Merge branch 'main' into rmsd_inertia

.github/workflows/pytest.yaml

@@ -3,11 +3,9 @@ name: Pytest
 on:
   push:
     branches:
-      - "master"
       - "main"
   pull_request:
     branches:
-      - "master"
       - "main"
 
 jobs:
@@ -17,12 +15,12 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.8"]
+        python-version: ["3.8", "3.10"]
     defaults:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Additional info about the build
       run: |
@@ -34,7 +32,7 @@ jobs:
       uses: josStorer/[email protected]
       id: current-time
     - name: Cache conda env
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       env:
         # Increase this value to reset cache if mols.yml has not changed
@@ -49,7 +47,7 @@ jobs:
 
     # More info on the whole conda setup: https://github.com/conda-incubator/setup-miniconda
     - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       id: conda-setup
       with:
         # mamba-version: "*" # uncomment to activate mamba
@@ -77,7 +75,7 @@ jobs:
         pytest --doctest-modules --ignore=molSimplify/Informatics/MOF --ignore=molSimplify/Informatics/protein --ignore=molSimplify/Scripts/in_b3lyp_usetc.py --ignore=molSimplify/Informatics/jupyter_vis.py --ignore=molSimplify/Informatics/macrocycle_synthesis.py --ignore=molSimplify/Informatics/organic_fingerprints.py molSimplify
 
     - name: Upload coverage report to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         directory: ./coverage/reports/
@@ -111,7 +109,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/python-linter.yaml

@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -51,11 +51,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/pycqa/flake8
-    rev: '7.0.0'
+    rev: '7.1.0'
     hooks:
     -   id: flake8
         args: ['--select=E9,F63,F7,F82', '--exclude=fragment_classes.py,frag_functionalizer.py,bridge_functionalizer.py']

molSimplify/Ligands/ligands.dict

@@ -183,7 +183,7 @@ ox:oxalate.mol,oxate,1 4,build bidentate,A,-2
 oxo:oxygen.mol,oxo,0,build small,N,-2
 pcy3:PCy3.mol,pcy3,0,build bulky big,BA,0
 pentacyanopentadienide:pentacyanocyclopentadienide.mol,pcyanopent,1,build bulky,A,-1
-pf3:phosphorustrifluoride.mol,pf3,1,build small,BA,0
+pf3:pf3.mol2,pf3,1,build small,BA,0
 ph2-:ph2-.mol,ph2-,0,build functionalize small,N,-1
 ph3:ph3.mol,ph3,0,build functionalize small,N,0
 phen:phen.mol,phen,9 12,build bidentate,BA,0

molSimplify/Ligands/pf3.mol2

@@ -0,0 +1,19 @@
+@<TRIPOS>MOLECULE
+pf3.mol2
+4	3	1
+SMALL
+PartialCharges
+****
+Generated from molSimplify
+
+@<TRIPOS>ATOM
+1 F1	1.215917934819222  0.0666657847598425  -0.005857293024108329 F	1 RES1 0.0
+2 P1	2.7546239026034516  -0.2682925621616243  -0.034209056581309884 P.3	1 RES1 0.0
+3 F2	3.1090617015157433  0.8313972878801463  -1.1045721415058223 F	1 RES1 0.0
+4 F3	3.1090574085440688  0.635819556544132  1.2057809186362327 F	1 RES1 0.0
+@<TRIPOS>BOND
+1 1 2 1
+1 2 3 1
+1 2 4 1
+@<TRIPOS>SUBSTRUCTURE
+1 RES1 4

molSimplify/Scripts/rmsd.py

@@ -486,7 +486,7 @@ def align_rmsd_project(mol_p, mol_q, rotation: str = "kabsch",
     - projecting the coordinates onto the principal axes
         Note that the projection may lead to reflections, which will break chirality.
     - reordering x, y, z such that Ixx < Iyy < Izz
-    (will allow for 180degree rotations about x, y, z, as well as
+    (will allow for 180 degree rotations about x, y, z, as well as
     reflections about the xy, xz, yz, and all three of those planes)
 
     Parameters
@@ -629,7 +629,6 @@ def align_rmsd_rotate(mol_p, mol_q, rotation: str = "kabsch",
 
     return rmsd
 
-
 def test_case():
     p_atoms = np.array(["N", "H", "H", "H"])
     q_atoms = np.array(["H", "N", "H", "H"])

molSimplify/python_nn/clf_analysis_tool.py

@@ -1,4 +1,4 @@
-# import matplotlib.pyplot as plt
+from typing import Callable
 import numpy as np
 from sklearn.metrics.pairwise import pairwise_distances
 from packaging import version
@@ -105,7 +105,7 @@ def get_layer_outputs(model, layer_index, input,
                                  [model.layers[layer_index].output])
         nn_outputs = get_outputs([input, training_flag])[0]
     else:
-        partial_model = Model(model.inputs, model.layers[layer_index].output)
+        partial_model = Model(model.inputs, model.layers[layer_index].output)  # type: Callable
         nn_outputs = partial_model([input], training=training_flag).numpy()  # runs the model in training mode
     return nn_outputs
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "molSimplify"
-version = "v1.7.4"
+version = "v1.7.5"
 license = {file = "LICENSE"}
 readme = "README.md"
 dependencies = [
@@ -41,10 +41,12 @@ build-backend = "setuptools.build_meta"
 where = ["."]
 
 [tool.setuptools.package-data]
-"molSimplify.Data" = ["*.dat"]
-"molSimplify.Bind" = ["*.dat"]
-"molSimplify.Ligands" = ["*.dict", "*.mol", "*.xyz", "*.smi"]
+"molSimplify.Bind" = ["*.dat", "*.dict"]
+"molSimplify.Cores" = ["*.dict"]
+"molSimplify.Data" = ["*.dat", "*.dict"]
+"molSimplify.Ligands" = ["*.dict", "*.mol", "*.smi", "*.xyz"]
+"molSimplify.Substrates" = ["*.dict", "*.mol", "*.xyz"]
 "molSimplify.icons" = ["*.png"]
-"molSimplify.python_nn" = ["*.csv"]
 "molSimplify.python_krr" = ["*.csv"]
+"molSimplify.python_nn" = ["*.csv"]
 "molSimplify.tf_nn" = ["*/*"]