org.biojava.nbio.structure.io

Class PDBBioAssemblyParser

java.lang.Object

org.biojava.nbio.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

Modifier and Type	Method and Description
java.util.Map<java.lang.Integer,BioAssemblyInfo>	getTransformationMap() Returns a map of bioassembly transformations
void	pdb_REMARK_350_Handler(java.lang.String line) Parses REMARK 350 line.
void	setMacromolecularSizes() Set the macromolecularSize fields of the parsed bioassemblies.

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,BioAssemblyInfo> getTransformationMap()

Returns a map of bioassembly transformations

Returns:

setMacromolecularSizes

public void setMacromolecularSizes()

Set the macromolecularSize fields of the parsed bioassemblies. This can only be called after the full PDB file has been read so that all the info for all bioassemblies has been gathered. Note that an explicit method to set the field is necessary here because in PDB files the transformations contain only the author chain ids, corresponding to polymeric chains, whilst in mmCIF files the transformations contain all asym ids of both polymers and non-polymers.