de.bioforscher.singa.structure.model.oak

Class OakChain

java.lang.Object

de.bioforscher.singa.structure.model.oak.OakChain

All Implemented Interfaces:

AtomContainer, Chain, LeafSubstructureContainer

public class OakChain
extends Object
implements Chain

Author:

cl

Constructor Summary

Constructors

Constructor and Description
OakChain(OakChain chain)
OakChain(String chainIdentifier)

Method Summary

Modifier and Type	Method and Description
void	addLeafSubstructure(OakLeafSubstructure leafSubstructure)
void	addLeafSubstructure(OakLeafSubstructure leafSubstructure, boolean consecutivePart)
void	connectChainBackbone()
void	connectNucleotideBonds(OakNucleotide source, OakNucleotide target)
void	connectPeptideBonds(OakAminoAcid source, OakAminoAcid target) Connects two residues, using the Backbone Carbon (C) of the source residue and the Backbone Nitrogen (N) of the target residue.
boolean	equals(Object o)
List<LeafSubstructure<?>>	getAllLeafSubstructures() Returns all LeafSubstructures.
Optional<Atom>	getAtom(Integer atomIdentifier) Returns an Optional of the Atom with the given identifier.
String	getChainIdentifier() Returns the chain identifier, a short sequence of alphabetic characters.
List<LeafSubstructure<?>>	getConsecutivePart()
OakChain	getCopy() Returns a copy of this chain.
LeafSubstructure<?>	getFirstLeafSubstructure()
Optional<LeafSubstructure<?>>	getLeafSubstructure(LeafIdentifier leafIdentifier) Returns an Optional of the LeafSubstructure with the given identifier.
LeafIdentifier	getNextLeafIdentifier()
List<LeafSubstructure<?>>	getNonConsecutivePart()
int	hashCode()
void	removeAtom(Integer atomIdentifier) Removes an atom from this container.
boolean	removeLeafSubstructure(LeafIdentifier leafIdentifier) Removes a LeafSubstructure from this container.
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface de.bioforscher.singa.structure.model.interfaces.Chain

flatToString

Methods inherited from interface de.bioforscher.singa.structure.model.interfaces.LeafSubstructureContainer

getAllAminoAcids, getAllAtoms, getAllLigands, getAllNucleotides, getAminoAcid, getAtom, getLigand, getNucleotide, getNumberOfLeafSubstructures, removeLeafSubstructure, removeLeafSubstructuresNotRelevantFor

Constructor Detail

OakChain

public OakChain(String chainIdentifier)

OakChain

public OakChain(OakChain chain)

Method Detail

getChainIdentifier

public String getChainIdentifier()

Description copied from interface: Chain

Returns the chain identifier, a short sequence of alphabetic characters.

Specified by:

getChainIdentifier in interface Chain

Returns:

The chain identifier.

getAllLeafSubstructures

public List<LeafSubstructure<?>> getAllLeafSubstructures()

Description copied from interface: LeafSubstructureContainer

Returns all LeafSubstructures.

Specified by:

getAllLeafSubstructures in interface LeafSubstructureContainer

Returns:

All LeafSubstructures.

getLeafSubstructure

public Optional<LeafSubstructure<?>> getLeafSubstructure(LeafIdentifier leafIdentifier)

Description copied from interface: LeafSubstructureContainer

Returns an Optional of the LeafSubstructure with the given identifier. If no LeafSubstructure with the identifier could be found, an empty optional is returned.

Specified by:

getLeafSubstructure in interface LeafSubstructureContainer

Parameters:

leafIdentifier - The identifier of the leaf.

Returns:

An Optional encapsulating the LeafSubstructure.

getFirstLeafSubstructure

public LeafSubstructure<?> getFirstLeafSubstructure()

Specified by:

getFirstLeafSubstructure in interface LeafSubstructureContainer

addLeafSubstructure

public void addLeafSubstructure(OakLeafSubstructure leafSubstructure,
                                boolean consecutivePart)

addLeafSubstructure

public void addLeafSubstructure(OakLeafSubstructure leafSubstructure)

removeLeafSubstructure

public boolean removeLeafSubstructure(LeafIdentifier leafIdentifier)

Description copied from interface: LeafSubstructureContainer

Removes a LeafSubstructure from this container.

Specified by:

removeLeafSubstructure in interface LeafSubstructureContainer

Parameters:

leafIdentifier - The identifier of the leaf.

Returns:

True if the LeafSubstructure was removed.

getAtom

public Optional<Atom> getAtom(Integer atomIdentifier)

Description copied from interface: AtomContainer

Returns an Optional of the Atom with the given identifier. If no Atom with the identifier could be found, an empty optional is returned.

Specified by:

getAtom in interface AtomContainer

Parameters:

atomIdentifier - The identifier of the atom.

Returns:

An Optional encapsulating the Atom.

removeAtom

public void removeAtom(Integer atomIdentifier)

Description copied from interface: AtomContainer

Removes an atom from this container.

Specified by:

removeAtom in interface AtomContainer

Parameters:

atomIdentifier - The identifier of the atom to be removed.

connectChainBackbone

public void connectChainBackbone()

connectPeptideBonds

public void connectPeptideBonds(OakAminoAcid source,
                                OakAminoAcid target)

Connects two residues, using the Backbone Carbon (C) of the source residue and the Backbone Nitrogen (N) of the target residue.

Parameters:

source - AminoAcid with Backbone Carbon.

target - AminoAcid with Backbone Nitrogen.

connectNucleotideBonds

public void connectNucleotideBonds(OakNucleotide source,
                                   OakNucleotide target)

getConsecutivePart

public List<LeafSubstructure<?>> getConsecutivePart()

getNonConsecutivePart

public List<LeafSubstructure<?>> getNonConsecutivePart()

getNextLeafIdentifier

public LeafIdentifier getNextLeafIdentifier()

getCopy

public OakChain getCopy()

Description copied from interface: Chain

Returns a copy of this chain.

Specified by:

getCopy in interface Chain

Specified by:

getCopy in interface LeafSubstructureContainer

Returns:

A copy of this chain.

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object