org.biojava.bio.structure.io

Class PDBBioAssemblyParser

java.lang.Object

org.biojava.bio.structure.io.PDBBioAssemblyParser

public class PDBBioAssemblyParser
extends java.lang.Object

Parses REMARK 350 records in a PDB file and creates transformations to construct the quaternary structure of a protein from an asymmetric unit

Author:

Peter Rose, Andreas Prlic

Constructor Summary

Constructors

Constructor and Description
PDBBioAssemblyParser()

Method Summary

Methods

Modifier and Type	Method and Description
int	getNrBioAssemblies() Returns the number of bioassemblies
java.util.Map<java.lang.Integer,java.util.List<BiologicalAssemblyTransformation>>	getTransformationMap() Returns a map of bioassembly transformations
void	pdb_REMARK_350_Handler(java.lang.String line) Parses REMARK 350 line.

Methods inherited from class java.lang.Object

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

Constructor Detail

PDBBioAssemblyParser

public PDBBioAssemblyParser()

Method Detail

pdb_REMARK_350_Handler

public void pdb_REMARK_350_Handler(java.lang.String line)

Parses REMARK 350 line. See format description: http://www.wwpdb.org/documentation/format33/remarks2.html

Parameters:

line -

getTransformationMap

public java.util.Map<java.lang.Integer,java.util.List<BiologicalAssemblyTransformation>> getTransformationMap()

Returns a map of bioassembly transformations

Returns:

getNrBioAssemblies

public int getNrBioAssemblies()

Returns the number of bioassemblies

Returns:

number of bioassemblies