nbehrnd

> I did some comparisons between fingerprints calculated with your code and those calculated with PyFingerprint which uses the cdk library and noticed some differences. If this is your observation,...

@kalinni In an instance of Linux Debian 13/trixie with openbabel 3.1.1., I run the addition of hydrogens by ```shell $ obabel 3lcs.pdb -h -O obabel_with_hydrogens.pdb ============================== *** Open Babel Warning...

In absence of working knowledge of C++, I lack insight how Openbabel's C++ code is organized, interacting, and eventually providing results. Your log shared by 2029-02-29 might indicate "something is...

@kalinni With `-p` I get records labeled either `UNL` or `UNK`: ```shell $ obabel 3lcs.pdb -O 3lcs_prot.pdb -p ============================== *** Open Babel Warning in PerceiveBondOrders Failed to kekulize aromatic bonds...

@kalinni Separate thought: perhaps your workflow does not require the addition of the complete set of hydrogens either; in a separate conversation I learned the (ligand) molecules submitted to /in...

@kalinni The page https://open-babel.readthedocs.io/en/latest/Installation/install.html compiles (...) some hints. I agree it merits to pull a chair to digest the steps required.

@kalinni A postscript: in my pane of «suggested projects», I just encountered a link to [reduce](https://github.com/rlabduke/reduce) by the Richardson group. It might be an interesting checkpoint for your reduction/addition of...

@cassguff Based on the [documentation](https://open-babel.readthedocs.io/en/latest/FileFormats/XYZ_cartesian_coordinates_format.html) flag `-b` is an option (`-xb`) of reading. Your input is a SMILES string and eventually you want to write .xyz coordinates only (i.e., the...

Yeah, https://open-babel.readthedocs.io/en/latest/Installation/install.html

Re executables: with Windows 64bit in hand, you might i) deinstall the current installation of openbabel (for 64bit) to ii) then try the installer for 32bit. No guarantee this then...