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Questions tagged [openbabel]

OpenBabel is a popular set of tools and a library used to read, write, analyze and modify chemical and biochemical structures.

OpenBabel is a popular set of tools and a library used to read, write, analyze and modify chemical and biochemical structures. Bindings are available for C++ and Python.

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How do I use python-openbabel in Travis CI?

I use Travis CI as part of a Toxicology mapping project. For this project I require python-openbabel as a dependency. As such, I have added the apt-get installer to the .travis.yml file, shown below ( comments removed ). language: python python: …
Stephan Heijl
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Why is this exception is being generated while running an OpenBabel hello-world program?

I am trying to compile and run the following OpenBabel test program supplied on their web page in 64bit mode. Program.cs using System; using OpenBabel; namespace MyConsoleApplication { class Program { static void Main(string[]…
user366312
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open babel: how to create multiple output files (split the input)?

I have a .pdb file containing multiple conformers of the same molecule. Now I want to convert each of those conformers to a separate .xyz file. According to the open babel help, this could be done with the -m option. -m Produces multiple output…
tmartin
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How to install the latest python module via pip?

I can see openbabel 3.0.0 with pip3 search. But when I install it with pip3 install, I get only 2.4.1. Is there anything wrong? How to get the latest version installed? Thanks. When I try to specify the version, pip does not find it. This is strange…
user1424739
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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 for Python 3.6 on macOS Sierra 10.12.3

I am using Python for making a script to work with some chemical structures in my PhD. I want to install openbabel libraries for python. I tried my best but I could not install it on Windows. I posted a question earlier about installing it on…
Hashmi
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How do I install openbabel for Python 3.6 in Windows 10?

I am using Python for making a script to work with some chemical structures in my PhD. I want to install openbabel libraries for python. I tried my best but I could not install it. It always gives error: Error: SWIG failed. Is Open Babel…
Hashmi
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Python CGI Premature end of script error depending on script parameters

I have a python script which should parse a file and produce some output to disk, as well as returning a webpage linking to the outputted files. When run with a file posted from the HTML form I get no HTML output back, just a 500 error page and the…
Nick
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g++ link to shared library not being compiled

I have these shared library files in /usr/local/lib: libopenbabel.so libopenbabel.so.4 libopenbabel.so.4.0.2 libopenbabel.so is actually a link to libopenbabel.so.4 and libopenbabel.so.4 is actually a link to libopenbabel.so.4.0.2 when I compile my…
kjh
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Registering a function in Django

I have a very simple python script that runs Tanimoto similarity index between a molecule sample and a molecule database: from openbabel import pybel def get_similar(targetmol): results = [] # calculate fingerprints of the sample …
Giuliano
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This page isn’t working 127.0.0.1 didn’t send any data Error in Flask

I am building a Flask webapp and it uses the OpenBabel API (chemistry toolkit) to generate some files for me. When I call this particular function it seems to work fine and generate the files in the directory that I want. However, once it gets back…
user21398
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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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installing openbabel with pip for linux in venv

I am trying to install openbabel with pip on a linux computer without root access and also using a virtual environment. I run the following command pip install openbabel --user --log LOG and then I get the following error: Collecting openbabel …
beliz
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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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install python openbabel package heroku

Trying to install openbabel on heroku. I placed this line in my requirements.txt file: openbabel==2.4.1. I normally install openbabel to my local computer using anaconda. Looks like it has a dependency named SWIG but a search online indicates SWIG…
Spencer Trinh
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