de.bioforscher.singa.structure.model.mmtf

Class MmtfChain

java.lang.Object

de.bioforscher.singa.structure.model.mmtf.MmtfChain

All Implemented Interfaces:

AtomContainer, Chain, LeafSubstructureContainer

public class MmtfChain
extends Object
implements Chain

The implementation of Chain for mmtf structures. Remembers the chain identifier, the leaf relevant for this chain, their respective leaf identifiers, and atom ranges.

Author:

cl

Method Summary

Modifier and Type	Method and Description
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.
Chain	getCopy() Returns a copy of this chain.
LeafSubstructure<?>	getFirstLeafSubstructure()
Optional<LeafSubstructure<?>>	getLeafSubstructure(LeafIdentifier leafIdentifier) Returns an Optional of the LeafSubstructure with the given identifier.
int	getNumberOfLeafSubstructures()
int	hashCode()
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.
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, removeLeafSubstructure

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

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)

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. Further, this method does not cache the leafs that are being removed in contrary to the default implementation.

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 Chain 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