymer

Returns:

number of monomers

getMonomer

IMonomer getMonomer(String monName,
                    String strandName)

Retrieve a Monomer object by specifying its name.

You have to specify the strand to enable monomers with the same name in different strands. There is at least one such case: every strand contains a monomer called "".

Parameters:

monName - The name of the monomer to look for

strandName - The name of the strand to look for

Returns:

The Monomer object which was asked for

getMonomerNames

Collection<String> getMonomerNames()

Returns a collection of the names of all Monomers in this BioPolymer.

Specified by:

getMonomerNames in interface IPolymer

Returns:

a Collection of all the monomer names.

getStrandCount

int getStrandCount()

Return the number of strands present in the BioPolymer.

Returns:

number of strands

getStrand

IStrand getStrand(String cName)

Retrieve a Monomer object by specifying its name.

Parameters:

cName - The name of the monomer to look for

Returns:

The Monomer object which was asked for

getStrandNames

Collection<String> getStrandNames()

Returns a collection of the names of all Strands in this BioPolymer.

Returns:

a Collection of all the strand names.

removeStrand

void removeStrand(String name)

Removes a particular strand, specified by its name.

Parameters:

name - The name of the strand to remove

getStrands

Map<String,IStrand> getStrands()

Returns a Map containing the strands in the Polymer.

Returns:

hashtable containing the strands in the Polymer

clone

IBioPolymer clone()
           throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IPolymer

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned