Merge master into TINKER

.github/workflows/actions.yml

@@ -6,7 +6,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Apply formatting
         uses: github/super-linter@v4
@@ -29,13 +29,13 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
-          miniforge-version: latest
+          miniforge-version: 4.9.2-4
           use-mamba: true
           environment-file: envs/linux.yml
           use-only-tar-bz2: true
@@ -59,13 +59,13 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
-          miniforge-version: latest
+          miniforge-version: 4.9.2-4
           use-mamba: true
           environment-file: envs/osx.yml
           use-only-tar-bz2: true
@@ -91,13 +91,13 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Mambaforge
-          miniforge-version: latest
+          miniforge-version: 4.9.2-4
           use-mamba: true
           python-version: 3.9
           channels: conda-forge,bioconda

conda-recipe/meta.yaml

@@ -33,7 +33,7 @@ requirements:
     - openmpi
     - pandas >=1.1.4
     - python =3.9
-    - rdkit <=2022.09.1
+    - rdkit >=2023.09.1
     - snakemake >=6.3.0
     - statsmodels >=0.11.1
     - xtb >=6.5.1

envs/linux.yml

@@ -14,7 +14,7 @@ dependencies:
   - openmpi
   - pandas >=1.1.4
   - python =3.9
-  - rdkit <=2022.09.1
+  - rdkit >=2023.09.1
   - snakemake >=6.3.0
   - statsmodels >=0.11.1
   - xtb >=6.5.1

envs/osx.yml

@@ -12,7 +12,7 @@ dependencies:
   - openmpi
   - pandas >=1.1.4
   - python =3.9
-  - rdkit <=2022.09.1
+  - rdkit >=2023.09.1
   - snakemake >=6.3.0
   - statsmodels >=0.11.1
   - xtb >=6.5.1

isicle/adducts.py

@@ -301,7 +301,7 @@ def set_charge(self):
         '''
 
         if self.geom.__dict__.get('charge') is None:
-            self.geom.__dict__.update(charge=self.geom.get_formal_charge())
+            self.geom.__dict__.update(charge=self.geom.get_charge())
 
     def _set_ions(self, ion_path=None, ion_list=None):
         '''
@@ -472,7 +472,7 @@ def _update_geometry_charge(self, geom):
         '''
         '''
 
-        geom.__dict__.update(charge=geom.get_formal_charge())
+        geom.__dict__.update(charge=geom.get_charge())
 
     def _add_ion(self, init_mol, base_atom_idx, ion_atomic_num, sanitize, forcefield, ff_iter):
         '''
@@ -983,9 +983,9 @@ def set_charge(self):
             if self.geom.load.get('filetype') == '.xyz':
                 # self.geom.__dict__.update(charge=charge)
                 raise ValueError(
-                    'Must first run geom.set_formal_charge for an xyz structure')
+                    'Must first run geom.set_charge for an xyz structure')
             else:
-                self.geom.__dict__.update(charge=self.geom.get_formal_charge())
+                self.geom.__dict__.update(charge=self.geom.get_charge())
 
     def _set_ions(self, ion_path=None, ion_list=None):
         cations, anions, complex = _parse_ions(