Re: [Open Babel] Unable to match hydronium ions (H3O+) and H5O2+ using SMARTS

I've been working on another system where oxygen frequently exceeds a standard valency of two (organometallics). So far, I've been getting around the automatic bond deletion in an older version of Open Babel by modifying the element.txt file. By changing the MaxBnd column for oxygen to a higher v

Re: [Open Babel] using Open Babel for virtual library generation

Hi Siavoush, To my understanding, in OBChemTsfm::Init (phmodel.cpp, around line 208), there's only options to delete atoms, change the atomic number or charge, or modify bonds. If your combinations have very simple rules, you might be able to use a workaround in Open Babel to get around these lim

Re: [Open Babel] Reading large coordinate files in C++ using Babel

Hi Sébastien, I have run into similar issues and eventually traced it back to the ring perception after using a profiler. Unfortunately, the ring perception can be triggered in unexpected places to avoid internal inconsistencies. (e.g. copying an OBMol in turn calculates OBAtom hybridization if n

Re: [Open Babel] Hello, I have a question for Openbabel GUI

Hello, I am not sure about the Openbabel GUI, but for your application maybe the Avogadro software would be more useful. It is built on top of the Openbabel API, so it still has access to the file formats. It can visualize and let you actually watch the optimization take place: https://avogadro.

Re: [Open Babel] Creating a Symmetric Disulfide Containing SMILES string

John, Is this the SMILES you're trying to generate from the first thiol? S(CCC(=O)NC1CCN(CC1)Cc1c1)SCCC(=O)NC1CCN(CC1)Cc1c1 Assuming so, my favorite shortcut is by using a dot-disconnected SMILES . Attaching the n