duello 0.1.6__py3-none-macosx_11_0_arm64.whl → 0.2.1__py3-none-macosx_11_0_arm64.whl

{duello-0.1.6.dist-info → duello-0.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: duello
-Version: 0.1.6
+Version: 0.2.1
 Requires-Dist: pdb2xyz>=0.1.2
 License-File: LICENSE
 Summary: Calculates the osmotic second virial coefficient (B2), and dissociation constant (Kd), for two rigid (macro)molecules, e.g. globular proteins. Done by explicit summation of the partition function in six dimensions (angular space and rigid-body separation). Calvados 3 parameters for use with coarsed grained amino acids are provided, but any pair-wise additivie potential can be used.
@@ -15,6 +15,9 @@ Project-URL: Source Code, https://github.com/mlund/duello
   <img src="assets/duello-logo.png" alt="crates.io", height="300">
 </p>
 <p align="center">
+    <a href="https://doi.org/10/p5d4">
+        <img src="https://img.shields.io/badge/doi-10.26434%2Fchemrxiv--2025--0bfhd-lightgrey" alt="DOI:10.26434/chemrxiv-2025-0bfhd">
+    </a>
     <a href="https://doi.org/10.5281/zenodo.15772003">
         <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.15772003.svg" alt="Zenodo">
     </a>
@@ -95,8 +98,6 @@ you may alternatively build and install directly from the source code:
 cargo install --git https://github.com/mlund/duello
 ```
 
-If you have compilation issues, try updating Rust with `rustup toolchain update`.
-
 # Usage
 
 The command-line tool `duello` does the 6D scanning and calculates
@@ -104,10 +105,9 @@ the angularly averaged potential of mean force, _A(R)_ which
 is used to derive the 2nd virial coefficient and twobody dissociation constant, $K_d$.
 The two input structures should be in `.xyz` format and all particle names must
 be defined in the topology file under `atoms`.
-The topology also defines the particular pair-potential to use.
+The topology also defines the particular pair-potential to use, see below.
 Note that currently, a coulomb potential is automatically added and should
 hence _not_ be specified in the topology.
-The program is written in Rust and attempts to use all available CPU cores.
 
 ```sh
 duello scan \
@@ -118,9 +118,57 @@ duello scan \
     --resolution 0.8 \
     --cutoff 1000 \
     --molarity 0.05 \
-    --temperature 298.15
+    --temperature 298.15 \
+    --backend auto \
+    --grid "type=powerlaw2,size=2000,shift=true"
+```
+
+## Spline Grid Options
+
+The `--grid` option controls interpolation of pair potentials:
+
+| Key     | Values               | Default     | Description                              |
+|---------|----------------------|-------------|------------------------------------------|
+| `type`  | `powerlaw2`, `invr2` | `powerlaw2` | Grid spacing (invr2 avoids sqrt in eval) |
+| `size`  | integer              | `2000`      | Number of grid points                    |
+| `shift` | `true`, `false`      | `true`      | Shift energy to zero at cutoff           |
+
+Example: `--grid "type=invr2,size=1500,shift=false"`
+
+## Backend Performance
+
+The program is written in Rust and attempts to use either GPU or all available CPU cores.
+The following backends are available, with performance measured on the Calvados3 lysozyme example
+(2.4M poses, 128 atoms per molecule, Apple M4):
+
+| Backend     | Description                    | Poses/ms | Speedup |
+|-------------|--------------------------------|----------|---------|
+| `reference` | Exact potentials (validation)  |       48 |    1.0x |
+| `cpu`       | Splined potentials             |      102 |    2.1x |
+| `simd`      | NEON (aarch64) / AVX2 (x86)    |      131 |    2.7x |
+| `gpu`       | wgpu compute shaders           |     1065 |     22x |
+
+The `auto` backend (default) selects GPU if available, otherwise SIMD.
+All but `reference` use Cubic Hermite splines for pair potentials.
+
+## Preparing PDB files
+
+The following uses `pdb2xyz` to create a coarse grained XYZ file and Calvados topology for Duello:
+
+```sh
+pip install pdb2xyz
+pdb2xyz -i 4lzt.pdb -o 4lzt.xyz --pH 7.0 --sidechains
+duello scan \
+  -1 4lzt.xyz -2 4lzt.xyz \
+  --rmin 24 --rmax 80 --dr 0.5 \
+  --resolution 0.6 \
+  --top topology.yaml \
+  --molarity 0.05
 ```
 
+If `pdb2xyz` give errors, you may be able to correct your PDB file with
+[pdbfixer](https://github.com/openmm/pdbfixer?tab=readme-ov-file).
+
 ## Examples
 
 Ready run scripts examples are provided in the `scripts/` directory:
@@ -130,12 +178,6 @@ Command                | Description
 `scripts/cppm.sh`      | Spherical, multipolar particles using the CPPM model
 `scripts/calvados3.sh` | Two coarse grained lysozyme molecules w. Calvados3 interactions
 
-## Converting PDB files
-
-A simple script to convert protein structure files to coarse grained, one bead
-per amino acid XYZ files is provided in `pdb2xyz` which can be installed with
-`pip install pdb2xyz`. This can also generate a corresponding `atomfile.yaml`
-with atom properties.
 
 ## Interaction models
 
@@ -152,7 +194,7 @@ The provided examples illustrate the following schemes:
 - Screened `Coulomb` + `WeeksChandlerAndersen` for the CPPM model.
 
 Many more pair-potentials are available through the
-[`interatomic`](https://crates.io/crates/interatomic) library,
+[`interatomic`](https://docs.rs/interatomic/latest/interatomic/twobody/index.html) library,
 _e.g._ `LennardJones`, `HardSphere` etc.
 
 __Warning:__ The electrostatic term, `Coulomb` is
@@ -165,19 +207,27 @@ binary package on pipy.org.
 
 ## Create `pip` package using Maturin via a Docker image:
 
+Run this on MacOS, linux (x86 and arm) to get all architectures:
+
 ```sh
-docker run --rm -v $(pwd):/io ghcr.io/pyo3/maturin publish -u __token__ -p ...
+docker run --rm -v $(pwd):/io ghcr.io/pyo3/maturin::v1.11.5 publish -u __token__ -p PYPI_TOKEN
 ```
 
+
 For local Maturin installs, follow the steps below.
 
 ```sh
 pip install ziglang pipx
 pipx install maturin # on ubuntu; then restart shell
-maturin publish -u __token__ --target=x86_64-unknown-linux-gnu --zig
+maturin publish -u __token__ -p PYPI_TOKEN --target=x86_64-unknown-linux-gnu --zig
 ```
 
 MacOS targets can be generated without `--zig` using the targets
 `x86_64-apple-darwin` and `aarch64-apple-darwin`.
-See list of targets with `rustup target list`.
+
+```sh
+rustup target list
+rustup target add x86_64-apple-darwin
+```
+
 

duello-0.2.1.dist-info/RECORD

@@ -0,0 +1,5 @@
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+duello-0.2.1.dist-info/WHEEL,sha256=xXrZFUZdUx5dZHQRUyNYMU2_RR2PioJ5KlyzYJq5nRk,101
+duello-0.2.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+duello-0.2.1.dist-info/RECORD,,

duello-0.1.6.dist-info/RECORD

@@ -1,5 +0,0 @@
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-duello-0.1.6.dist-info/METADATA,sha256=7ZWIaH1XA-2zG9fOwADVPilgG1BgXSpD9mVtJNHEDow,6882
-duello-0.1.6.dist-info/WHEEL,sha256=xXrZFUZdUx5dZHQRUyNYMU2_RR2PioJ5KlyzYJq5nRk,101
-duello-0.1.6.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-duello-0.1.6.dist-info/RECORD,,