bugBKChem - Bugs: bug #16432, the "Fetch from Webbook"...


bug #16432: the "Fetch from Webbook" plugin has difficulties with some compounds

Submitter:  david a thompson <thomp>
Submitted:  Mon 24 Apr 2006 08:20:15 PM UTC
Category:  None Severity:  3 - Normal
Item Group:  import Status:  Confirmed
Privacy:  Public Assigned to:  beda
Open/Closed:  Open
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Thu 27 Apr 2006 06:54:14 AM UTC, comment #1: 

The problem is that the molfile contains in fact two independent molecules and the Molfile import cannot handle this properly and loops infinitely. As soon as I have time I will try to fix it.

As for the batch conversion etc. - have a look at http://bkchem.zirael.org/batch_mode_en.html, this could be exactly what you need.

Beda Kosata <beda>
Group administrator
Mon 24 Apr 2006 08:20:15 PM UTC, original submission:  

I just discovered the Fetch from Webbook plugin. Great stuff! However, if I start up bkchem 0.11.4 (on Fedora Core 5) and then use the Fecth from Webbook plugin with the query "Penicillin, o-cyclohexylphenyl-, sodium salt, dihydrate  ", bkchem seems to have a hard time. This doesn't seem to be unique to this query since "Penicillin g procaine  " produces a similar result.

After entering the query, it looks like the molecule is found and then the molfile is downloaded but, after that, bkchem freezes. This seems to be reproducible. (I would have tried to download the MOL file to see it if it's an import issue but I didn't see a way to do that from the web interface to NIST webbook.)

If, after bkchem freezes, I press CTRL-C in the terminal I used to start bkchem, a popup window appears titled "Error in background function". The window contained the text below.

Error: 1
KeyboardInterrupt Exception in Tk callback
  Function: <function <lambda> at 0xb6c366f4> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "/usr/lib/python2.4/site-packages/bkchem/Pmw.py", line 1788, in _call_
    return apply(self.func, args)
  File "/usr/lib/python2.4/site-packages/bkchem/misc.py", line 114, in <lambda>
    return lambda: apply( function, arguments)
  File "/usr/lib/python2.4/site-packages/bkchem/main.py", line 1369, in run_plugin
    self.plug_man.run_plugin( name)
  File "/usr/lib/python2.4/site-packages/bkchem/plugin_support.py", line 90, in run_plugin
    execfile( filename, the_globals)
  File "/usr/share/bkchem/plugins/fetch_from_webbook.py", line 66, in ?
  File "/usr/lib/python2.4/site-packages/bkchem/molecule.py", line 408, in draw
    [a.draw( automatic=automatic) for a in copy.copy( self.bonds)]
  File "/usr/lib/python2.4/site-packages/bkchem/bond.py", line 301, in draw
    sign, center = self._compute_sign_and_center()
  File "/usr/lib/python2.4/site-packages/bkchem/bond.py", line 1316, in _compute_sign_and_center
    for ring in self.molecule.get_smallest_independent_cycles():
  File "/usr/lib/python2.4/site-packages/bkchem/oasa/oasa/graph/graph.py", line 368, in get_smallest_independent_cycles
    return map( self.edge_subgraph_to_vertex_subgraph, self.get_smallest_independent_cycles_e())
  File "/usr/lib/python2.4/site-packages/bkchem/oasa/oasa/graph/graph.py", line 543, in get_smallest_independent_cycles_e
    cs.insert( 0, c)

Best wishes with a great program. It really has become very usable (I think my only remaining "wishlist feature" would be some way to invoke it in the context of processing batches of files (i.e., without the GUI and with some sort of ability to direct bkchem to load/save/export files)). Well, apologies for the digression... Please let me know if you need any additional information...


david a thompson <thomp>


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Follow 3 latest changes.

Date Changed by Updated Field Previous Value => Replaced by
2006-04-27 beda Item GroupNone import
    StatusNone Confirmed
    Assigned toNone beda

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