Lester Hedges

On my local machine, it's specifically the required RDKit pin that's causing the issue. Using the following diff works: ``` diff --git a/requirements_host.txt b/requirements_host.txt index ef32ada64..a06788fc6 100644 --- a/requirements_host.txt +++...

The environment is resolvable if you create it in one go, e.g: ``` conda create -n openbiosim -c conda-forge python=3.12 "cmake>=3.30.0" git libtool make sysroot_linux-64==2.17 gsl "kartograf>=1.0.0" lazy_import libboost-devel libboost-python-devel...

My thought is that we replace the build with a `create_environment` script that sets up the initial environment with everything installed and resolved in one go. Then the user activates...

In the absence of stereochemistry, the converter uses an inference routine based on one from MDAnalysis. This works well in many cases, but clearly isn't ideal for everything. I'll take...

I also think the fallback relies on appropriate 3D coordinates, so might not work as intended for structures that aren't well minimised.

Thanks for the update. I've tried using some of the RDKit stereochemistry inference routines, but those fail to assign the correct formal charges too. I'll take a look at some...

Looks like `gemmi` is causing CI failures on all platforms: ``` [ 97%] Building CXX object Convert/SireGemmi/CMakeFiles/SireGemmi.dir/_SireGemmi.main.cpp.o cd $SRC_DIR/build/conda_build_wrapper/Convert/SireGemmi && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++ -DBOOST_NO_CXX98_FUNCTION_BASE -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DGEMMI_SHARED -DQT_CORE_LIB -DQT_NO_DEBUG -DSireGemmi_EXPORTS -I$PREFIX/pkgs/sire-2025.1.0/include/Sire -I$SRC_DIR/build/conda_build_wrapper...

Presumably there are some breaking changes with version 0.7, although that did appear to come out over 3 months ago :man_shrugging:

I've added a fix to handle negative residue numbers in the parser [here](https://github.com/OpenBioSim/sire/commit/3e8f4b779c96834dbf19bb8ee8487cfc5847b6ad). This appears to work and I see the correct numbers on load, e.g.: ```python In [1]: import...

It is possible to construct a new `ResNum` using an existing one with value -1, e.g. `res_num = ResNum(negative_res_num)`, but explicitly passing a negative integer doesn't work: ```python C++ signature:...