# pymol-open-source

Open-Source PyMOL, compiled from the GitHub source. Free for everyone,
no license file — unlike the `pymol` module (Schrodinger incentive
bundle).

- Upstream: https://github.com/schrodinger/pymol-open-source
- License: Open-Source PyMOL license (BSD-like)

## How it is built

uv route (careless-style): uv fetches a standalone Python 3.12 into
`$PREFIX/python`, creates `$PREFIX/venv`, then `uv pip install` compiles
the sha-pinned source tarball into it with the gcc/12.3.0 module
(`CC=gcc CXX=g++`; gcc is also a runtime dep for its libstdc++). glm
(header-only) is fetched as a second pinned tarball and staged via
`PREFIX_PATH`. PyQt5 is pip-installed for the GUI.

Build options passed as `uv pip install -C k=v` (upstream
`_custom_build/backend.py` turns them into `build_ext --k=v`):

- `use-msgpackc=no` — no msgpack-c/mmtf-cpp on Ra; disables fast MMTF load
- `no-libxml=true` — disables COLLADA export
- `no-vmd-plugins=false` — disables VMD molfile plugins (needs libnetcdf).
  `false` is correct: upstream stores the value straight into `vmd_plugins`.

Boolean flags take ONLY `true`/`false` — upstream `str2bool` rejects
`yes`/`no` with "Boolean value expected".

Required system RPMs on the build host (if the compile fails, ask
sysadmins for): `glew-devel libpng-devel freetype-devel mesa-libGL-devel`.

`uv` must be on the build host (default `~/.local/bin/uv`, override with
`UV=/path/to/uv`).

## Building on Ra

```sh
module use unstable && module load modbuild/2.1.3
cd pymol-open-source
modbuild build \
    --tmpdir=/das/work/p21/p21515/.cache/Pmodules \
    --distdir=/das/work/p21/p21515/.cache/Pmodules \
    3.1.0
module use MX unstable && module load pymol-open-source/3.1.0
```

## Verifying the install

```sh
which pymol                              # -> .../pymol-open-source/3.1.0/venv/bin/pymol
readlink -f "$PYMOL_ENV/bin/python"      # system /usr/bin/python3.12 (RPM) is fine;
                                         # inside $PREFIX/python if uv had to download one
pymol -cq                                # headless no-op: exits 0 without X
pymol                                    # Qt GUI check, needs X
```

## Adding a new version

Add the version + tarball sha256 in `files/config.yaml`
(`sha256sum` the downloaded `v<ver>.tar.gz`), then build as above.