de.bioforscher.singa.structure.model.mmtf

Class MmtfStructure

java.lang.Object

de.bioforscher.singa.structure.model.mmtf.MmtfStructure

All Implemented Interfaces:

AtomContainer, ChainContainer, LeafSubstructureContainer, Structure

public class MmtfStructure
extends Object
implements Structure

The implementation of Structures for mmtf structures.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
MmtfStructure(byte[] bytes) Creates a new MmtfStructure
MmtfStructure(byte[] bytes, boolean deflate) Creates a new MmtfStructure

Method Summary

Modifier and Type	Method and Description
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).
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.
int	getNumberOfLeafSubstructures()
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.
void	removeAtom(Integer atomIdentifier) Removes an atom from this container.
boolean	removeLeafSubstructure(LeafIdentifier leafIdentifier) Removes a LeafSubstructure from this container.
void	removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep) Removes all LeafSubstructures from this container that are not referenced in the given LeafSubstructureContainer.
void	removeModel(int modelIdentifier) Removes a Model with the given identifier from the structure.
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, 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, removeLeafSubstructure

Constructor Detail

MmtfStructure

public MmtfStructure(byte[] bytes)

Creates a new MmtfStructure

Parameters:

bytes - The original undecoded bytes.

MmtfStructure

public MmtfStructure(byte[] bytes,
                     boolean deflate)

Creates a new MmtfStructure

Parameters:

bytes - The original undecoded bytes.

deflate - Signifies if the byte array should be deflated.

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

getTitle

public String getTitle()

Description copied from interface: Structure

Returns the title.

Specified by:

getTitle in interface Structure

Returns:

The title of the structure.

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.

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.

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.

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.

removeLeafSubstructuresNotRelevantFor

public void removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)

Description copied from interface: LeafSubstructureContainer

Removes all LeafSubstructures from this container that are not referenced in the given LeafSubstructureContainer. Basically all LeafSubstructures are removed that do not match any of the given containers families. This method also keeps exchangeable families if any are defined.

Specified by:

removeLeafSubstructuresNotRelevantFor in interface LeafSubstructureContainer

Parameters:

leafSubstructuresToKeep - The leaf structures that are kept.

getNumberOfLeafSubstructures

public int getNumberOfLeafSubstructures()

Specified by:

getNumberOfLeafSubstructures in interface LeafSubstructureContainer

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.

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.

toString

public String toString()

Overrides:

toString in class Object