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branch: development
Seems to me that graph.__all__ is missing in python2.7. No problem in python 3.5. But that's strange because graph.__all__ exists.
```
In [1]: import pybel
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cebel updated
7 years ago
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Hi,
The conversion to json crashes if a required document metadata field is not available. (eg. ContactInfo)
We have a many BEL files from commercial vendors and some do not have all requiered m…
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Most miRNA can be written with `g(HGNC:YFG) transcribedTo m(HGNC:YFG)` so the inference of the central dogma should also make these edges.
I'm also curious about miRNA's themselves, since there's …
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This was reported on the list by Bjoern Gruening. Here's a test case in Python, using the attached test.mol:
mol = pybel.readfile("mol", "test.mol").next().OBMol
bond = mol.GetBond(1, 28)
mol…
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(See also: http://sourceforge.net/mailarchive/forum.php?thread_name=464DC438.5020604%40dl.ac.uk&forum_name=openbabel-scripting)
)
I've hit what I think is a bug with the readers for NWChem and Gau…
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>>> text = """InChI=1S/C14H23N5O2/c1-11(2)5-4-6-12(3)7-8-18-19-14(21)9-16-13(20)
10-17-15/h5,8,10,12,16H,4,6-7,9H2,1-3H3,(H-,19,20,21)/p+1/b13-10?,18-8-"""
>>> print pybel.readstring("inchi", text).…
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Hi,
I have created a new molfile with DeleteBond() - Separate(). Afterwards i get the following error if i try to read that file.
Openbabel Version is 2.2.1b.
In [2]: mol = pybel.readfile("mol"…
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1. The PDB parser fails to parse some structures correctly, e.g. in 1XAJ chain B is not included in the OBMol object:
import pybel
from openbabel import *
mol = pybel.readfile('pdb', '1xaj.pdb'…
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Hello,
I think you should have a bad answer when you aske for GetAtomicNum in class OBElementTable.
Because of strncascmp (line 331) with only 5 char. comparison made (With 6 the answer is good…
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In the graph manager class, add a convenience function that will ensure a network by URL function that will go and download a network and stick it in the database