Add yaml config for easier installation

.github/workflows/pre-commit.yml

@@ -0,0 +1,16 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - uses: pre-commit/action@v3.0.1

.gitignore

@@ -0,0 +1,4 @@
+.venv/
+__pycache__/
+*.pyc
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: >-
+          (?x)^(
+            force_field_library/.*|
+            molecular_dynamics/.*|
+            parameterisation_scripts/.*\.(mol2|frcmod|pdb|csv)
+          )$
+      - id: end-of-file-fixer
+        exclude: >-
+          (?x)^(
+            force_field_library/.*|
+            molecular_dynamics/.*|
+            parameterisation_scripts/.*\.(mol2|frcmod|pdb|csv)
+          )$
+      - id: check-yaml
+      - id: check-merge-conflict
+      - id: check-added-large-files
+        args: ["--maxkb=5000"]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.4
+    hooks:
+      - id: ruff
+        args: ["--select=E9,F", "--fix"]

README.md

@@ -1,16 +1,21 @@
 # Stapline
 
-## A pipeline for the parameterisation of stapled peptide residues and for the analysis of their secondary structure preferences via molecular dynamics simulations
+A pipeline for the parameterisation of stapled peptide residues and for the
+analysis of their secondary structure preferences via molecular dynamics
+simulations.
 
-### Requirements
+## Requirements
 
-We recommend creating separate conda environments for the residue fragmentation, QM torsion scans and MM energy decomposition. For details on how to create and work with conda environments, refer to: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
+We recommend creating separate conda environments for the residue
+fragmentation, QM torsion scans and MM energy decomposition. For details on
+how to create and work with conda environments, refer to the
+[conda user guide](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html).
 
-**1. Residue Fragmentation**
+### 1. Residue Fragmentation
 
-Refer to https://docs.openforcefield.org/projects/bespokefit/en/stable/getting-started/installation.html for instructions for bespokefit.
+Refer to the [bespokefit installation guide](https://docs.openforcefield.org/projects/bespokefit/en/stable/getting-started/installation.html).
 
-```
+```bash
 conda create -n bespokefit-env
 conda activate bespokefit-env
 conda install mamba
@@ -19,50 +24,54 @@ mamba install -c conda-forge ambertools
 mamba install -c conda-forge nglview
 ```
 
-**2. QM Scans**
-
-Execute the commands below in the specified order:
+Or, equivalently:
 
-```
-conda create -n qm_scans python=3.8
-conda activate qm_scans
+```bash
+conda env create -f conda-environment-bespokefit.yml
 ```
 
-[ambertools](https://ambermd.org/GetAmber.php#ambertools) 18.0 
+### 2. QM Scans
 
-``conda install -c omnia ambertools=18.0``
-
-[rdkit](https://github.com/rdkit/rdkit) 2022.09.5 
-
-``conda install -c conda-forge rdkit=2022.09.5``
-
-``conda install mamba``
+```bash
+conda create -n qm_scans python=3.8
+conda activate qm_scans
 
-[psi4](https://github.com/psi4/psi4) 1.6.1 
+# ambertools 18.0 - https://ambermd.org/GetAmber.php#ambertools
+conda install -c omnia ambertools=18.0
 
-``mamba install -c psi4 psi4=1.6.1``
+# rdkit 2022.09.5 - https://github.com/rdkit/rdkit
+conda install -c conda-forge rdkit=2022.09.5
 
-[psiresp](https://github.com/lilyminium/psiresp) 0.4.2 
+conda install mamba
 
-``mamba install -c conda-forge psiresp=0.4.2``
+# psi4 1.6.1 - https://github.com/psi4/psi4
+mamba install -c psi4 psi4=1.6.1
 
-[papermill](https://github.com/nteract/papermill) 2.5.0
+# psiresp 0.4.2 - https://github.com/lilyminium/psiresp
+mamba install -c conda-forge psiresp=0.4.2
 
-``pip install papermill``
+# papermill 2.5.0 - https://github.com/nteract/papermill
+pip install papermill
 
-[parmed](https://github.com/ParmEd/ParmEd)
+# parmed - https://github.com/ParmEd/ParmEd
+pip install parmed
 
-``pip install parmed``
+# downgrade pydantic last, since the packages above pull in a newer version
+conda install -c conda-forge pydantic=1.10.8
+```
 
-After installing the above packages, pydantic will need to be downgraded to 1.10.8
+Or, equivalently:
 
-``conda install -c conda-forge pydantic=1.10.8``
+```bash
+conda env create -f conda-environment-qm-scans.yml
+```
 
-**3. MM Energy Decomposition**
+### 3. MM Energy Decomposition
 
-Refer to https://sire.openbiosim.org/install.html for instructions for Sire. The version of Sire used in this work is 2023.5.1
+Refer to the [Sire installation guide](https://sire.openbiosim.org/install.html).
+The version of Sire used in this work is 2023.5.1.
 
-```
+```bash
 conda create -n openbiosim "python<3.13"
 conda activate openbiosim
 conda install -n openbiosim -c conda-forge -c openbiosim sire
@@ -71,25 +80,32 @@ conda install rdkit
 conda install scikit-learn
 ```
 
-**4. MD Simulations**
-
-Refer to https://ambermd.org/AmberMD.php for installing the latest version of AMBER.
+Or, equivalently:
 
-### Contents
-
-**Force Field Library**
-
-Contains the force field parameters for the stapled residues in this work, along with peptide PDB templates and tleap scripts to generate MD simulation inputs.
-
-**Parameterisation Scripts**
+```bash
+conda env create -f conda-environment-mm-decomp.yml
+```
 
-Contains code to prepare force field parameters for other stapled residues and/or non-proteinogenic amino acids.
+### 4. MD Simulations
 
-**Molecular Dynamics**
+Refer to [AMBER](https://ambermd.org/AmberMD.php) for installing the latest
+version of AMBER.
 
-Contains the SAH-p53 peptide PDB input files and scripts to prepare, run and analyse MD simulations, as well MD trajectories and output from helicity analyses.
+## Contents
 
+- **Force Field Library** — force field parameters for the stapled residues
+  in this work, along with peptide PDB templates and tleap scripts to
+  generate MD simulation inputs.
+- **Parameterisation Scripts** — code to prepare force field parameters for
+  other stapled residues and/or non-proteinogenic amino acids.
+- **Molecular Dynamics** — SAH-p53 peptide PDB input files and scripts to
+  prepare, run and analyse MD simulations, as well as MD trajectories and
+  output from helicity analyses. Also available on the
+  [`molecular-dynamics-only`](../../tree/molecular-dynamics-only) branch as a
+  standalone snapshot.
 
-### Citation
+## Citation
 
-Notari E, Bluntzer MTJ, Michel J, Hulme AN. Stapline: Development of a Force Field Library for Stapled Peptide Residues. ChemRxiv. 2025; [doi:10.26434/chemrxiv-2025-xfcnm](https://chemrxiv.org/engage/chemrxiv/article-details/68c3511c23be8e43d6760a9c)
+Notari E, Bluntzer MTJ, Michel J, Hulme AN. Stapline: Development of a Force
+Field Library for Stapled Peptide Residues. ChemRxiv. 2025;
+[doi:10.26434/chemrxiv-2025-xfcnm](https://chemrxiv.org/engage/chemrxiv/article-details/68c3511c23be8e43d6760a9c)

conda-environment-bespokefit.yml

@@ -0,0 +1,8 @@
+name: bespokefit-env
+channels:
+  - conda-forge
+dependencies:
+  - mamba
+  - openff-bespokefit
+  - ambertools
+  - nglview

conda-environment-mm-decomp.yml

@@ -0,0 +1,13 @@
+# sire=2023.5.1 is currently only published for linux-64; on macOS the
+# closest available builds are 2023.4.2/2023.5.2 (osx-64) or 2024.1.0+
+# (osx-arm64).
+name: openbiosim
+channels:
+  - conda-forge
+  - openbiosim
+dependencies:
+  - python<3.13
+  - sire=2023.5.1
+  - matplotlib
+  - rdkit
+  - scikit-learn

conda-environment-qm-scans.yml

@@ -0,0 +1,23 @@
+# Tested by solving against linux-64: ambertools=18.0 is linux-64/osx-64
+# only (no osx-arm64 build), and psi4=1.6.1 has since been pruned from the
+# psi4 channel entirely (only 1.9+ remains) - on Apple Silicon, run this
+# under an x86_64 subdir (`CONDA_SUBDIR=osx-64 conda env create -f ...`)
+# and expect to substitute a still-available psi4 version.
+name: qm_scans
+channels:
+  - omnia
+  - psi4
+  - conda-forge
+dependencies:
+  - python=3.8
+  - ambertools=18.0
+  - rdkit=2022.09.5
+  - mamba
+  - psi4=1.6.1
+  - psiresp=0.4.2
+  - pip
+  - pip:
+      - papermill==2.5.0
+      - parmed
+  # installed last: downgrades pydantic pulled in by the packages above
+  - pydantic=1.10.8