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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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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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drawing of chemical structures -Any plugin in C# for these?

I want to represent the chemical structure drawing in my windows application. I found some softwares are available in the market like "BKChem","Metlab","ChemDraw","SMILE (Simplified molecular input line entry specification)","BioChemDraw". but…
Red Swan
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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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unexpected list appearing in python loop

I am new to python and have the following piece of test code featuring a nested loop and I'm getting some unexpected lists generated: import pybel import math import openbabel search = ["CCC","CCCC"] matches = [] #n = 0 #b = 0 print…
Shughes
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Error in installing openbabel (could not build wheels)

I typed pip install openbabel in the terminal, and it gave me this error: Failed to build openbabel ERROR: Could not build wheels for openbabel, which is required to install pyproject.toml-based projects What could be wrong here? I tried updating…
Veronica Angelin Setiyo
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Open Babel Warning in PerceiveBondOrders

I try to gnina docking tool for protein-ligand docking But I can get output file just included ligand. (there is no protein in pdb) Is there problem at openbabel in gnina? Or at input file format? Command is gnina -r 6vl4/6vl4.pdb -l…
JeongSoo Na
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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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installing openbabel3 with pip

I tried pip install openbabel --log log_file and I got the following error: Collecting openbabel Using cached openbabel-2.4.1.tar.gz (74 kB) Building wheels for collected packages: openbabel Building wheel for openbabel (setup.py) ... error …
beliz
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Why wxWidgets cannot be found during compiling openbabel?

I am trying to install openbabel-2.4.1 in my centos 7 system. The the cmake command (cmake ..) gives information that wxWidgets and Eigen cannot be found: -- Using included inchi library. -- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES)…
Yeping Sun
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Open Babel running .Net C# Process, doesn't work on deployed website

Due to some circumstances, I was ask to develop a page that uses Process in .Net C# to call the function through command prompt. The code works perfectly Fine on visual studio, but when deployed on an IIS server. the Process doesn't seems to work,…
SilvarCraw
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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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Run external program to each element of list

I'm trying to call an external program (Openbabel) to each element (molecule) in a list of molecules (SMILES format). However, I keep getting the same error: /bin/sh: 1: Syntax error: "(" unexpected (expecting ")"). What is wrong with my code? from…
Marcos Santana
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Open Babel can't convert from mol2 to png because Cairo library is not loaded

I first installed Open Babel through brew. When I tried to run the command: "obabel -:"CC(=O)Cl" -opng -O mymol.png", I got this error message: " Open Babel Error in PNG Format PNG2Format not found. Probably the Cairo library is not loaded." I…
Tyson Chen
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Implement babel on c++ but it cannot convert the chemical file

I'm jira. I try to implement babel in c++ in order to convert a file of chemical structures in 'mol' format to that in 'smiles' format. I wrote the code similar to the one provided in documentation of openbabel (…
Jira
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Is there a PhP wrapper of OpenBabel?

We are using this for customer to generate images, but we have to serve the images in round-about way. It will be nice if OpenBabel gives us as Stream that can be redirected automatically.
Adway Lele
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