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I read a mol2 file with pybel.
I want to rename some atoms (name, type) in some special cases.
For this, I test if the type (atom.GetType()) equals a given string. The problem is that pybel assigns …
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The following script reads the attached mol2 file but wrongly outputs 0
for the charge. Openbabel is version 2.3.
import pybel
mol = pybel.readfile('mol2', 'amm.mol2').next()
print mol.charge
…
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This is a new change made by `conda-build` (https://github.com/conda/conda-build/pull/1630). Basically, the source files (SRC_DIR) will be deleted right before testing phase starts for some safety pur…
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head.sdf is included in scripts/python/examples
OBMol.DeleteData causes a segfault for "NSC" in head.sdf, but not for "Comment". Here's the code:
import pybel
pymol = pybel.readfile("sdf", "hea…
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I've set this a high priority because I think it needs to be fixed before the impending release.
With the latest beta 2 snapshot, the Pybel test suite fails due to the following result:
pybel.re…
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Get hooks for more validator plugins. For example, Reagon asked for the statements that don't have a disease state (normal, AD, etc) to get flagged.
This could either be done on compile time, or t…
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importing pybel and matplotlib.backends.backend_qt4agg crashes with error
"AccessInit: hash collision: 3 for both 1 and 1"
On windows XP, I have the latest pythonxy with python 2.7.3 and matplotli…
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Does this work in C++? Setting the torsion in a 3d structure of butane segfaults.
import pybel
import openbabel as ob
mol = pybel.readstring("smi", "CCCC")
mol.make3D()
atoms = [x.OBAtom fo…
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The following Python code shows that the default fingerprinter (FP2?) does not set any bits for methane:
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import openbabel as ob
import pybel
mol = pybel.readstring("sm…
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Given the attached mol2 (which has some dodgy atom types I must admit) which contains 85 molecules, only half of the molecules are returned by an iterator. In fact, every second molecule is skipped.
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