openbabel

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docs: fix man format

1

e-kwsm

FindPythonInterp and FindPythonLibs are deprecated since CMake 3.12; use FindPython instead - https://cmake.org/cmake/help/v3.12/module/FindPython.html - https://cmake.org/cmake/help/v3.12/module/FindPythonInterp.html - https://cmake.org/cmake/help/v3.12/module/FindPythonLibs.html This requires CMake 3.12 or later

e-kwsm

ability to have a consistent 3D orientation from SMILES with `openbabel.pybel.readstring()` and `make3D()`

3

Using the `SMILES` `readstring` converter in `pybel` gives a different orientation of the molecule each time it is run. Is there a way to consistently have the same orientation /...

badw

QA Warning: -Wuninitialized, /src/formats/mdffformat.cpp:135:50 (path)

1

## Environment Information Open Babel version: git version Operating system and version: Linux/Clang-19 ## Actual Behavior /src/formats/mdffformat.cpp:135:50: warning: variable 'path' is uninitialized when used within its own initialization [-Wuninitialized]

PPN-SD

Bug: wrong Z/E configuration on long carbon chains

5

Edit : I want to generate 2D depiction of molecules using SMILES as input, and some long carbon chains containing double bonds are incrorrectly generated. I have thousands of molecules...

Ghriann

## Environment Information Open Babel version: 3.1.0 Operating system and version: Ubuntu (WSL) ## Expected Behavior smiles = '[O:301]=[C:302]([n:303]1[c:304][n:305]cc1)[n:306]2cc[n:307][c:308]2' mol = pybel.readstring("smiles", smiles) smiles1 = mol.write('smiles') print(smiles1) should print O=C(n1cncc1)n1ccnc1...

gregmagdits

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 7.0.5 to 7.0.8. Release notes Sourced from peter-evans/create-pull-request's releases. Create Pull Request v7.0.8 What's Changed build(deps-dev): bump ts-jest from 29.2.5 to 29.2.6 by @​dependabot in peter-evans/create-pull-request#3751 build(deps-dev):...

dependabot[bot]

Unable to run openbabel using the python module

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## Environment Information Open Babel version: Open Babel 3.1.0 and python module openbabel-3.1.1.1 Operating system and version: MacOS Sequoia 15.3.1 (24D70) Python 3.9.6 ## Expected Behavior Successfully run the example...

cgaimoli

-p fails when --gen3d also specified

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## Environment Information Open Babel version: 3.1.0 Operating system and version: WSL Ubuntu 22.04.5 ## Expected Behavior For an input molecule with charged groups, I expect output with protons added...

ken-lind

Error in ComputeCharges

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## Environment Information Open Babel version: 3.1.1 Operating system and version: Windows 11 PRO ## Expected Behavior Using the ComputeCharges function, open babel should calculate the charges of the molecule....

VicenteMartiCentelles