Class pmr.chemime.PDB
All Packages Class Hierarchy This Package Previous Next Index
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
-
PDB(String, StringList)
- create a CMLTree from a PDB file
-
PDB(String, StringList, boolean)
- as above, but allow for 'pdb-like' files if strict = false
-
getSEQUENCENodes()
- extract SEQUENCENodes from PDB object
-
main(String[])
- this is only run when an application.
-
process()
- the standard SGMLNode 'process' routine
-
process1()
- additional processing after whole file has been read in
-
readATOMHETATM(boolean)
-
-
readAUTHOR(boolean)
-
-
readBIB(boolean)
-
-
readCOMPND(boolean)
-
-
readCONECT(boolean)
-
-
readCRYST1(boolean)
-
-
readFORMUL(boolean)
-
-
readFTNOTE(boolean)
-
-
readHELIX(boolean)
-
-
readHET(boolean)
-
-
readORIGXSCALEMTRIX(boolean)
-
-
readREMARK(boolean)
-
-
readREVDAT(boolean)
-
-
readSEQRES(boolean)
-
-
readSHEET(boolean)
-
-
readSITE(boolean)
-
-
readSOURCE(boolean)
-
-
readSSBOND(boolean)
-
-
readTURN(boolean)
-
-
showHelp()
- display Help (includes ATOMS and BONDS)
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
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
showHelp
public void showHelp()
- display Help (includes ATOMS and BONDS)
- Overrides:
- showHelp in class ChemTree
process
public void process() throws BadPDBFileException
- the standard SGMLNode 'process' routine
- Throws: BadPDBFileException
- corrupt PDB file
readCOMPND
protected void readCOMPND(boolean ignore)
readSOURCE
protected void readSOURCE(boolean ignore)
readAUTHOR
protected void readAUTHOR(boolean ignore)
readREVDAT
protected void readREVDAT(boolean ignore)
readBIB
protected void readBIB(boolean ignore) throws BadPDBFileException
readREMARK
protected void readREMARK(boolean ignore)
readSEQRES
protected void readSEQRES(boolean ignore)
getSEQUENCENodes
public SEQUENCENode[] getSEQUENCENodes()
- extract SEQUENCENodes from PDB object
readFTNOTE
protected void readFTNOTE(boolean ignore)
readHET
protected void readHET(boolean ignore)
readFORMUL
protected void readFORMUL(boolean ignore)
readHELIX
protected void readHELIX(boolean ignore)
readSHEET
protected void readSHEET(boolean ignore)
readTURN
protected void readTURN(boolean ignore)
readSSBOND
protected void readSSBOND(boolean ignore)
readSITE
protected void readSITE(boolean ignore)
readCRYST1
protected void readCRYST1(boolean ignore)
readORIGXSCALEMTRIX
protected void readORIGXSCALEMTRIX(boolean ignore)
readATOMHETATM
protected void readATOMHETATM(boolean ignore) throws BadPDBFileException
readCONECT
protected void readCONECT(boolean ignore)
process1
protected void process1()
- additional processing after whole file has been read in
main
public static void main(String args[])
- this is only run when an application.
All Packages Class Hierarchy This Package Previous Next Index