Package pl.poznan.put.pdb.analysis

Class ResidueCollection.CifBuilder

java.lang.Object

pl.poznan.put.pdb.analysis.ResidueCollection.CifBuilder

Enclosing interface:

ResidueCollection

public static final class ResidueCollection.CifBuilder
extends Object

A builder that can merge many residue collections in one mmCIF file.

Constructor Summary

Constructors

Constructor	Description
CifBuilder()	Creates an instance of this build and initializes it with an audit, citation and citation_author headers.

Method Summary

Modifier and Type	Method	Description
ResidueCollection.CifBuilder	add(ResidueCollection residueCollection)	Add a residue collection to be serialized into mmCIF format.
ResidueCollection.CifBuilder	add(ResidueCollection residueCollection, String name)	Add a residue collection to be serialized into mmCIF format.
ResidueCollection.CifBuilder	add(ResidueCollection residueCollection, String name, String description)	Add a residue collection to be serialized into mmCIF format.
ResidueCollection.CifBuilder	add(ResidueCollection residueCollection, String name, String description, int modelNumber)	Add a residue collection to be serialized into mmCIF format.
String	build()

Methods inherited from class java.lang.Object

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

Constructor Details

CifBuilder

public CifBuilder()

Creates an instance of this build and initializes it with an audit, citation and citation_author headers.

Method Details

add

public ResidueCollection.CifBuilder add(ResidueCollection residueCollection)

Add a residue collection to be serialized into mmCIF format. Model number defaults to 1 and entity block is omitted entirely.

Parameters:

residueCollection - The residue collection to store.

Returns:

This instance of builder.

add

public ResidueCollection.CifBuilder add(ResidueCollection residueCollection,
 String name)

Add a residue collection to be serialized into mmCIF format. Model number defaults to 1 and description is empty.

Parameters:

residueCollection - The residue collection to store.

name - The name of the residue collection.

Returns:

This instance of builder.

add

public ResidueCollection.CifBuilder add(ResidueCollection residueCollection,
 String name,
 String description)

Add a residue collection to be serialized into mmCIF format. Model number defaults to 1.

Parameters:

residueCollection - The residue collection to store.

name - The name of the residue collection.

description - An optional description (for example, the dot-bracket representation of the entity).

Returns:

This instance of builder.

add

public ResidueCollection.CifBuilder add(ResidueCollection residueCollection,
 String name,
 String description,
 int modelNumber)

Add a residue collection to be serialized into mmCIF format.

Parameters:

residueCollection - The residue collection to store.

name - The name of the residue collection.

description - An optional description (for example, the dot-bracket representation of the entity).

modelNumber - The model number to store together with the coordinates.

Returns:

This instance of builder.

build

public String build()
             throws IOException

Returns:

The string content in PDBx/mmCIF format.

Throws:

IOException - When serializing the mmCIF to string fails.