Class pmr.chemime.PDB
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Class pmr.chemime.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.CMLTree
                                                                   |
                                                                   +----pmr.chemime.ChemTree
                                                                           |
                                                                           +----pmr.chemime.PDB

public class PDB
extends ChemTree

Constructor Index

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

Method Index

 o getSEQUENCENodes()
extract SEQUENCENodes from PDB object
 o main(String[])
this is only run when an application.
 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)
 o showHelp()
display Help (includes ATOMS and BONDS)

Constructors

 o PDB
  public PDB(String filename,
             StringList lines) throws BadPDBFileException
create a CMLTree from a PDB file
Parameters:
filename - name of file to read from (or title if lines != null)
lines - if lines != null, use this as file content instead of filename
Throws: BadPDBFileException
missing or corrupt PDB file
 o PDB
  public PDB(String filename,
             StringList lines,
             boolean strict) throws BadPDBFileException
as above, but allow for 'pdb-like' files if strict = false
Throws: BadPDBFileException
missing or corrupt PDB file

Methods

 o showHelp
  public void showHelp()
display Help (includes ATOMS and BONDS)
Overrides:
showHelp in class ChemTree
 o process
  public void process() throws BadPDBFileException
the standard SGMLNode 'process' routine
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 getSEQUENCENodes
  public SEQUENCENode[] getSEQUENCENodes()
extract SEQUENCENodes from PDB object
 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
 o main
  public static void main(String args[])
this is only run when an application.

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