bugBKChem - Bugs: bug #22005, Batch Script Errors Out

 
 

bug #22005: Batch Script Errors Out

Submitted by:  None
Submitted on:  Sat 12 Jan 2008 07:58:20 AM UTC  
 
Category: NoneSeverity: 3 - Normal
Item Group: NoneStatus: Fixed
Privacy: PublicAssigned to: Beda Kosata <beda>
Open/Closed: Closed

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Mon 14 Jan 2008 06:32:37 AM UTC, comment #1:

Hi,
thanks for reporting it. It is a bug in the Molfile import. I have it fixed in my repository and it will be fixed in the next release.

Beda Kosata <beda>
Project AdministratorIn charge of this item.
Sat 12 Jan 2008 07:58:20 AM UTC, original submission:

I have a batch script to convert mol files to png files. This currently errors out with the latest version of bkchem. I temporarily hacked a fix for my project but I'd like to see a more elegant solution eventually done.

The batch script is attached.

The messages I get from running the batch script:

Running bkchem to draw /tmp/tmpQ4pVp5.mol file ...
Reading /tmp/tmpQ4pVp5.mol ...
Traceback (most recent call last):
File "/usr/lib/python2.5/site-packages/bkchem/bkchem.py", line 138, in <module>
myapp.process_batch( opts)
File "/usr/lib/python2.5/site-packages/bkchem/main.py", line 1487, in process_batch
execfile( plugin, the_globals)
File "/home/tburdick/development/naprabase/naprabase/scripts/mol_to_png.py", line 33, in <mod ule>
mol_to_png( Args[0], Args[1])
File "/home/tburdick/development/naprabase/naprabase/scripts/mol_to_png.py", line 17, in mol_ to_png
if App.plugin_import("Molfile", inf ):
File "/usr/lib/python2.5/site-packages/bkchem/main.py", line 1086, in plugin_import
self.paper.start_new_undo_record()
File "/usr/lib/python2.5/site-packages/bkchem/paper.py", line 1410, in start_new_undo_record
self.before_undo_record()
File "/usr/lib/python2.5/site-packages/bkchem/paper.py", line 1420, in before_undo_record
checks.check_linear_fragments( self)
File "/usr/lib/python2.5/site-packages/bkchem/checks.py", line 34, in check_linear_fragments
last_record = paper.um.get_last_record()
File "/usr/lib/python2.5/site-packages/bkchem/undo.py", line 164, in get_last_record
rec = self._records[ self._pos]
IndexError: list index out of range

Hopefully its an easy fix!

Anonymous

 

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Attached Files
file #14788:  mol_to_png.py added by None (932B - application/x-python)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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  • -unavailable- added by beda (Posted a comment)
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    Follow 4 latest changes.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon 14 Jan 2008 06:32:37 AM UTCbedaStatusNone=>Fixed
      Assigned toNone=>beda
      Open/ClosedOpen=>Closed
    Sat 12 Jan 2008 07:58:20 AM UTCNoneAttached File-=>Added mol_to_png.py, #14788

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