disvis 3.0.0__tar.gz

disvis-3.0.0/CHANGELOG.md

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+# Changelog
+
+## 3.0.0
+
+Changes compared with 2.3.0, the last Python 2 release.
+
+### Requirements and installation
+
+- Python 3.11 or newer and NumPy 2; Python 2 is no longer supported.
+- pyFFTW is now a requirement, installed automatically; it is about twice as
+  fast as the NumPy FFT.
+- Cython 3 is needed to build; the generated `src/libdisvis.c` was removed.
+- The package metadata, dependencies and build requirements are in
+  `pyproject.toml`; `setup.py` only defines the compiled extensions. New `dev`
+  extra (`pip install '.[dev]'`: ruff and cython-lint).
+- src layout: the package is in `src/disvis/` (with the extension sources), the
+  unit tests in `tests/`; run them from the repository root with
+  `python -m unittest`. The sdist includes the tests.
+- GPU FFTs with VkFFT through pyvkfft, instead of clFFT and gpyfft, which had
+  to be built by hand. New `gpu` extra (`pip install '.[gpu]'`: pyopencl,
+  Mako and pyvkfft). The coarse test cases give byte-identical output with
+  VkFFT and clFFT.
+- Docker image based on Python 3.12.
+- The source distribution (sdist) includes the extension sources, so it can
+  be built and installed.
+- Published on PyPI (`pip install disvis`), with wheels for Linux (x86_64,
+  aarch64), macOS (arm64) and Windows (x86_64), Python 3.11 to 3.14, and a
+  WebAssembly wheel for Pyodide (Python 3.14, NumPy FFT instead of pyfftw).
+
+### Fixes and changes
+
+- New `--version` option, and `disvis.__version__`.
+- A zero or negative voxel spacing (`-vs`) is rejected; DisVis used to hang.
+- `-p` works with the spawn start method (macOS and Windows).
+- With `-p`, one progress line for all processes, updated in place.
+- `disvis.log` is overwritten instead of appended to, and is also written
+  with `-g`.
+- `args.json` (the command-line options) is written to the output directory.
+- Clear error message when `-g` is used without the GPU packages.
+- `-g` uses another OpenCL device (e.g. pocl on the CPU) when there is no
+  OpenCL GPU, and writes the device to `disvis.log`.
+- `-np`/`--no-progress` turns off the progress line.
+- GPU: OpenCL kernels are built once, the search no longer waits for the GPU
+  after every step, and fused kernels launch fewer per rotation: together
+  1.3–2.6× faster on the fine grid, with the same output.
+- GPU interaction analysis (`-g -is`): the interaction cutoff was 10 grid
+  units instead of 10 Å, so with a voxel spacing other than 1 Å the counts
+  were wrong (at 2 Å, 6–87× too high, median 13×, for PRE5-PUP2). It now
+  agrees with the CPU.
+- MRC files are closed after reading; `MRCFile` closes a file it opened by
+  name (`close()` or a `with` block), also when its header cannot be read.
+- `volume.erode` writes the erosion into the given `out` volume.
+- `scripts/analyze.py` and `scripts/analyze_interactions.py` were rewritten
+  for the current code and output format.
+- New `scripts/interactions_to_bfactor.py` writes the average number of
+  interactions of each residue into the B-factor column of a PDB file, for
+  coloring the most contacted residues (#12).
+
+### Results
+
+- The CPU output is byte-identical across Python 3.11–3.14, NumPy FFT or
+  pyFFTW, and macOS or Linux; the GPU output agrees with it to about 1e-5.
+
+### Documentation and tests
+
+- Updated `README.md` and `INSTALLATION.md` (GPU set-up on macOS and Linux).
+- `CITATION.cff`, and the Zenodo DOI of all versions (10.5281/zenodo.7775093)
+  in `README.md`.
+- New CPU and GPU reference results for the test cases, and
+  `test-cases/README.md` with benchmarks.
+- Fixed the outdated GPU unit tests; they are skipped without pyopencl,
+  pyvkfft or an OpenCL GPU.
+- Code formatted and linted with ruff (configuration in `pyproject.toml`),
+  with docstrings throughout.
+- GitHub workflow running the linters, the unit tests (Linux, macOS and
+  Windows, Python 3.11–3.14), the coarse test cases against the CPU
+  references (`test-cases/check_test_cases.py`), and the GPU unit tests on the CPU
+  with pocl. Ruff also limits the complexity of functions (C901).
+- Issue and pull-request templates, and `CONTRIBUTING.md` for developers.
+- AI declaration (`aidecl.yaml`, see https://ai-declaration.org/).

disvis-3.0.0/INSTALLATION.md

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+# Installation instructions for GPU-accelerated DisVis
+
+This document shows how to set up GPU-accelerated DisVis using the OpenCL
+framework, with [pyopencl](https://github.com/inducer/pyopencl) and the VkFFT
+library through [pyvkfft](https://github.com/vincefn/pyvkfft) for the Fourier
+transforms. These instructions were tested with Python 3.14 on macOS 15 (Apple
+M2 Pro GPU) and on Rocky Linux 9 (NVIDIA GeForce GTX 1080 Ti and RTX 6000 Ada
+GPUs, NVIDIA driver 555). Note that the speed-up depends on the GPU: a
+power-efficient integrated card may not be much faster than the multi-processor
+CPU version (`-p`).
+
+## Requirements
+
+* An OpenCL 1.2+ enabled GPU and its OpenCL driver (included in macOS; on Linux
+  with NVIDIA GPUs, part of the NVIDIA driver).
+* A C++ compiler (on macOS, the Xcode command line tools), as pyvkfft is built
+  from source.
+* On Linux, the OpenCL headers (`CL/cl.h`) and loader (`libOpenCL.so`), e.g.
+  the `opencl-headers` and `ocl-icd-opencl-dev` (Debian/Ubuntu) or
+  `opencl-headers` and `ocl-icd-devel` (Rocky/RHEL) packages.
+* DisVis installed in a virtual environment, as described in README.md.
+
+On a cluster, the OpenCL headers and libraries may only be installed on the
+GPU nodes: install the GPU requirements there.
+
+## Installation
+
+With the virtual environment activated, install the optional GPU requirements
+of DisVis (the `gpu` extra in `pyproject.toml`)
+
+```bash
+pip install 'disvis[gpu]'
+```
+
+(or `pip install '.[gpu]'` from the DisVis directory, for a source install)
+
+and check that your GPU is found
+
+```bash
+python -c "import pyopencl as cl; print([d.name for p in cl.get_platforms() for d in p.get_devices()])"
+```
+
+## Test
+
+From the DisVis directory, run the GPU tests
+
+```bash
+python -m unittest tests/test_kernels.py tests/test_cpu_vs_gpu.py
+```
+
+and run DisVis with the `-g` option, e.g. on the PRE5-PUP2 test case
+
+```bash
+cd test-cases/PRE5-PUP2-complex
+disvis O14250.pdb Q9UT97.pdb restraints.dat -a 9.72 -vs 2 -g -d gpu-results
+```
+
+The results should agree with the GPU results in `example-results/gpu/coarse`
+and the CPU results in `example-results/cpu/coarse` to within single-precision
+rounding (relative differences of about 1e-5). Timings on several GPUs are
+listed in `test-cases/README.md`.

disvis-3.0.0/LICENSE

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disvis-3.0.0/MANIFEST.in

@@ -0,0 +1,6 @@
+# Sources of the compiled extensions, needed to build from the sdist
+include src/disvis/libdisvis.pyx
+include src/disvis/_extensions.c
+include CHANGELOG.md INSTALLATION.md
+# The unit tests, with their data
+recursive-include tests *.py *.pdb *.dat *.res

disvis-3.0.0/PKG-INFO

@@ -0,0 +1,309 @@
+Metadata-Version: 2.4
+Name: disvis
+Version: 3.0.0
+Summary: Quantifying and visualizing the interaction space of distance-constrained macromolecular complexes
+Author-email: "Gydo C.P. van Zundert" <gvanzundert51@gmail.com>
+Maintainer-email: BonvinLab <bonvinlab.support@uu.nl>
+License-Expression: Apache-2.0
+Project-URL: homepage, https://github.com/haddocking/disvis
+Project-URL: source, https://github.com/haddocking/disvis
+Project-URL: issues, https://github.com/haddocking/disvis/issues
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pyfftw; platform_machine != "wasm32"
+Provides-Extra: gpu
+Requires-Dist: pyopencl; extra == "gpu"
+Requires-Dist: mako; extra == "gpu"
+Requires-Dist: pyvkfft; extra == "gpu"
+Provides-Extra: dev
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: cython-lint; extra == "dev"
+Dynamic: license-file
+
+# DisVis
+
+[![PyPI - Version](https://img.shields.io/pypi/v/disvis)](https://pypi.org/project/disvis/)
+[![DOI](https://zenodo.org/badge/30263463.svg)](https://doi.org/10.5281/zenodo.7775093)
+[![ci](https://github.com/haddocking/disvis/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/disvis/actions/workflows/ci.yml)
+[![SBGrid Badge](https://img.shields.io/badge/DisVis-blue?label=SBGrid&labelColor=%3D)](https://sbgrid.org/software/titles/disvis)
+[![bio.tools](https://img.shields.io/badge/bio.tools-disvis-orange)](https://bio.tools/disvis)
+[![AI Declaration](https://img.shields.io/badge/AI_Declaration-aidecl.yaml-blue)](aidecl.yaml)
+
+## About DisVis
+
+**DisVis** is a Python package and command line tool to visualize and quantify 
+the accessible interaction space of distance restrained binary biomolecular complexes.
+It performs a full and systematic 6 dimensional search of the three translational
+and rotational degrees of freedom to determine the number of complexes consistent
+with the restraints. In addition, it outputs the percentage of restraints being violated
+and a density that represents the center-of-mass position of the scanning chain corresponding 
+to the highest number of consistent restraints at every position in space.
+
+
+## Requirements
+
+* Python 3.11+
+* A C compiler (to build the extension modules)
+
+The Python packages DisVis needs are listed in `pyproject.toml` and installed
+automatically by *pip*. GPU acceleration also needs an OpenCL 1.2+ enabled GPU
+and the optional `gpu` packages (see INSTALLATION.md).
+
+
+## Installation
+
+**DisVis** is best installed in a virtual environment. Open a terminal and type
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+pip install disvis
+```
+
+After installation, the command line tool *disvis* should be at your disposal.
+To install from the source instead, clone the repository and run `pip install .`
+in it.
+
+For GPU acceleration, install the optional GPU requirements with
+
+```bash
+pip install 'disvis[gpu]'
+```
+
+See INSTALLATION.md for the requirements and for checking the GPU set-up.
+
+
+### Linux
+
+Make sure git, the Python header files and a C compiler are available, e.g. on
+Debian/Ubuntu
+
+```bash
+sudo apt-get install git python3-dev python3-venv build-essential
+```
+
+If you are working on a Fedora system, use *dnf* and the *python3-devel* and *gcc* packages.
+Follow the general instructions above to install **DisVis**.
+
+
+### MacOSX
+
+Install the Xcode command line tools, which provide git and a C compiler
+
+```bash
+xcode-select --install
+```
+
+and a recent Python 3, e.g. with [*brew*](https://brew.sh)
+
+```bash
+brew install python
+```
+
+Follow the general instructions above to install **DisVis**.
+
+
+### Windows
+
+Install [*git*](https://git-scm.com/download) for Windows, a Python 3
+distribution, such as [Anaconda](https://www.anaconda.com/download), and the
+[Microsoft C++ Build Tools](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+Follow the general instructions above to install **DisVis**.
+
+
+## Usage
+
+The general pattern to invoke *disvis* is
+
+```bash
+disvis <pdb1> <pdb2> <distance-restraints-file>
+```
+
+where `<pdb1>` is the fixed chain, `<pdb2>` is the scanning chain and 
+`<distance-restraints-file>` is a text-file
+containing the distance restraints in the following format
+
+```text
+<chainid 1> <resid 1> <atomname 1> <chainid 2> <resid 2> <atomname 2> <mindis> <maxdis>
+```
+
+As an example
+    
+```text
+A 18 CA F 27 CB 10.0 20.0
+```
+
+This puts a distance restraint between the CA-atom of residue 18 of 
+chain A of pdb1 and the CB-atom of residue 27 of chain F of pdb2 that 
+should be longer than or equal to 10A and smaller than or equal to 20A.
+Comments can be added by starting the line with the pound sign (#) and empty
+lines are ignored.
+
+
+### Options
+
+To get a help screen with available options and explanation type
+            
+```bash
+disvis --help
+```
+
+Some examples to get you started. To perform a 5.27 degree rotational search and store the results
+in the directory *results/*
+
+```bash
+disvis 1wcm_A.pdb 1wcm_E.pdb restraints.dat -a 5.27 -d results
+```
+
+Note that the directory is created if it doesn't exist.
+
+To perform a 9.72 degree rotational search with 16 processors and a voxel spacing of 2A
+
+```bash
+disvis O14250.pdb Q9UT97.pdb restraints.dat -a 9.72 -p 16 -vs 2
+```
+
+To offload computations to the GPU (if the requirements are met) and increase
+the maximum allowed volume of clashes as well as the minimum required volume of
+interaction, and set the interaction radius to 2A
+
+```bash
+disvis 1wcm_A.pdb 1wcm_E.pdb restraints.dat -g -cv 6000 -iv 7000 -ir 2
+```
+
+To perform a grid occupancy analysis for complexes consistent with at least N
+restraints, include the `-oa` or `--occupancy-analysis` flag to the command. By
+default, the analysis is only performed on complexes consistent with
+either *all* and *all - 1* restraints. If you want to perform an occupancy
+analysis for complexes consistent with a lower number of restraints, use the
+`-ic` or `--interaction-restraints-cutoff` option, followed by the minimum
+number of required consistent restraints. Thus the command
+
+```bash
+disvis 1wcm_A.pdb 1wcm_E.pdb restraints.dat -oa -ic 5
+```
+
+will make an occupancy grid for complexes consistent with at least 5
+restraints, and higher.
+
+Finally, to perform an interaction analysis to determine which residues
+are most likely at the interface, the `-is` or `--interaction-selection`
+options can be used with an additional file giving the residue numbers of the
+receptor and ligand for which the interaction analysis will be performed. The
+input file consists of two lines, where the two lines are a space separated
+sequence of residue numbers for the receptor and ligand, respectively. As the
+interaction analysis is particularly expensive, only complexes consistent with
+*all*, or *all - 1* are considered. To lower the barrier, the `-ic` option can
+again be used. Also limit the selected residues to only the solvent accessible
+ones. A simple example for the selection-file
+
+```text
+1 2 3 4
+101 302 888
+```
+
+This will select residue numbers 1, 2, 3, and 4 for the receptor, and 101, 302,
+and 888 for the ligand.
+
+
+### Output
+
+Standard *disvis* outputs 5 files:
+
+* *accessible_complexes.out*: a text file containing the number of complexes
+  consistent with a number of restraints. 
+* *violations.out*: a text file showing how often a specific restraint is
+  violated for each number of consistent restraints. This helps in identifying
+  which restraint is most likely a false-positive if any.
+* *accessible_interaction_space.mrc*: a density file in MRC format. The density
+  represents the center of mass of the scanning chain conforming to the maximum
+  found consistent restraints at every position in space. The density can be
+  inspected by opening it together with the fixed chain in a molecular viewer
+  (UCSF Chimera is recommended for its easier manipulation of density
+  data, but also PyMol works).
+* *z-score.out*: a text file giving the Z-score for each restraint. The higher
+  the score, the more likely the restraint is a false-positive. Z-scores above
+  1.0 are explicitly mentioned in the output.
+* *disvis.log*: a log file showing all the parameters used, together with date
+  and time indications.
+
+If an occupancy and/or interaction analysis was requested, *disvis* also
+outputs the following files:
+
+* *occupancy_N.mrc*: a volume file giving a normalized indication of how
+  frequent a grid point is occupied by the ligand, where *N* indicates the minimal
+  required number of consistent restraints that resulted in the occupancy grid.
+* *[receptor|ligand]_interactions.txt*: a text file containing the average
+  number of interactions per complex each selected residue made, for both the
+  receptor and ligand molecule. Each column denotes the minimal number of
+  consistent restraints of each complex for which interactions were counted.
+
+To visualize the most contacted residues, write the average number of
+interactions into the B-factor column of the receptor or ligand PDB file
+
+```bash
+python scripts/interactions_to_bfactor.py receptor.pdb receptor_interactions.txt N
+```
+
+where *N* is one of the column numbers of the interaction file. This writes
+*receptor_interactions.pdb*, which can be colored on B-factor, e.g. with
+`spectrum b, blue_red` in PyMOL or `color bfactor` in ChimeraX.
+
+
+Licensing
+---------
+
+If this software was useful to your research please cite us
+
+**Van Zundert, G.C.P. and Bonvin, A.M.J.J.** (2015) DisVis: Visualizing and
+quantifying accessible interaction space of distance restrained biomolecular complexes.
+*Bioinformatics 31*, 3222-3224.
+
+The software itself can be cited with its Zenodo DOI,
+[10.5281/zenodo.7775093](https://doi.org/10.5281/zenodo.7775093), and
+[`CITATION.cff`](https://github.com/haddocking/disvis/blob/main/CITATION.cff)
+gives both references.
+
+Apache License Version 2.0
+
+The elements.py module is licenced under the MIT License, Copyright Christoph
+Gohlke.
+
+
+## Tested platforms
+
+| Operating System| CPU single | CPU multi | GPU |
+| --------------- | ---------- | --------- | --- |
+|Linux            | Yes        | Yes       | Yes |
+|MacOSX           | Yes        | Yes       | Yes |
+|Windows          | Yes        | Yes       | No  |
+
+The GPU version has been tested on:
+NVIDIA GeForce GTX 1080 Ti and RTX 6000 Ada for Linux, and Apple M2 Pro for
+macOS (and, with the earlier Python 2 version, NVIDIA GeForce GTX 680 and AMD
+Radeon HD 7730M for Linux)
+
+Reference results and timings for the test cases, on CPUs and GPUs, are in
+`test-cases/README.md`.
+
+
+## Contributing
+
+See `CONTRIBUTING.md` for the development setup, code style, tests and pull
+requests.
+
+
+## AI Declaration
+
+Large language models (LLM) were used in this repository since
+[v3.0.0](CHANGELOG.md), for the port to Python 3 and the later changes. The
+changes were always reviewed by a human before being merged. See
+[aidecl.yaml](aidecl.yaml) for machine-readable details of the LLM usage.