de.bioforscher.singa.structure.model.oak

Class OakStructure

java.lang.Object

de.bioforscher.singa.structure.model.oak.OakStructure

All Implemented Interfaces:

AtomContainer, ChainContainer, LeafSubstructureContainer, Structure

public class OakStructure
extends Object
implements Structure

Author:

cl

Constructor Summary

Constructors

Constructor and Description
OakStructure()
OakStructure(OakStructure structure)

Method Summary

Modifier and Type	Method and Description
void	addAtom(String chainIdentifier, String threeLetterCode, Vector3D position) Adds an Atom to the Structure FIXME: atom serial overflow may happen (if exceeds 9999)
void	addModel(OakModel model)
boolean	equals(Object o)
List<Chain>	getAllChains() Returns all Chains.
List<LeafSubstructure<?>>	getAllLeafSubstructures() Returns all LeafSubstructures.
Set<Integer>	getAllModelIdentifiers() Returns all model identifiers referenced in the model.
List<Model>	getAllModels() Returns all Models.
Optional<Atom>	getAtom(Integer atomIdentifier) Returns an Optional of the Atom with the given identifier.
Optional<Chain>	getChain(int modelIdentifier, String chainIdentifier) Returns an Optional of the Chain with the given identifier from the model with the given identifier.
Structure	getCopy() Returns a copy of this structure.
Chain	getFirstChain() Returns the first Chain.
LeafSubstructure<?>	getFirstLeafSubstructure()
Model	getFirstModel() Returns the first Model (with the smallest identifier).
int	getLastAddedAtomIdentifier()
Optional<LeafSubstructure<?>>	getLeafSubstructure(LeafIdentifier leafIdentifier) Returns an Optional of the LeafSubstructure with the given identifier.
Optional<Model>	getModel(int modelIdentifier) Returns an Optional of the Model with the given identifier.
String	getPdbIdentifier() Returns the PDB identifier, a 4 character code, where the first character is any number followed by three alphanumeric characters.
String	getTitle() Returns the title.
Optional<Map.Entry<UniqueAtomIdentifer,Atom>>	getUniqueAtomEntry(int atomSerial)
int	hashCode()
void	removeAtom(Integer atomIdentifier) Removes an atom from this container.
boolean	removeLeafSubstructure(LeafIdentifier leafIdentifier) Removes a LeafSubstructure from this container.
void	removeModel(int modelIdentifier) Removes a Model with the given identifier from the structure.
void	setLastAddedAtomIdentifier(int lastAddedAtomIdentifier)
void	setPdbIdentifier(String pdbIdentifier)
void	setTitle(String title)
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.Structure

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

OakStructure

public OakStructure()

OakStructure

public OakStructure(OakStructure structure)

Method Detail

getPdbIdentifier

public String getPdbIdentifier()

Description copied from interface: Structure

Returns the PDB identifier, a 4 character code, where the first character is any number followed by three alphanumeric characters.

Specified by:

getPdbIdentifier in interface Structure

Returns:

The PDB identifier.

See Also:

PDBIdentifier

setPdbIdentifier

public void setPdbIdentifier(String pdbIdentifier)

getTitle

public String getTitle()

Description copied from interface: Structure

Returns the title.

Specified by:

getTitle in interface Structure

Returns:

The title of the structure.

setTitle

public void setTitle(String title)

getAllModels

public List<Model> getAllModels()

Description copied from interface: Structure

Returns all Models.

Specified by:

getAllModels in interface Structure

Returns:

All models.

getAllModelIdentifiers

public Set<Integer> getAllModelIdentifiers()

Description copied from interface: Structure

Returns all model identifiers referenced in the model.

Specified by:

getAllModelIdentifiers in interface Structure

Returns:

All model identifiers referenced in the model.

getFirstModel

public Model getFirstModel()

Description copied from interface: Structure

Returns the first Model (with the smallest identifier).

Specified by:

getFirstModel in interface Structure

Returns:

The first model.

getModel

public Optional<Model> getModel(int modelIdentifier)

Description copied from interface: Structure

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

Specified by:

getModel in interface Structure

Parameters:

modelIdentifier - The identifier of the model.

Returns:

An Optional encapsulating the Model.

removeModel

public void removeModel(int modelIdentifier)

Description copied from interface: Structure

Removes a Model with the given identifier from the structure.

Specified by:

removeModel in interface Structure

Parameters:

modelIdentifier - The identifier of the model.

addModel

public void addModel(OakModel model)

getChain

public Optional<Chain> getChain(int modelIdentifier,
                                String chainIdentifier)

Description copied from interface: Structure

Returns an Optional of the Chain with the given identifier from the model with the given identifier. If no chain or model with the identifier could be found, an empty optional is returned.

Specified by:

getChain in interface Structure

Parameters:

modelIdentifier - The identifier of the model.

chainIdentifier - The identifier of the chain.

Returns:

An Optional encapsulating the Chain.

getAllChains

public List<Chain> getAllChains()

Description copied from interface: ChainContainer

Returns all Chains.

Specified by:

getAllChains in interface ChainContainer

Returns:

All Chains.

getFirstChain

public Chain getFirstChain()

Description copied from interface: ChainContainer

Returns the first Chain.

Specified by:

getFirstChain in interface ChainContainer

Returns:

The first Chain.

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

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.

getUniqueAtomEntry

public Optional<Map.Entry<UniqueAtomIdentifer,Atom>> getUniqueAtomEntry(int atomSerial)

addAtom

public void addAtom(String chainIdentifier,
                    String threeLetterCode,
                    Vector3D position)

Adds an Atom to the Structure FIXME: atom serial overflow may happen (if exceeds 9999)

Parameters:

chainIdentifier - The identifier of the Chain to which it should be added.

threeLetterCode - The three-letter code of the associated LeafSubstructure.

position - The position of 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.

getLastAddedAtomIdentifier

public int getLastAddedAtomIdentifier()

setLastAddedAtomIdentifier

public void setLastAddedAtomIdentifier(int lastAddedAtomIdentifier)

getCopy

public Structure getCopy()

Description copied from interface: Structure

Returns a copy of this structure.

Specified by:

getCopy in interface LeafSubstructureContainer

Specified by:

getCopy in interface Structure

Returns:

A copy of this structure.

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