Bugs item #3469904, was opened at 2012-01-05 10:03
Message generated for change (Tracker Item Submitted) made by ssorgatem
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Category: Pybel
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: ssorgatem (ssorgatem)
Assigned to: Noel O'Boyle (baoilleach)
Summary: HBA1 descriptor calculation goes crazy, but only sometimes
Initial Comment:
I was doing some tests with a file for a software I'm developing, and when I
did certain unrelated changes, the HBA calculation went crazy.
I haven't been able to reproduce the normal behaviour, only the buggy one.
I'm using OpenBabel 2.3.1 on Debian. This happens using both pybel from
OpenBabel and from cinfony 1.0.
So i've written a little script which shows what happens:
from cinfony import pybel # or just 'import pybel', the result is the same for
me
testfile = 'test/test_ligands.sdf.gz'
print [mol.calcdesc(['HBA1'])['HBA1'] for mol in pybel.readfile('sdf',
testfile)]
print [mol.calcdesc(['HBA2'])['HBA2'] for mol in pybel.readfile('sdf',
testfile)]
When I run it it prints the following:
[35.0, 43.0, 37.0, 46.0, 37.0, 37.0]
[6.0, 6.0, 6.0, 7.0, 6.0, 6.0]
There can be seen that the HBA1 values are extremely high in comparison. The
most annoying part is that I was getting sensible values from HBA1 calculation
in my program, but I'm not able to reproduce them (they were values almost
identical to the ones of HBA2).
Thank you,
Adrià <[email protected]>
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