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Questions tagged [pybel]

Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python. Source: Python Pybel page on openbabel.

What is Pybel?

Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python, especially for file input/output and for accessing the attributes of atoms and molecules. The Atom and Molecule classes used by Pybel can be converted to and from the OBAtom and OBMol used by the openbabel module. These features are discussed in more detail below.

The rationale and technical details behind Pybel are described in O’Boyle et al [omh2008]. To support further development of Pybel, please cite this paper if you use Pybel to obtain results for publication.

More informations

Information on the Pybel API can be found at the interactive Python prompt using the help() function. The full API is also listed in the next section (see Pybel API).

Source: Python Pybel home page on openbabel.org

http://openbabel.org/docs/2.3.1/UseTheLibrary/Python_Pybel.html

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How to install pybel in conda enviorment?

I tried to install pybel in conda, but it doesn't really work, even though the installation looks ok, all the module's API function aren't present. me$ conda create --name py34 python=3.4 Fetching package metadata ................. Solving package…
0x90
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Saving and Organizing Multiple .svg Files to Multi-Paged PDF, PNG, or Other Common Image File Types in Python

Goal: I want to be able to organize many SVG images of Lewis/Kekulé structures into a coherent list of reactions displayed in some common viewing file, like PDF or PNG; that is, each reaction might take up one line with the reactants and products…
Mihoi
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Redirect logs to file in Pybel?

Similar to this post, but rather than change the logging level, I would like to redirect all logging information to a file. I believe the relevant API call…
Sean Colby
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How to install openbabel

I installed OpenBabel for Mac using: brew install open-babel I tried to work with pyenv version 3.9.0 and got the following error : ImportError:…
user14499583
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importing openbabel wrapper pybel for macos without conda

Previously I asked how to install openbabel for macos here. Now I also need to install the openbabel python wrapper pybel. I tried pip install pybel and it was installed. Then, while I was following the tutorial, import openbabel import pybel mymol…
beliz
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Can I capture warning messages during format conversion in pybel?

I have a list of molecules in SMILES format that I am converting to InChIKey format. However, a number of them are generating warnings. I would like to be able to generate a file showing the warnings generated in the process of converting each…
Aniket Schneider
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How to disable logged warnings in Pybel?

I am using Pybel - a Python wrapper around the OpenBabel API, and I am trying to disable warnings such as these: ============================== *** Open Babel Warning in ParseComplex Illegal aromatic element b- My warnings were raised…
The Aelfinn
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TypeError: '>=' not supported between instances of 'tuple' and 'float'

I am trying to write a little python script that calculates the Tanimoto similarity index between a molecule of interest and a database of molecules. I am using pybel. The database, in the .smi format, have chemical information of molecules on the…
Giuliano
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"IndexError: list index out of range" on "import pybel"

I'm working on a web app django, when I install openbabel and try to import pybel i've got an error I'm using a venv that was activate when I did all this commands I install openbabel like this: sudo apt-get install python-openbabel I also tried…
Zineb Lazrak
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Fingerprinting using python module called pybel

I want to get fingerprints using smiles of compounds. I did but the problem is I want to get in a higher bit and a list format so I can calculate the length of lists. In this case I just get classes. Any solution in python using pybel? I did this…
Gozde Kibar
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to get properties of a residue from pdb file

I have a pdb file and I want to parse the pdb using python and I want to find the following for residues in pdb: 1. hydrophobicity 2. interface topology 3. solvent accessible surface area I have tried using pybel file_name = "4hhb.pdb" allmols =…
sam
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error in creating executable for python script

I have created a application using python2.7 also used pyqt for gui. I have also used pybel module for computations. my application python file works properly. but when I try to create executable from that python file it gives me error. I have…
sam
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