de.bioforscher.singa.structure.model.mmtf

Class MmtfModel

java.lang.Object

de.bioforscher.singa.structure.model.mmtf.MmtfModel

All Implemented Interfaces:

AtomContainer, ChainContainer, LeafSubstructureContainer, Model

public class MmtfModel
extends Object
implements Model

The implementation of Model for mmtf structures. Remembers the index of the model and a mapping of chain identifiers relevant for this model, as well as their respective identifiers in the chain data arrays.

Author:

cl

Method Summary

Modifier and Type	Method and Description
Set<String>	getAllChainIdentifiers() Returns A set of all chin identifiers referenced in th model.
List<Chain>	getAllChains() Returns all Chains.
List<LeafSubstructure<?>>	getAllLeafSubstructures() Returns all LeafSubstructures.
Optional<Atom>	getAtom(Integer atomIdentifier) Returns an Optional of the Atom with the given identifier.
Optional<Chain>	getChain(String chainIdentifier) Returns an Optional of the Chain with the given identifier.
Model	getCopy() Returns a copy of this model.
Chain	getFirstChain() Returns the first Chain.
LeafSubstructure<?>	getFirstLeafSubstructure()
Optional<LeafSubstructure<?>>	getLeafSubstructure(LeafIdentifier leafIdentifier) Returns an Optional of the LeafSubstructure with the given identifier.
Integer	getModelIdentifier() Returns the model identifier, an integer greater or equal to 1.
int	getNumberOfLeafSubstructures()
void	removeAtom(Integer atomIdentifier) Removes an atom from this container.
void	removeChain(String chainIdentifier) Removes a Chain with the given identifier from the structure.
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.
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.Model

flatToString

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

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

Method Detail

getModelIdentifier

public Integer getModelIdentifier()

Description copied from interface: Model

Returns the model identifier, an integer greater or equal to 1.

Specified by:

getModelIdentifier in interface Model

Returns:

The model identifier.

getAllChains

public List<Chain> getAllChains()

Description copied from interface: ChainContainer

Returns all Chains.

Specified by:

getAllChains in interface ChainContainer

Returns:

All Chains.

getAllChainIdentifiers

public Set<String> getAllChainIdentifiers()

Description copied from interface: Model

Returns A set of all chin identifiers referenced in th model.

Specified by:

getAllChainIdentifiers in interface Model

Returns:

A set of all chin identifiers referenced in th model.

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(String chainIdentifier)

Description copied from interface: Model

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

Specified by:

getChain in interface Model

Parameters:

chainIdentifier - The identifier of the chain.

Returns:

An Optional encapsulating the Chain.

removeChain

public void removeChain(String chainIdentifier)

Description copied from interface: Model

Removes a Chain with the given identifier from the structure.

Specified by:

removeChain in interface Model

Parameters:

chainIdentifier - The identifier of 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 Model getCopy()

Description copied from interface: Model

Returns a copy of this model.

Specified by:

getCopy in interface LeafSubstructureContainer

Specified by:

getCopy in interface Model

Returns:

A copy of this model.

toString

public String toString()

Overrides:

toString in class Object