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update qfit to make qligand working

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duan_j
2026-09-02 09:26:34 +02:00
parent 11d171f75d
commit 77494991a6
4 changed files with 66 additions and 42 deletions
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qfit/README.md
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@@ -2,34 +2,36 @@
qFit 3 — automated multiconformer model building for X-ray
crystallography and cryo-EM (`qfit_protein`, `qfit_ligand`,
`qfit_covalent_ligand`, `edia`, ...). Repo is named `qfit-3.0`; module
`qfit_covalent_ligand`, ...). Repo is named `qfit-3.0`; module
follows the name/version rule as `qfit/<version>`.
- Upstream: https://github.com/ExcitedStates/qfit-3.0
- License: MIT
## Versions
- **2025.3** (Dec 2025) — current. Post-2024-paper qFit-ligand
(RDKit `-sm SMILES` route, `-em` flag). Python 3.12, solvers
cvxpy + pyscipopt (SCIP) declared in `install_requires` — no
extras, no CPLEX size cap.
- **3.2.2** (Aug 2022) — legacy, pre-paper qfit_ligand algorithm.
Python 3.10 (`numpy<1.22`), cvxopt + CPLEX Community Edition
pip-installed as extras. Last upstream tag with the `v` prefix —
its `urls:` is overridden per-version in `config.yaml`.
## How it is built
uv route (careless-style) from the sha-pinned GitHub tag tarball into
`$PREFIX/venv`, Python **3.10** (upstream pins `numpy<1.22`, which has
no 3.11+ wheels). The small C extension builds with the gcc/12.3.0
module (plain C, no gcc runtime dep). Upstream quirks the recipe
handles:
`$PREFIX/venv`. The small C extension (`_extensions.c`) builds with
the gcc/12.3.0 module (plain C, no gcc runtime dep). Both eras need
`SETUPTOOLS_SCM_PRETEND_VERSION` (`use_scm_version=True` but the
tarball has no `.git`). 3.x-only quirks (solver extras, `setuptools<81`
for the runtime `pkg_resources` import) are branched on `V_PKG` in
`build`; upstream fixed both by 2024.3.
- `use_scm_version=True` but the tarball has no `.git` →
`SETUPTOOLS_SCM_PRETEND_VERSION=<version>` is exported for the build.
- MIQP solvers are only listed in upstream's conda `environment.yml`,
not in `install_requires` → `cvxopt` and `cplex` are pip-installed
explicitly.
- `logtools.py` imports `pkg_resources` at runtime but upstream never
declares setuptools (conda/virtualenv always shipped it, uv venvs
don't) — and setuptools ≥81 removed `pkg_resources` entirely →
`setuptools<81` is pip-installed explicitly.
**CPLEX caveat**: the pip `cplex` wheel is the IBM Community Edition,
limited to 1000 variables/constraints. Large residues/ligands may hit
the cap; the fix is a full academic CPLEX install into the venv
(https://www.ibm.com/academic/) — documented by upstream.
**CPLEX caveat (3.x only)**: the pip `cplex` wheel is the IBM Community
Edition, limited to 1000 variables/constraints. 2024.3+ uses SCIP and
has no such cap.
`uv` must be on the build host (default `~/.local/bin/uv`, override
with `UV=/path/to/uv`).
@@ -42,16 +44,17 @@ cd qfit
modbuild build \
--tmpdir=/das/work/p21/p21515/.cache/Pmodules \
--distdir=/das/work/p21/p21515/.cache/Pmodules \
3.2.2
module use MX unstable && module load qfit/3.2.2
2025.3
module use MX unstable && module load qfit/2025.3
```
## Verifying the install
```sh
which qfit_protein # -> .../qfit/3.2.2/venv/bin/qfit_protein
which qfit_protein # -> .../qfit/2025.3/venv/bin/qfit_protein
qfit_protein --help # argparse usage, no traceback
"$QFIT_ENV/bin/python" -c "import qfit, cplex, cvxopt; print(qfit.__version__)"
qfit_ligand --help # should list -sm/--smiles (2024.3+)
"$QFIT_ENV/bin/python" -c "import qfit, pyscipopt, cvxpy; print(qfit.__version__)"
```
The post-refinement scripts (`qfit_final_refine_xray.sh`) call phenix:
@@ -60,6 +63,6 @@ The post-refinement scripts (`qfit_final_refine_xray.sh`) call phenix:
## Adding a new version
Add version + tarball sha256 in `files/config.yaml` (`sha256sum` the
downloaded `v<ver>.tar.gz`), check whether upstream unpinned
numpy/pandas (a newer pin may allow a newer venv Python), then build as
above.
downloaded `<ver>.tar.gz` — tags have no `v` prefix since 2024), check
whether upstream relaxed the numpy pin further (may allow a newer venv
Python), then build as above.
qfit/build
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@@ -1,18 +1,27 @@
#!/usr/bin/env modbuild
# qFit (multiconformer model building), uv route from the sha-pinned GitHub
# tarball. Three upstream traps handled here:
# - use_scm_version needs git metadata the tarball lacks -> SETUPTOOLS_SCM_PRETEND_VERSION
# - numpy pinned <1.22 -> newest CPython with wheels is 3.10
# - MIQP solvers (cvxopt, cplex) are only in environment.yml, not
# install_requires -> pip them explicitly or qfit dies at runtime
# tarball. Upstream traps differ by era, so both hooks branch on V_PKG:
# - 3.x (2022): numpy<1.22 caps Python at 3.10; MIQP solvers (cvxopt, cplex)
# only in environment.yml -> pip explicitly; logtools imports pkg_resources
# at runtime and uv venvs ship no setuptools -> pin setuptools<81
# (>=81 removed pkg_resources entirely).
# - 2024.3+ : numpy relaxed to <2 -> Python 3.12; solvers switched to
# cvxpy+pyscipopt and moved into install_requires (no CPLEX size cap);
# pkg_resources import removed -> no extras needed at all.
# - both eras: use_scm_version needs git metadata the tarball lacks
# -> SETUPTOOLS_SCM_PRETEND_VERSION
pbuild::configure() {
# modbuild's shell strips ~/.local/bin from PATH; override with UV=/path/to/uv if needed
UV="${UV:-$HOME/.local/bin/uv}"
export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
export UV_PYTHON_INSTALL_DIR="$PREFIX/python"
"$UV" venv --python 3.10 "$PREFIX/venv" || std::die 42 "uv venv failed - is uv at \$UV?"
case "$V_PKG" in
3.*) PY=3.10 ;; # numpy<1.22 has no 3.11+ wheels
*) PY=3.12 ;; # numpy<2 -> 1.26.x wheels up to 3.12
esac
"$UV" venv --python "$PY" "$PREFIX/venv" || std::die 42 "uv venv failed - is uv at \$UV?"
}
pbuild::compile() {
@@ -24,13 +33,14 @@ pbuild::install() {
export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
export CC=gcc
export SETUPTOOLS_SCM_PRETEND_VERSION="${V_PKG}"
# cplex is the IBM Community Edition pip wheel (problem-size limited);
# full CPLEX needs an academic license, see README.
# setuptools<81: qfit's logtools.py imports pkg_resources at RUNTIME; uv venvs
# don't ship setuptools, and setuptools >=81 removed pkg_resources entirely
# (verified: the 84.0.0 wheel has zero pkg_resources files, 80.9.0 has them)
local extras=()
case "$V_PKG" in
# cplex is the IBM Community Edition pip wheel (problem-size limited);
# full CPLEX needs an academic license, see README.
3.*) extras=('setuptools<81' cvxopt cplex) ;;
esac
"$UV" pip install --python "$PREFIX/venv/bin/python" \
'setuptools<81' cvxopt cplex "$SRC_DIR" || \
"${extras[@]}" "$SRC_DIR" || \
std::die 42 "qfit install failed - check build log above"
[[ -x "$PREFIX/venv/bin/qfit_protein" ]] || std::die 42 "qfit_protein missing from venv"
}
qfit/files/config.yaml
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@@ -7,14 +7,25 @@ qfit:
relstage: unstable
urls:
# repo is named qfit-3.0 but the tool/module is qfit (name/version guardrail)
- url: https://github.com/ExcitedStates/qfit-3.0/archive/refs/tags/v${V_PKG}.tar.gz
# upstream dropped the "v" tag prefix from 2024v1 on; 3.x overrides below
- url: https://github.com/ExcitedStates/qfit-3.0/archive/refs/tags/${V_PKG}.tar.gz
name: qfit-${V_PKG}.tar.gz
strip_dirs: 1
shasums:
qfit-3.2.2.tar.gz: b3c37a45598c31aabfb0a0024710b8e22ea6ffd49355ad69a17b93a7777e699d
qfit-2025.3.tar.gz: 40e31b49828eaeb4575e3535f0c4b93c4d82bc3cbd502f8d9f3b7bd4ff99fafa
versions:
3.2.2:
config:
relstage: unstable
# gcc for the small C extension (_extensions.c); plain C, so no runtime dep
build_requires: [gcc/12.3.0]
# last release with the old "v" tag prefix
urls:
- url: https://github.com/ExcitedStates/qfit-3.0/archive/refs/tags/v${V_PKG}.tar.gz
name: qfit-${V_PKG}.tar.gz
strip_dirs: 1
2025.3:
config:
relstage: unstable
build_requires: [gcc/12.3.0]
qfit/modulefile
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@@ -6,9 +6,9 @@ module-license "MIT"
module-maintainer "MX Data <jiaxin.duan@psi.ch>"
module-help "
qFit 3: qfit_protein, qfit_ligand, qfit_covalent_ligand, edia and
friends, in a private Python venv with cvxopt + IBM CPLEX Community
Edition as MIQP solvers. The post-refinement scripts
qFit 3: qfit_protein, qfit_ligand, qfit_covalent_ligand and friends,
in a private Python venv. MIQP solvers: cvxopt + IBM CPLEX Community
Edition (3.x) or cvxpy + SCIP (2024.3+). The post-refinement scripts
(qfit_final_refine_xray.sh) expect phenix on PATH - load a phenix
module for those.
"