duan_jandClaude Fable 5
4ffc1b152d
Separate module from PanDDA (different library): self-contained python 3.9 venv (torch==1.13.1 caps at py3.10), torch from the pytorch CPU wheel index, ~1 GB of CNN scoring models pre-fetched at build time because the package dir is read-only for users under /opt/psi. ccp4/9.0 runtime dep only, for pandda.inspect / pandda.export. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0152MuuYUaapP7CtxrDAfvBh
29 lines
1.2 KiB
Markdown
29 lines
1.2 KiB
Markdown
# PanDDA2
|
|
|
|
PanDDA 2 (`pandda_2_gemmi`) — multi-dataset density analysis for fragment
|
|
screening. <https://github.com/xchem/PanDDA2>
|
|
|
|
Not on PyPI: installed with uv into a self-contained python 3.9 venv from a
|
|
sha-pinned commit of xchem/PanDDA2 master (no usable release tags upstream;
|
|
module version 1.0.0 follows the README's announced version — bump the sha in
|
|
`build` to update). Torch comes from the pytorch CPU wheel index to avoid the
|
|
~2 GB CUDA build.
|
|
|
|
The ~1 GB of CNN scoring models that PanDDA2 normally gdown-fetches on first
|
|
run are downloaded at build time into the installed package dir, because that
|
|
dir is read-only for users under /opt/psi. If Ra blocks Google Drive, download
|
|
the 5 files by hand (ids in `build`) and copy them into the dir named in the
|
|
die message.
|
|
|
|
ccp4/9.0 is a runtime dependency (auto-loaded) for `pandda.inspect` /
|
|
`pandda.export`. The build needs no ccp4 — the venv is self-contained.
|
|
Upstream README claims inspect/export "do not function correctly" outside
|
|
ccp4/7.0.067; verify with 9.0 before trusting exports.
|
|
|
|
Verify after load:
|
|
|
|
```bash
|
|
pandda2.analyse --help
|
|
$PANDDA2_ENV/bin/python -c 'from pandda_gemmi.cnn import LitEventScoring'
|
|
```
|