Hi,
I was writing an application in python which reads and writes some data
stored in gzipped sdf and mol2 files. These files are gzipped, and I can use
them directly with pybel.readfile in linux without problems with OB 2.3.
However, when I try the same on MS Windows with OB 2.3 and python 2.7.1,
when I try to read a sdf file I just get a warning like this:
-------------
>>> mols = pybel.readfile('sdf','test_file.sdf.gz')
>>> mols.next().title()
==============================
*** Open Babel Warning in OpenBabel::MDLFormat::ReadMolecule
WARNING: Problems reading a MDL file
Missing data following atom specification in atom block
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
StopIteration
>>>
--------------------
With other formats (such as mol2) I don't even get a warning; it just
silently fails and returns an empty iterator:
--------------------
>>> mols = pybel.readfile('mol2','test_file.mol2.gz')
>>> mols.next().title()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
StopIteration
>>>
----------------------
Is this behaviour a known bug or limitation or am I doing something wrong?
I've tested it in windows XP, Windows 7 and even on wine, always with latest
packages of OB, python and OB python bindings, and is always reproducible.
Thanks in advance,
Adrià Cereto-Massagué
--
*Adrià Cereto Massagué*
Biotechnology student
Universitat Rovira i Virgili
Languages: Català, Español, English, Français, Deutsch, Português, Esperanto
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