Class pmr.cml.PDB 
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Class pmr.cml.PDB 

java.lang.Object
   |
   +----java.awt.Component
           |
           +----java.awt.Container
                   |
                   +----java.awt.Panel
                           |
                           +----java.applet.Applet
                                   |
                                   +----pmr.simplegraph.SimpleApplet
                                           |
                                           +----pmr.sgml.SGMLApplet
                                                   |
                                                   +----pmr.sgml.SGMLTree
                                                           |
                                                           +----pmr.cml.CMLObj
                                                                   |
                                                                   +----pmr.cml.PDB
public class PDB
extends CMLObj

Constructor Index

o PDB(String)
create a CMLObj from a PDB file
o PDB(String, boolean)
as above, but allow for 'pdb-like' files if strict = false

Method Index

o process()
the standard SGMLNode 'process' routine
o process1()
additional processing after whole file has been read in
o readATOMHETATM(boolean)
o readAUTHOR(boolean)
o readBIB(boolean)
o readCOMPND(boolean)
o readCONECT(boolean)
o readCRYST1(boolean)
o readFORMUL(boolean)
o readFTNOTE(boolean)
o readHELIX(boolean)
o readHET(boolean)
o readORIGXSCALEMTRIX(boolean)
o readREMARK(boolean)
o readREVDAT(boolean)
o readSEQRES(boolean)
o readSHEET(boolean)
o readSITE(boolean)
o readSOURCE(boolean)
o readSSBOND(boolean)
o readTURN(boolean)

Constructors

o PDB 
  public PDB(String filename) throws BadPDBFileException
create a CMLObj from a PDB file
Throws: throws
BadPDBFileException missing or corrupt PDB file
o PDB 
  public PDB(String filename,
             boolean strict) throws BadPDBFileException
as above, but allow for 'pdb-like' files if strict = false
Throws: throws
BadPDBFileException missing or corrupt PDB file

Methods

o process 
  public void process() throws BadPDBFileException
the standard SGMLNode 'process' routine
Throws: throws
BadPDBFileException corrupt PDB file
o readCOMPND 
  protected void readCOMPND(boolean ignore)
o readSOURCE 
  protected void readSOURCE(boolean ignore)
o readAUTHOR 
  protected void readAUTHOR(boolean ignore)
o readREVDAT 
  protected void readREVDAT(boolean ignore)
o readBIB 
  protected void readBIB(boolean ignore) throws BadPDBFileException
o readREMARK 
  protected void readREMARK(boolean ignore)
o readSEQRES 
  protected void readSEQRES(boolean ignore)
o readFTNOTE 
  protected void readFTNOTE(boolean ignore)
o readHET 
  protected void readHET(boolean ignore)
o readFORMUL 
  protected void readFORMUL(boolean ignore)
o readHELIX 
  protected void readHELIX(boolean ignore)
o readSHEET 
  protected void readSHEET(boolean ignore)
o readTURN 
  protected void readTURN(boolean ignore)
o readSSBOND 
  protected void readSSBOND(boolean ignore)
o readSITE 
  protected void readSITE(boolean ignore)
o readCRYST1 
  protected void readCRYST1(boolean ignore)
o readORIGXSCALEMTRIX 
  protected void readORIGXSCALEMTRIX(boolean ignore)
o readATOMHETATM 
  protected void readATOMHETATM(boolean ignore) throws BadPDBFileException
o readCONECT 
  protected void readCONECT(boolean ignore)
o process1 
  protected void process1()
additional processing after whole file has been read in 
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