Good day all. I understand that I use pybel to manipulate structures
that are larger than what the code is intended to do. So I am testing
the limits of this.
I write because if I execute a 'make3D' function on a molecule that is
too large, pybel (or openbabel) crashes python.
Here is what a good execution looks like when I use 'make3D' on a large
molecule.
Python 2.7 (r27:82525, Jul 4 2010, 09:01:59) [MSC v.1500 32 bit
(Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
>>> smiles='O'+'CCO'*300
>>> mol=pybel.readstring('smi',smiles)
>>> mol.make3D()
>>> ^Z
And here is what a bad execution looks like
Python 2.7 (r27:82525, Jul 4 2010, 09:01:59) [MSC v.1500 32 bit
(Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pybel
>>> smiles='O'+'CCO'*400
>>> mol=pybel.readstring('smi',smiles)
>>> mol.make3D()
This application has requested the Runtime to terminate it in an unusual
way.
Please contact the application's support team for more information.
As you can see, I am running a 32-bit version of python on Windows. It
is a 64-bit version of Windows 7 with 12 GB of memory.
I investigated whether the error is memory-based. It seems that this
error is shown when python asks for about 490 MB of memory. This is
well below the limits of this machine, since I have run scripts on this
same machine that fail when it is ~1.7 GB of memory, something more
meaningful when I run a 32-bit application on Windows 7.
Two questions... Why is this happening? And is there a more graceful
way to fail, so that I can wrap the command with a try loop and execute
the rest of my script if 'make3D' fails?
Thanks for your help.
Steve
Steven G. Arturo
Core R&D - E&PS
The Dow Chemical Company
727 Norristown Road
Spring House, PA 19477
7B/207P 979.238.5749
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