> I found their interfaces especially for simple things (traversing atoms/bonds in a molecule) quite unwieldy.
Somehow the same for me, this is part of why I started my own project (http://chemfiles.org). I have the impression that for cheminformatics you want to see molecules as graphes, is this true or is a list of bonds enough for usual purposes?
I have heard of OEChem but never used it. I'll try to find some documentation to have a look.
What do you think is missing in the current offering (OpenBabel, RDKIT, maybe some other I am missing)?
Context: I do research in computational chemistry, and write an open source library for this, that could be used for cheminformatics too. I don't really know what is needed for this though, since I never touched cheminformatics.
Better distributed computing libraries and semantics (MPI, OpenSHMEM, ...). At the language level, it is not completely clear how RMDA and lifetimes/references should interact.
Better GPGPU support, for CUDA and OpenCL, ideally with direct compilation of Rust code to GPU assembly.
I have a C++ project that is available in multiple languages (Python, Rust, Fortran, Julia and JS), and I decided not to use SWIG partly because of this issue. Instead, I manually maintain a clean C API with everything that I need, and manually wrap this API using whatever is available in other languages. It is a bit more work (and thus incentivize me not to break the API ^^), but allow me to mix and match various ownership semantics throughout the API.
Somehow the same for me, this is part of why I started my own project (http://chemfiles.org). I have the impression that for cheminformatics you want to see molecules as graphes, is this true or is a list of bonds enough for usual purposes?
I have heard of OEChem but never used it. I'll try to find some documentation to have a look.