de.bioforscher.singa.structure.model.interfaces

Interface Model

All Superinterfaces:

AtomContainer, ChainContainer, LeafSubstructureContainer

All Known Implementing Classes:

MmtfModel, OakModel

public interface Model
extends LeafSubstructureContainer, ChainContainer

Models represent macro molecular structures. Models are most often grouped in Structures where they are different dynamic states of the same molecule.

Author:

cl

Method Summary

Modifier and Type	Method and Description
default String	flatToString()
Set<String>	getAllChainIdentifiers() Returns A set of all chin identifiers referenced in th model.
Optional<Chain>	getChain(String chainIdentifier) Returns an Optional of the Chain with the given identifier.
Model	getCopy() Returns a copy of this model.
Integer	getModelIdentifier() Returns the model identifier, an integer greater or equal to 1.
void	removeChain(String chainIdentifier) Removes a Chain with the given identifier from the structure.

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

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

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

getAtom, removeAtom

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

getAllChains, getFirstChain

Method Detail

getModelIdentifier

Integer getModelIdentifier()

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

Returns:

The model identifier.

getAllChainIdentifiers

Set<String> getAllChainIdentifiers()

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

Returns:

A set of all chin identifiers referenced in th model.

getChain

Optional<Chain> getChain(String chainIdentifier)

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

Parameters:

chainIdentifier - The identifier of the chain.

Returns:

An Optional encapsulating the Chain.

removeChain

void removeChain(String chainIdentifier)

Removes a Chain with the given identifier from the structure.

Parameters:

chainIdentifier - The identifier of the chain.

getCopy

Model getCopy()

Returns a copy of this model.

Specified by:

getCopy in interface LeafSubstructureContainer

Returns:

A copy of this model.

flatToString

default String flatToString()