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@bioconda/all,
We just rolled out some changes to the build system that will reduce workload for the core team, reduce build times on travis-ci, and ensure high-quality recipes. New recipes will n…
daler updated
7 years ago
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First reported on the list by Bjoern Gruening on 27 Jul.
The following code exhibits causes a segfault on Windows (inchi.sdf attached):
==============
from cinfony import pybel
mols = list(pyb…
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If I read the first entry in head.sdf (including in OB distribution), and write it out as SMI, I get a segfault, but only on Windows. I can read a SMI string, and write it out as SMI, no problem. This…
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Openbabel 2.1.1 compiled on Mac OS X 10.5.1/intel
== CONTEXT
pybel implements a ReadFile generator in order to read every molecule from a single file. It relies on OBConversion.Readfile which is…
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Pybel sometimes doens't save properly a mol2 file. It adds a space in the name of the atom => shift of columns in the mol2 parsing (split on spaces).
I am using openbabel 2.2.1 with Pybel
Pymol …
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Write a Jupyter Notebook outlining how the process of Citation Correction worked in AETIONOMY. Provide a few examples of common incorrect citations, and show how your code fixes them. Later, we can in…
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A molecule with 0 atoms was contained in an SDF download from the PDB of all ligands. OpenBabel 2.2.3 segfaulted on Windows when used through the Python interface as follows:
>>> import pybel
>>> …
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The attached file contains a single fullerene molecule in MOL2 format. It looks pretty cool in Avogadro (Stick format). Calling OBMol::Separate causes a segfault on Windows after a minute or two.
>…
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Make a Jupyter Notebook describing where to get named protein complex information from the BEL Framework. Parse this information and use it to post-process a graph. Later, this code can be written as …
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Good day,
I would like to simulate the small positive charge on halides (Chlorine, Bromine and Iodine, but not Fluorine) on ligands for docking (Autodock) and molecular dynamics simulations (Gromac…