ffe.parsers
Class PDBFilter

java.lang.Object
  ffe.parsers.SystemFilter
      ffe.parsers.PDBFilter

All Implemented Interfaces:

java.lang.Runnable

public final class PDBFilter

extends SystemFilter

The PDBFilter class parses data from a Protein DataBank (*.PDB) file. The following records are recognized: HEADER, ATOM, HETATM, LINK, SSBOND, HELIX, SHEET, TURN. The rest are ignored.

Field Summary

(package private) static java.util.Hashtable

mmatoms

Fields inherited from class ffe.parsers.SystemFilter

ARC, atomList, bondList, file_read, filetype, fpanel, fsystem, INT, mmfilter, NED, PDB, SIM, statusBar, XYZ

Constructor Summary

PDBFilter()
Default Constructor

PDBFilter(FSystem f, MainPanel tink)
Parse the PDB File form a local disk

PDBFilter(FSystem f, java.lang.String pdb, java.lang.String vrml, MainPanel tink)
Parse the PDB File from a URL

Method Summary

static MMAtom	getMMAtom(java.lang.String s)
boolean	readfile() Parse the PDB File
boolean	writefile()

Methods inherited from class ffe.parsers.SystemFilter

FileRead, getFSystem, getType, run, setFileRead, setFSystem, setType, toFileString, version

Methods inherited from class java.lang.Object

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

Field Detail

mmatoms

static java.util.Hashtable mmatoms

Constructor Detail

PDBFilter

public PDBFilter()

Default Constructor

PDBFilter

public PDBFilter(FSystem f,
                 MainPanel tink)

Parse the PDB File form a local disk

PDBFilter

public PDBFilter(FSystem f,
                 java.lang.String pdb,
                 java.lang.String vrml,
                 MainPanel tink)

Parse the PDB File from a URL

Method Detail

readfile

public boolean readfile()

Parse the PDB File

Specified by:

readfile in class SystemFilter

writefile

public boolean writefile()

Specified by:

writefile in class SystemFilter

getMMAtom

public static MMAtom getMMAtom(java.lang.String s)