change .gnina indexing to match pymol

.github/workflows/CI.yml

@@ -1,42 +1,48 @@
 name: CI
 
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
-  build-linux:
-    runs-on: ubuntu-latest
+  tests:
+    name: Test on ${{ matrix.os }}, 🐍=${{ matrix.python-version }}, Program=${{ matrix.conda-env }}
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest" ]
+        python-version: ["3.10", "3.11"]
       max-parallel: 5
 
+    defaults:
+      run:
+        shell: bash -l {0}
+
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
     - name: Create Environment
-      uses: conda-incubator/setup-miniconda@v2.1.1
+      uses: mamba-org/setup-micromamba@v2
       with:
-        activate-environment: fegrow
-        environment-file: env.yml
-        python-version: 3.8
-        auto-update-conda: true
-        auto-activate-base: false
-        show-channel-urls: true
-        mamba-version: "*"
-        miniforge-version: latest
-        miniforge-variant: Mambaforge
-        use-mamba: true
+        environment-file: environment.yml
+        create-args: >-
+          python=${{ matrix.python-version }}
+
     - name: env summary
-      shell: bash -l {0}
       run: conda list
+
+    - name: dry install fegrow
+      run: pip install --dry-run .
+
     - name: install fegrow
-      shell: bash -l {0}
       run: pip install .
+
     - name: install pytest
-      shell: bash -l {0}
-      run: mamba install pytest
+      run: $MAMBA_EXE install pytest
+
     - name: pytest
-      shell: bash -l {0}
       run: pytest fegrow/testing
+
     - name: Run tutorial.py
-      shell: bash -l {0}
       run: |
         cd notebooks
         obabel sarscov2/lig.pdb -O sarscov2/coreh.sdf -p 7

.github/workflows/docs.yml

@@ -0,0 +1,54 @@
+name: Publish Docs to branch
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - '*'
+
+jobs:
+  deploy-docs:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Create FEgrow Environment
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-file: environment.yml
+
+    - name: Install FEgrow
+      run: pip install --no-deps .
+
+    - name: Add docs-generating packages
+      run: $MAMBA_EXE env update --file docs/environment.yml
+
+    - name: Determine Version
+      run: |
+        if [ "$GITHUB_REF" = "refs/heads/master" ]; then
+          echo "VERSION=latest" >> $GITHUB_ENV
+        elif [ "${GITHUB_REF#refs/tags/}" != "$GITHUB_REF" ]; then
+          VERSION=$(echo $GITHUB_REF | sed 's/refs\/tags\///')
+          echo "VERSION=$VERSION stable" >> $GITHUB_ENV
+        else
+          echo "Invalid ref: $GITHUB_REF"
+          exit 1
+        fi
+        echo "Docs version: $VERSION" 
+
+    - name: Build and Deploy Documentation
+      run: |
+        git config --global user.name 'GitHub Actions'
+        git config --global user.email 'actions@github.com'
+        git config --global --add safe.directory "$PWD"
+        git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}
+
+        git fetch --all --prune
+
+        mike deploy --push --update-aliases $VERSION

.github/workflows/nice.yml

@@ -0,0 +1,25 @@
+name: Nice
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        pip install ruff
+    - name: Check formatting with ruff
+      run: ruff format --check
+    - name: Run ruff
+      run: ruff check

.gitignore

@@ -0,0 +1,3 @@
+ignore_git
+.idea
+fegrow.egg-info/

CHANGELOG

@@ -1,7 +1,41 @@
 
 Authors: Mateusz K. Bieniek, Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum, Daniel J. Cole
 
-** [UNPUBLISHED] version 1.*.***
+**version 2.0.1 **
+ - The scaffold's R atom breaks the constrained embedding. The R atom is now omitted. (#74)
+
+**version 2.0.0 **
+ - The new FEgrow with ChemSpace (AL) and Dask support
+
+**version 1.4.0 **
+ - rmol.to_file now writes all conformers into the PDB using the "MODEL / ENDMDL" flavour which can be ready by
+    MDAnalysis.
+ - ANI in some cases explodes. Remove the bad conformers with bonds that have lengths larger than 3A.
+ - The user now has to import the libraries (RGroupGrid) and instantiate first.
+ - Libraries (linkers, rgroups) are now single .sdf files to avoid problems on clusters with many small files
+ - A growing vector can now be any molecule-separating atom in the molecule.
+ - Lipinski now uses the initial definitions of HBD: "sum of Ns and Os" and HBA: "sum of OHs and NHs",
+    (thanks to @RPirie96)
+ - When growing a molecule C multiple time in the same session (e.g. +linker +R), the .template attribute will
+    always be the original C
+ - Lipinski now uses the initial definitions of HBD: "sum of Ns and Os" and HBA: "sum of OHs and NHs",
+    (thanks to @RPirie96)
+ - R-group without coordinates are now using by default Chem.rdDistGeom.EmbedMolecule
+ - Do not cache openff parameters into db.json which right now crashes when multiple threads are used (same filename)
+ - using a tempfile with the anipotential .pt model file for for thread safety
+ - gnina column is renamed from "CNNaffinity->IC50s" to "Kd" with nM unit. We added pint-pandas package for units.
+ - rgroups and linkers are now dataframe (simpler API access)
+
+**version 1.3.0**
+
+ - Compatibility with openff-toolkit >=0.11 (thanks to @jeeberhardt for #29 #30)
+
+
+**version 1.2.1**
+
+ - refined library coordinates (Ben)
+ - visualisations with pandas
+ - error handling
 
 
 **version 1.2.0**

MANIFEST.in

@@ -1,6 +1,8 @@
-include fegrow/data/rgroups/library/*.mol
-include fegrow/data/linkers/library/*.sdf
+include fegrow/data/rgroups/library.sdf
+include fegrow/data/linkers/library.sdf
 include fegrow/data/fpscores.pkl.gz
 include fegrow/version.txt
 include LICENSE.txt
 include fegrow/testing/data/*sdf
+include fegrow/testing/data/cs50k_scored49578_unique47710.csv.zip
+include fegrow/testing/data/5R83_rec.pdb

README.md

@@ -1,7 +1,20 @@
-# FEgrow
-An interactive workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations.
+# FEgrow 2.0.0: Active Learning and acceleration
+
+![CI](https://github.com/cole-group/FEgrow/actions/workflows/CI.yml/badge.svg)![Anaconda-Server Badge](https://anaconda.org/conda-forge/fegrow/badges/downloads.svg)
+
+A new release of FEgrow that adds active learning together with acceleration powered by Dask (multi -cpu, -node, -cluster).
+
+To get started with the new functionality, see the [tutorials](https://github.com/cole-group/FEgrow/tree/master/tutorials) folder, which contains examples of i) basic interactive molecular design, ii) an introduction to the chemspace functionality, and iii) an example of active learning for inhibitor design.
+
+These notebooks are based on the functionality described in:
 
-![CI](https://github.com/cole-group/FEgrow/actions/workflows/CI.yml/badge.svg)
+Cree B, Bieniek M, Amin S, Kawamura A, Cole D. [Active learning driven prioritisation of compounds from on-demand libraries targeting the SARS-CoV-2 main protease.](https://doi.org/10.26434/chemrxiv-2024-xczfb) ChemRxiv (2024).
+
+Scripts used to create Figures 2-6 in the above paper can be accessed [here.](https://github.com/cole-group/FEgrow_AL_data)
+
+
+# FEgrow (1.*)
+An interactive workflow for building user-defined congeneric series of ligands in protein binding pockets for input to free energy calculations.
 
 Bieniek, Mateusz K., Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum, and Daniel J. Cole. "An open-source molecular builder and free energy preparation workflow." Communications Chemistry 5, no. 1 (2022): 136.
 
@@ -11,4 +24,3 @@ Bieniek, Mateusz K., Ben Cree, Rachael Pirie, Joshua T. Horton, Natalie J. Tatum
 
 Please see [cole-group.github.io/fegrow](https://cole-group.github.io/FEgrow) for full installation instructions, documentation and acknowledgements.
 
-To get started see the [online tutorial](https://cole-group.github.io/FEgrow/tutorial/tutorial/) for which the IPython Notebook is available [here](https://github.com/cole-group/FEgrow/tree/master/notebooks).