duello 0.1.4__py3-none-macosx_11_0_arm64.whl → 0.1.6__py3-none-macosx_11_0_arm64.whl

{duello-0.1.4.dist-info → duello-0.1.6.dist-info}/METADATA

@@ -1,6 +1,8 @@
 Metadata-Version: 2.4
 Name: duello
-Version: 0.1.4
+Version: 0.1.6
+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.
 Keywords: pairwise_interaction,bioinformatics,virial_coefficient,dissociation_constant
 Author: Mikael Lund <lyssky@icloud.com>
@@ -13,6 +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/10.5281/zenodo.15772003">
+        <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.15772003.svg" alt="Zenodo">
+    </a>
     <a href="https://colab.research.google.com/github/mlund/duello/blob/master/scripts/colab.ipynb">
         <img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab">
     </a>
@@ -35,7 +40,7 @@ Project-URL: Source Code, https://github.com/mlund/duello
 
 # Introduction
 
-Duello is a tool to calculate the potential of mean force (PMF) between two ridig bodies, performing a
+Duello is a tool to calculate the potential of mean force (PMF) between two rigid bodies, performing a
 statistical mechanical average over inter-molecular orientations using subdivided icosahedrons.
 For each mass center separation, _R_, the static contribution to the partition function,
 $\mathcal{Z}(R) = \sum_{\mathbf{\Omega}} e^{-V(R,\mathbf{\Omega})/k_BT}$, is explicitly
@@ -62,6 +67,7 @@ R^2 dR d\mathbf{\Omega}\\
 & = B_2^{hs} -2\pi \int_{\sigma}^{\infty} \left ( e^{-w(R)/k_BT} -1 \right )R^2 dR\\
 \end{align}
 $$
+
 where $B_2^{hs} = 2\pi\sigma^3/3$ is the hard-sphere contribution and $\sigma$ is a distance
 of closest approach where $w(R\lt \sigma)=\infty$ is assumed.
 For systems with net attractive interactions, the dissociation constant, $K_d$, can be estimated by,
@@ -76,27 +82,20 @@ $$
 
 # Installation
 
-## Using pip (linux x86)
+Binary packages are available for Linux and MacOS through PyPI.org:
 
 ```console
 pip install duello
 ```
 
-## Using Cargo (all platforms)
-
-This requires prior installation of the [Rust](https://www.rust-lang.org/learn/get-started) toolchain.
+If you have a [Rust toolchain](https://www.rust-lang.org/learn/get-started) installed,
+you may alternatively build and install directly from the source code:
 
 ```sh
-cargo install duello
+cargo install --git https://github.com/mlund/duello
 ```
 
-Alternatively you may compile and run directly from the source code:
-
-```sh
-git clone https://github.com/mlund/duello
-cd duello/
-cargo run --release -- <args...>
-```
+If you have compilation issues, try updating Rust with `rustup toolchain update`.
 
 # Usage
 
@@ -112,7 +111,6 @@ The program is written in Rust and attempts to use all available CPU cores.
 
 ```sh
 duello scan \
-    --icotable \
     --mol1 cppm-p18.xyz \
     --mol2 cppm-p18.xyz \
     --rmin 37 --rmax 50 --dr 0.5 \
@@ -132,6 +130,13 @@ 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
 
 Each macromolecule is represented by a rigid constellation of beads with
@@ -155,13 +160,24 @@ always automatically added and should therefore _not_ be specified in the topolo
 
 # Development
 
-This is for development purposes only.
+This is for development purposes only and details how to create and publish a
+binary package on pipy.org.
+
+## Create `pip` package using Maturin via a Docker image:
+
+```sh
+docker run --rm -v $(pwd):/io ghcr.io/pyo3/maturin publish -u __token__ -p ...
+```
 
-## Create `pip` package using Maturin
+For local Maturin installs, follow the steps below.
 
 ```sh
 pip install ziglang pipx
 pipx install maturin # on ubuntu; then restart shell
-maturin publish --target=x86_64-unknown-linux-gnu --zig
+maturin publish -u __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`.
+

duello-0.1.6.dist-info/RECORD

@@ -0,0 +1,5 @@
+duello-0.1.6.data/scripts/duello,sha256=rUkqI9IGuQ0b_Mc0AarG86kHfCLrHo1ZzpIUqnJ1kSo,5690208
+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,,

{duello-0.1.4.dist-info → duello-0.1.6.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: maturin (1.7.6)
+Generator: maturin (1.9.0)
 Root-Is-Purelib: false
 Tag: py3-none-macosx_11_0_arm64

duello-0.1.6.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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duello-0.1.4.dist-info/RECORD

@@ -1,4 +0,0 @@
-duello-0.1.4.dist-info/METADATA,sha256=NFVOsi3zVL3pEf27ktAbKHuLQVfTf_RuImPWhMww0eU,5990
-duello-0.1.4.dist-info/WHEEL,sha256=kZa2AJPQTDmndETGEqExjvAJdFgQXIAry5haCtjamfI,101
-duello-0.1.4.data/scripts/duello,sha256=3ZcsEN5MwdAK0Z20s4N9k8hiBNi7VK2DlIGVklOJe1U,5137304
-duello-0.1.4.dist-info/RECORD,,