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http://resources.openbel.org/belframework/ and http://resource.belframework.org/belframework/ are both down
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Lots of people are going to think it's pybel's fault that the BEL framework site is down. Put a snotty logging message for when it fails.
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Hi,
the conversion to CX format crashes with the following error message.
I am using ByBEL Version: 0.4.2
Regrads,
INFO:pybel:Outputting CX to t.cx
Traceback (most recent call last):
Fil…
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Pybel doesn't seem to support OBReaction, although the other OBBase subclasses are supported. I have installed openbabel and pybel 2.2.3 via fink (see below).
$ /sw/bin/python2.6
Python 2.6.5 (…
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The global error handler obErrorLog is not wrapped by SWIG (e.g., "import openbabel; dir(openbabel)".)
This means that users cannot turn off warnings or errors using OBMessageHandler.
Reported by:…
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This is the monolithic to-do for the data manager portion of the project. This consists of translating the `Django` models used in the AETIONOMY Knowledgebase to use `SQLlchemy`.
For the first try…
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I believe this to be a bug with openbabel/openbabel/scripts/python/pybel.py in line 172 for function readstring
## Expected Behavior
Example:
```
input = "C1=CC=CS1"
mymol = readstring("smi", …
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Compare the atom4refs for the chiral atom in the following two SMILES strings (which encode the exact same molecule):
>>> import pybel
>>> mol = pybel.readstring("smi","C1CN[C@]12CCCN2")
>>> at…
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From Ahmet Bakan on the openbabel-scripting mailing list:
I am using pybel to process several thousand MOL2.gz files and having a problem. When I read the 1022nd file my script does not read any m…
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It seems that separating a methane is fine,
but separating ethane causes a segault.
>>> import pybel
>>> pybel.readstring("smi", "C").OBMol.Separate()
(,)
>>> pybel.readstring("smi", "CC").OBMo…