org.biojava.nbio.structure.io.cif

Class AbstractCifFileSupplier<S>

java.lang.Object

org.biojava.nbio.structure.io.cif.AbstractCifFileSupplier<S>

All Implemented Interfaces:

CifFileSupplier<S>

Direct Known Subclasses:

CifChainSupplierImpl, CifStructureSupplierImpl

public abstract class AbstractCifFileSupplier<S>
extends Object
implements CifFileSupplier<S>

Convert a BioJava object to a CifFile.

Since:

5.3.0

Author:

Sebastian Bittrich

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AbstractCifFileSupplier.WrappedAtom Wrapped atoms represent individual atoms enriched with model- and chain-level information.

Constructor Summary

Constructors

Constructor and Description
AbstractCifFileSupplier()

Method Summary

Modifier and Type	Method and Description
protected org.rcsb.cif.model.CifFile	getInternal(Structure structure, List<AbstractCifFileSupplier.WrappedAtom> wrappedAtoms)
protected void	handleChain(Chain chain, int model, List<AbstractCifFileSupplier.WrappedAtom> wrappedAtoms)
static Collector<AbstractCifFileSupplier.WrappedAtom,?,org.rcsb.cif.model.Category>	toAtomSite() Collects AbstractCifFileSupplier.WrappedAtom instances into one AtomSite.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.nbio.structure.io.cif.CifFileSupplier

get

Constructor Detail

AbstractCifFileSupplier

public AbstractCifFileSupplier()

Method Detail

getInternal

protected org.rcsb.cif.model.CifFile getInternal(Structure structure,
                                                 List<AbstractCifFileSupplier.WrappedAtom> wrappedAtoms)

handleChain

protected void handleChain(Chain chain,
                           int model,
                           List<AbstractCifFileSupplier.WrappedAtom> wrappedAtoms)

toAtomSite

public static Collector<AbstractCifFileSupplier.WrappedAtom,?,org.rcsb.cif.model.Category> toAtomSite()

Collects AbstractCifFileSupplier.WrappedAtom instances into one AtomSite.

Returns:

an atom site record containing all atoms