[Biopython-dev] bug-request

Thu Dec 5 07:07:11 EST 2002

Dear Coleagues!

Trying to apply the PDB-Biopython-module with all PDB structures alvailable 
to me, I recognized that the job will sometimes be killed while processing a 
file, especially when processing large PDB files.
The cause seems to be a lack of memory. Seemingly the problem files are read 
several times (-due to an error within the header reading routine?--> I came 
upon this, because the program is printing the same discontinuations several 
times to the screen.)

Here is an example output for (pdb file) "1htq">
WARNING: Chain A is discontinuous at line 96431.
WARNING: Chain B is discontinuous at line 96432.
WARNING: Chain C is discontinuous at line 96433.
WARNING: Chain D is discontinuous at line 96434.
WARNING: Chain E is discontinuous at line 96435.
WARNING: Chain F is discontinuous at line 96436.
WARNING: Chain G is discontinuous at line 96437.
WARNING: Chain H is discontinuous at line 96438.
WARNING: Chain I is discontinuous at line 96439.
WARNING: Chain J is discontinuous at line 96440.
WARNING: Chain K is discontinuous at line 96441.
WARNING: Chain L is discontinuous at line 96442.
WARNING: Chain M is discontinuous at line 96443.
WARNING: Chain N is discontinuous at line 96444.
WARNING: Chain O is discontinuous at line 96445.
WARNING: Chain P is discontinuous at line 96446.
WARNING: Chain Q is discontinuous at line 96447.
WARNING: Chain R is discontinuous at line 96448.
WARNING: Chain S is discontinuous at line 96449.
WARNING: Chain T is discontinuous at line 96450.
WARNING: Chain U is discontinuous at line 96451.
WARNING: Chain V is discontinuous at line 96452.
WARNING: Chain W is discontinuous at line 96453.
WARNING: Chain X is discontinuous at line 96454.
WARNING: Chain A is discontinuous at line 194329.
WARNING: Chain B is discontinuous at line 194330.
WARNING: Chain C is discontinuous at line 194331.
WARNING: Chain D is discontinuous at line 194332.
WARNING: Chain E is discontinuous at line 194333.
WARNING: Chain F is discontinuous at line 194334.
WARNING: Chain G is discontinuous at line 194335.
WARNING: Chain H is discontinuous at line 194336.
WARNING: Chain I is discontinuous at line 194337.
WARNING: Chain J is discontinuous at line 194338.
WARNING: Chain K is discontinuous at line 194339.
WARNING: Chain L is discontinuous at line 194340.
WARNING: Chain M is discontinuous at line 194341.
WARNING: Chain N is discontinuous at line 194342.
WARNING: Chain O is discontinuous at line 194343.
WARNING: Chain P is discontinuous at line 194344.
WARNING: Chain Q is discontinuous at line 194345.
WARNING: Chain R is discontinuous at line 194346.
WARNING: Chain S is discontinuous at line 194347.
WARNING: Chain T is discontinuous at line 194348.
WARNING: Chain U is discontinuous at line 194349.
WARNING: Chain V is discontinuous at line 194350.
WARNING: Chain W is discontinuous at line 194351.
WARNING: Chain X is discontinuous at line 194352.
WARNING: Chain A is discontinuous at line 292227.
WARNING: Chain B is discontinuous at line 292228.
WARNING: Chain C is discontinuous at line 292229.
WARNING: Chain D is discontinuous at line 292230.
WARNING: Chain E is discontinuous at line 292231.
WARNING: Chain F is discontinuous at line 292232.
WARNING: Chain G is discontinuous at line 292233.
WARNING: Chain H is discontinuous at line 292234.
WARNING: Chain I is discontinuous at line 292235.
WARNING: Chain J is discontinuous at line 292236.
WARNING: Chain K is discontinuous at line 292237.
WARNING: Chain L is discontinuous at line 292238.
WARNING: Chain M is discontinuous at line 292239.
WARNING: Chain N is discontinuous at line 292240.
WARNING: Chain O is discontinuous at line 292241.
WARNING: Chain P is discontinuous at line 292242.
WARNING: Chain Q is discontinuous at line 292243.
WARNING: Chain R is discontinuous at line 292244.
WARNING: Chain S is discontinuous at line 292245.
WARNING: Chain T is discontinuous at line 292246.
WARNING: Chain U is discontinuous at line 292247.
WARNING: Chain V is discontinuous at line 292248.
WARNING: Chain W is discontinuous at line 292249.
WARNING: Chain X is discontinuous at line 292250.
WARNING: Chain A is discontinuous at line 390125.
WARNING: Chain B is discontinuous at line 390126.
WARNING: Chain C is discontinuous at line 390127.
WARNING: Chain D is discontinuous at line 390128.
WARNING: Chain E is discontinuous at line 390129.
WARNING: Chain F is discontinuous at line 390130.
WARNING: Chain G is discontinuous at line 390131.
WARNING: Chain H is discontinuous at line 390132.
WARNING: Chain I is discontinuous at line 390133.
WARNING: Chain J is discontinuous at line 390134.
WARNING: Chain K is discontinuous at line 390135.
WARNING: Chain L is discontinuous at line 390136.
WARNING: Chain M is discontinuous at line 390137.
WARNING: Chain N is discontinuous at line 390138.
WARNING: Chain O is discontinuous at line 390139.
WARNING: Chain P is discontinuous at line 390140.
WARNING: Chain Q is discontinuous at line 390141.
WARNING: Chain R is discontinuous at line 390142.
WARNING: Chain S is discontinuous at line 390143.
WARNING: Chain T is discontinuous at line 390144.
WARNING: Chain U is discontinuous at line 390145.
WARNING: Chain V is discontinuous at line 390146.
WARNING: Chain W is discontinuous at line 390147.
WARNING: Chain X is discontinuous at line 390148.
WARNING: Chain A is discontinuous at line 488023.
WARNING: Chain B is discontinuous at line 488024.
WARNING: Chain C is discontinuous at line 488025.
WARNING: Chain D is discontinuous at line 488026.
WARNING: Chain E is discontinuous at line 488027.
WARNING: Chain F is discontinuous at line 488028.
WARNING: Chain G is discontinuous at line 488029.
WARNING: Chain H is discontinuous at line 488030.
WARNING: Chain I is discontinuous at line 488031.
WARNING: Chain J is discontinuous at line 488032.
WARNING: Chain K is discontinuous at line 488033.
WARNING: Chain L is discontinuous at line 488034.
WARNING: Chain M is discontinuous at line 488035.
WARNING: Chain N is discontinuous at line 488036.
WARNING: Chain O is discontinuous at line 488037.
WARNING: Chain P is discontinuous at line 488038.
WARNING: Chain Q is discontinuous at line 488039.
WARNING: Chain R is discontinuous at line 488040.
WARNING: Chain S is discontinuous at line 488041.
WARNING: Chain T is discontinuous at line 488042.
WARNING: Chain U is discontinuous at line 488043.
WARNING: Chain V is discontinuous at line 488044.
WARNING: Chain W is discontinuous at line 488045.
WARNING: Chain X is discontinuous at line 488046.
WARNING: Chain A is discontinuous at line 585921.
WARNING: Chain B is discontinuous at line 585922.
WARNING: Chain C is discontinuous at line 585923.
WARNING: Chain D is discontinuous at line 585924.
WARNING: Chain E is discontinuous at line 585925.
WARNING: Chain F is discontinuous at line 585926.
WARNING: Chain G is discontinuous at line 585927.
WARNING: Chain H is discontinuous at line 585928.
WARNING: Chain I is discontinuous at line 585929.
WARNING: Chain J is discontinuous at line 585930.
WARNING: Chain K is discontinuous at line 585931.
WARNING: Chain L is discontinuous at line 585932.
WARNING: Chain M is discontinuous at line 585933.
WARNING: Chain N is discontinuous at line 585934.
WARNING: Chain O is discontinuous at line 585935.
WARNING: Chain P is discontinuous at line 585936.
WARNING: Chain Q is discontinuous at line 585937.
WARNING: Chain R is discontinuous at line 585938.
WARNING: Chain S is discontinuous at line 585939.
WARNING: Chain T is discontinuous at line 585940.
WARNING: Chain U is discontinuous at line 585941.
WARNING: Chain V is discontinuous at line 585942.
WARNING: Chain W is discontinuous at line 585943.
WARNING: Chain X is discontinuous at line 585944.
WARNING: Chain A is discontinuous at line 683819.
WARNING: Chain B is discontinuous at line 683820.
WARNING: Chain C is discontinuous at line 683821.
WARNING: Chain D is discontinuous at line 683822.
WARNING: Chain E is discontinuous at line 683823.
WARNING: Chain F is discontinuous at line 683824.
WARNING: Chain G is discontinuous at line 683825.
WARNING: Chain H is discontinuous at line 683826.
WARNING: Chain I is discontinuous at line 683827.
WARNING: Chain J is discontinuous at line 683828.
WARNING: Chain K is discontinuous at line 683829.
WARNING: Chain L is discontinuous at line 683830.
WARNING: Chain M is discontinuous at line 683831.
WARNING: Chain N is discontinuous at line 683832.
WARNING: Chain O is discontinuous at line 683833.
WARNING: Chain P is discontinuous at line 683834.
WARNING: Chain Q is discontinuous at line 683835.
WARNING: Chain R is discontinuous at line 683836.
WARNING: Chain S is discontinuous at line 683837.
WARNING: Chain T is discontinuous at line 683838.
WARNING: Chain U is discontinuous at line 683839.
WARNING: Chain V is discontinuous at line 683840.
WARNING: Chain W is discontinuous at line 683841.
WARNING: Chain X is discontinuous at line 683842.
WARNING: Chain A is discontinuous at line 781717.
WARNING: Chain B is discontinuous at line 781718.
WARNING: Chain C is discontinuous at line 781719.
WARNING: Chain D is discontinuous at line 781720.
WARNING: Chain E is discontinuous at line 781721.
WARNING: Chain F is discontinuous at line 781722.
WARNING: Chain G is discontinuous at line 781723.
WARNING: Chain H is discontinuous at line 781724.
WARNING: Chain I is discontinuous at line 781725.
WARNING: Chain J is discontinuous at line 781726.
WARNING: Chain K is discontinuous at line 781727.
WARNING: Chain L is discontinuous at line 781728.
WARNING: Chain M is discontinuous at line 781729.
WARNING: Chain N is discontinuous at line 781730.
WARNING: Chain O is discontinuous at line 781731.
WARNING: Chain P is discontinuous at line 781732.
WARNING: Chain Q is discontinuous at line 781733.
WARNING: Chain R is discontinuous at line 781734.
WARNING: Chain S is discontinuous at line 781735.
WARNING: Chain T is discontinuous at line 781736.
WARNING: Chain U is discontinuous at line 781737.
WARNING: Chain V is discontinuous at line 781738.
WARNING: Chain W is discontinuous at line 781739.
WARNING: Chain X is discontinuous at line 781740.
WARNING: Chain A is discontinuous at line 879615.
WARNING: Chain B is discontinuous at line 879616.
WARNING: Chain C is discontinuous at line 879617.
WARNING: Chain D is discontinuous at line 879618.
WARNING: Chain E is discontinuous at line 879619.
WARNING: Chain F is discontinuous at line 879620.
WARNING: Chain G is discontinuous at line 879621.
WARNING: Chain H is discontinuous at line 879622.
WARNING: Chain I is discontinuous at line 879623.
WARNING: Chain J is discontinuous at line 879624.
WARNING: Chain K is discontinuous at line 879625.
WARNING: Chain L is discontinuous at line 879626.
WARNING: Chain M is discontinuous at line 879627.
WARNING: Chain N is discontinuous at line 879628.
WARNING: Chain O is discontinuous at line 879629.
WARNING: Chain P is discontinuous at line 879630.
WARNING: Chain Q is discontinuous at line 879631.
WARNING: Chain R is discontinuous at line 879632.
WARNING: Chain S is discontinuous at line 879633.
WARNING: Chain T is discontinuous at line 879634.
WARNING: Chain U is discontinuous at line 879635.
WARNING: Chain V is discontinuous at line 879636.
WARNING: Chain W is discontinuous at line 879637.
WARNING: Chain X is discontinuous at line 879638.
Killed

-----------------------------------------------------------------------------------------

The code for checking out what I experienced should be (I give you a python 
file here) >

#!usr/bin/python2.0

import os, sys, string

sys.path.append('/home/people/clemens/BIOPYTHON/BIO/PDB/')
import PDBParser
from PDBParser import *

def main():
    Testparser = PDBParser()
    self.Struktur = 
Testparser.get_structure('Stru','/usr/local/CAME/PDB/PDBFILES/pdb1htq')
    Testparser.file.close()

if __name__ == "__main__" :
    main()

------------------------------------------------------------------------------------------

Again the core problem: Note that for example  "1htq"  and "1bxr" will not be 
processed correctly, but be killed after some time.

Thank you for your help,

Clemens (@CAME, Salzburg)