de.bioforscher.singa.structure.model.interfaces

Interface Structure

All Superinterfaces:

AtomContainer, ChainContainer, LeafSubstructureContainer

All Known Implementing Classes:

MmtfStructure, OakStructure

public interface Structure
extends LeafSubstructureContainer, ChainContainer

Structures represent chemical objects in three dimensional space.

Structures may contain one ore more Models that represent the same structure but in different situations (e.g. at different time steps for MD trajectories or dynamics for NMR)
Structures may contain one or more Chains that represent one continuous macro molecule (most often the biggest macro molecules and its ligands are collected in one model).

Author:

cl

Method Summary

Modifier and Type	Method and Description
default String	flatToString()
Set<Integer>	getAllModelIdentifiers() Returns all model identifiers referenced in the model.
List<Model>	getAllModels() Returns all Models.
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.
Model	getFirstModel() Returns the first Model (with the smallest 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.
void	removeModel(int modelIdentifier) Removes a Model 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

getPdbIdentifier

String getPdbIdentifier()

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

Returns:

The PDB identifier.

See Also:

PDBIdentifier

getTitle

String getTitle()

Returns the title.

Returns:

The title of the structure.

getAllModels

List<Model> getAllModels()

Returns all Models.

Returns:

All models.

getAllModelIdentifiers

Set<Integer> getAllModelIdentifiers()

Returns all model identifiers referenced in the model.

Returns:

All model identifiers referenced in the model.

getFirstModel

Model getFirstModel()

Returns the first Model (with the smallest identifier).

Returns:

The first model.

getModel

Optional<Model> getModel(int modelIdentifier)

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

Parameters:

modelIdentifier - The identifier of the model.

Returns:

An Optional encapsulating the Model.

removeModel

void removeModel(int modelIdentifier)

Removes a Model with the given identifier from the structure.

Parameters:

modelIdentifier - The identifier of the model.

getChain

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

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.

Parameters:

modelIdentifier - The identifier of the model.

chainIdentifier - The identifier of the chain.

Returns:

An Optional encapsulating the Chain.

getCopy

Structure getCopy()

Returns a copy of this structure.

Specified by:

getCopy in interface LeafSubstructureContainer

Returns:

A copy of this structure.

flatToString

default String flatToString()