[Biopython-dev] [Bug 1897] New: In IsoelectricPoint.py infinite loop observed.

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1897

           Summary: In IsoelectricPoint.py infinite loop observed.
           Product: Biopython
           Version: 1.24
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: clowney.lester at aist.go.jp


Using getIsoElectricPoint some proteins (just one for me)  can put you into an
infinite loop. There is a stopping condition that apparently is to coarse.
Using smaller pH increments increments allows the test to pass and not
oscillate.

This is the fixed fragment I used where delta pH was changed from 0.001to
0.0005.


Frag of IsoelectricPoint.py:

    while abs(Charge) > 0.01:
                if Charge > 0:
                    pH += 0.0005 # was 0.001
                else:
                    pH -= 0.0005  # 0.001
                Charge = self._chargeR(pH, Cterm, Nterm)
                print Charge
            print "returning pH", pH



Regards,
Les




------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.