Package pl.poznan.put.pdb.analysis

Class CifContainer

java.lang.Object

pl.poznan.put.pdb.analysis.CifContainer

All Implemented Interfaces:

Closeable, AutoCloseable, ModelContainer

Direct Known Subclasses:

ImmutableCifContainer

@Immutable
public abstract class CifContainer
extends Object
implements ModelContainer

A container of one or more PDB files converted from a single mmCIF file.

Constructor Summary

Constructors

Constructor	Description
CifContainer()

Method Summary

Modifier and Type	Method	Description
abstract File	cifFile()
void	close()	Deletes all files (PDB and mmCIF) maintained by this instance.
String	convertedPdbChainName(File pdbFile, String cifChain)	Checks mapping of chains to get the generated PDB chain name from the original mmCIF chain name.
static ModelContainer	emptyInstance(File cifFile)	Creates an empty instance (without any chain mapping).
abstract Map<File,org.apache.commons.collections4.BidiMap<String,String>>	fileChainMap()
String	originalCifChainName(File pdbFile, String pdbChain)	Checks mapping of chains to get the original mmCIF chain name from the generated PDB chain name.
List<File>	pdbFiles()

Methods inherited from class java.lang.Object

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

Constructor Detail

CifContainer

public CifContainer()

Method Detail

emptyInstance

public static ModelContainer emptyInstance(File cifFile)

Creates an empty instance (without any chain mapping).

Parameters:

cifFile - Path to the mmCIF file.

Returns:

An instance without any chain mapping.

fileChainMap

@Parameter(order=2)
public abstract Map<File,org.apache.commons.collections4.BidiMap<String,String>> fileChainMap()

Returns:

The mapping of chain name in PDB and mmCIF for a specific file.

cifFile

@Parameter(order=1)
public abstract File cifFile()

Returns:

The value of the cifFile attribute,

pdbFiles

public final List<File> pdbFiles()

Specified by:

pdbFiles in interface ModelContainer

Returns:

A list of PDB files corresponding to this container.

originalCifChainName

public final String originalCifChainName(File pdbFile,
                                         String pdbChain)

Description copied from interface: ModelContainer

Checks mapping of chains to get the original mmCIF chain name from the generated PDB chain name.

Specified by:

originalCifChainName in interface ModelContainer

Parameters:

pdbFile - A PDB file.

pdbChain - Chain name in the PDB file.

Returns:

Original chain name in the mmCIF file.

convertedPdbChainName

public final String convertedPdbChainName(File pdbFile,
                                          String cifChain)

Description copied from interface: ModelContainer

Checks mapping of chains to get the generated PDB chain name from the original mmCIF chain name.

Specified by:

convertedPdbChainName in interface ModelContainer

Parameters:

pdbFile - A PDB file.

cifChain - Chain name in the mmCif file.

Returns:

Original chain name in the PDB file.

close

public final void close()

Deletes all files (PDB and mmCIF) maintained by this instance.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable