Merge pull request #193 from andrewtarzia/clean_deps

Clean dependencies to save install time.

.github/workflows/tests.yml

@@ -55,7 +55,7 @@ jobs:
       - name: Build environment
         run: |
           conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
+          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
           python -m pip install -e '.[dev]'
@@ -79,7 +79,7 @@ jobs:
       - name: Build environment
         run: |
           conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
+          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
           conda install -c conda-forge mdanalysis openbabel
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools
@@ -104,7 +104,7 @@ jobs:
       - name: Build environment
         run: |
           conda activate pytest
-          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
+          conda install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
           conda install -c conda-forge mdanalysis openbabel
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools

README.rst

@@ -35,7 +35,7 @@ Some optional dependencies are only available through conda:
   # for OpenMM and espaloma charge
   # note the temporary issue with rdkit versions and conda will overwrite pip
   # installed software
-  mamba install openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
+  mamba install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4 espaloma_charge
   # for xtb
   mamba install xtb
   # for openbabel

docs/source/index.rst

@@ -41,7 +41,7 @@ Some optional dependencies are only available through conda:
   # for OpenMM and espaloma charge
   # note the temporary issue with rdkit versions and conda will overwrite pip
   # installed software
-  mamba install openff-toolkit openmm openmmtools dgl rdkit==2024.3.4
+  mamba install -c conda-forge openff-toolkit openmm openmmtools dgl rdkit==2024.3.4  espaloma_charge
   # for xtb
   mamba install xtb
   # for openbabel

examples/cage_openmm_example.py

@@ -44,7 +44,6 @@ def main() -> None:
 
     # Settings.
     force_field = ForceField("openff_unconstrained-2.1.0.offxml")
-    partial_charges = "espaloma-am1bcc"
     temperature = 700 * openmm.unit.kelvin
     friction = 10 / openmm.unit.picoseconds
     time_step = 1 * openmm.unit.femtoseconds
@@ -55,15 +54,15 @@ def main() -> None:
         stko.OpenMMForceField(
             force_field=force_field,
             restricted=True,
-            partial_charges_method=str(partial_charges),
+            partial_charges_method="espaloma-am1bcc",
         ),
         # Unrestricted optimisation.
         stko.OpenMMForceField(
             # Load the openff-2.1.0 force field appropriate for
             # vacuum calculations (without constraints)
             force_field=force_field,
             restricted=False,
-            partial_charges_method=partial_charges,
+            partial_charges_method="espaloma-am1bcc",
         ),
         # Molecular dynamics, short for equilibration.
         stko.OpenMMMD(
@@ -75,7 +74,7 @@ def main() -> None:
                 time_step=time_step,
             ),
             random_seed=275,
-            partial_charges_method=partial_charges,
+            partial_charges_method="espaloma-am1bcc",
             # Frequency here is not related to the num confs tested.
             reporting_freq=100,
             trajectory_freq=100,
@@ -86,7 +85,7 @@ def main() -> None:
             conformer_optimiser=stko.OpenMMForceField(
                 force_field=force_field,
                 restricted=False,
-                partial_charges_method=partial_charges,
+                partial_charges_method="espaloma-am1bcc",
             ),
         ),
         # Long MD, for collecting lowest energy conformers.
@@ -99,7 +98,7 @@ def main() -> None:
                 time_step=time_step,
             ),
             random_seed=275,
-            partial_charges_method=partial_charges,
+            partial_charges_method="espaloma-am1bcc",
             # Frequency here is not related to the num confs tested.
             reporting_freq=100,
             trajectory_freq=100,
@@ -111,7 +110,7 @@ def main() -> None:
             conformer_optimiser=stko.OpenMMForceField(
                 force_field=force_field,
                 restricted=False,
-                partial_charges_method=partial_charges,
+                partial_charges_method="espaloma-am1bcc",
             ),
         ),
     )

justfile

@@ -11,6 +11,11 @@ docs:
 # Install development environment.
 dev:
   pip install -e '.[dev]'
+  mamba install -y -c conda-forge openff-toolkit openmm openmmtools rdkit==2024.3.4 dgl espaloma_charge
+  mamba install -y xtb
+  mamba install -y openbabel
+  mamba install -y mdanalysis
+
 
 # Run code checks.
 check:

pyproject.toml

@@ -11,11 +11,11 @@ maintainers = [
 dependencies = [
   # Remove pin once openmm infrastructure is safely moved to >= 2.
   "numpy < 2",
-  "rdkit != 2024.3.5",
+  # Pinned while rdkit changes stk results.
+  "rdkit == 2024.3.4",
   "stk",
   "networkx",
   "rmsd",
-  "espaloma-charge",
 ]
 requires-python = ">=3.11"
 dynamic = ["version"]
@@ -59,8 +59,6 @@ line-length = 79
 [tool.ruff.lint]
 select = ["ALL"]
 ignore = [
-  "ANN101",
-  "ANN102",
   "ANN401",
   "COM812",
   "ISC001",
@@ -137,5 +135,6 @@ module = [
   "openmmforcefields.*",
   "rmsd.*",
   "espaloma_charge.*",
+  "traitlets.*",
 ]
 ignore_missing_imports = true

src/stko/__init__.py

@@ -126,99 +126,99 @@
 """Type parameter matching :class:`stk.ConstructedMolecule` or subclasses."""
 
 __all__ = [
-    "functional_groups",
-    "molecule_analysis",
-    "OrcaExtractor",
-    "OpenBabelEnergy",
-    "OrcaEnergy",
-    "PlanarityCalculator",
-    "MMFFEnergy",
-    "UFFEnergy",
-    "EnergyResults",
-    "ConstructedMoleculeTorsionResults",
-    "TorsionResults",
-    "XTBResults",
-    "RmsdCalculator",
-    "RmsdMappedCalculator",
-    "KabschRmsdCalculator",
-    "ShapeCalculator",
-    "OrcaResults",
-    "PlanarityResults",
-    "RmsdResults",
-    "ShapeResults",
-    "ConstructedMoleculeTorsionCalculator",
-    "MatchedTorsionCalculator",
-    "TorsionCalculator",
-    "XTBExtractor",
-    "XTBEnergy",
-    "Du",
-    "PositionedAtom",
-    "MDAnalysis",
-    "ZMatrix",
-    "MoleculeSplitter",
-    "MoleculeTransformer",
-    "Network",
-    "UnitCell",
-    "cap_absolute_value",
-    "get_approximate_cell_size",
-    "get_from_parameters",
-    "TopologyExtractor",
-    "TopologyInfo",
-    "Torsion",
-    "TorsionInfo",
-    "Aligner",
-    "AlignmentPotential",
-    "Collapser",
-    "CollapserMC",
-    "GulpUFFMDOptimizer",
-    "GulpUFFOptimizer",
-    "MacroModelForceField",
-    "MacroModelMD",
-    "Optimizer",
-    "OptimizerSequence",
-    "OptWriterSequence",
-    "TryCatchOptimizer",
-    "NullOptimizer",
     "ETKDG",
     "MMFF",
     "UFF",
-    "MetalOptimizer",
-    "MAEExtractor",
-    "get_metal_atoms",
-    "move_generated_macromodel_files",
-    "mol_from_mae_file",
     "XTB",
-    "XTBFF",
     "XTBCREST",
+    "XTBFF",
     "XTBFFCREST",
+    "Aligner",
+    "AlignmentPotential",
+    "CalculatorError",
+    "Collapser",
+    "CollapserMC",
     "ConstructedMoleculeT",
-    "MoleculeT",
-    "OpenBabel",
-    "OpenMMForceField",
-    "OpenMMMD",
-    "OpenMMEnergy",
-    "WrapperNotInstalledError",
-    "DifferentMoleculeError",
-    "DifferentAtomError",
-    "InputError",
-    "PathError",
+    "ConstructedMoleculeTorsionCalculator",
+    "ConstructedMoleculeTorsionResults",
     "ConvergenceError",
-    "CalculatorError",
     "ConversionError",
+    "DifferentAtomError",
+    "DifferentMoleculeError",
+    "Du",
+    "EnergyResults",
     "ExpectedMetalError",
     "ForceFieldError",
     "ForceFieldSetupError",
+    "GulpUFFMDOptimizer",
+    "GulpUFFOptimizer",
+    "InputError",
+    "InvalidSolventError",
+    "KabschRmsdCalculator",
     "LewisStructureError",
+    "MAEExtractor",
+    "MDAnalysis",
+    "MMFFEnergy",
+    "MacroModelForceField",
+    "MacroModelMD",
+    "MatchedTorsionCalculator",
+    "MetalOptimizer",
+    "MoleculeSplitter",
+    "MoleculeT",
+    "MoleculeTransformer",
+    "Network",
     "NotCompletedError",
     "NotStartedError",
-    "SettingConflictError",
-    "InvalidSolventError",
+    "NullOptimizer",
+    "OpenBabel",
+    "OpenBabelEnergy",
+    "OpenMMEnergy",
+    "OpenMMForceField",
+    "OpenMMMD",
+    "OptWriterSequence",
+    "Optimizer",
     "OptimizerError",
-    "get_torsion_info_angles",
+    "OptimizerSequence",
+    "OrcaEnergy",
+    "OrcaExtractor",
+    "OrcaResults",
+    "PathError",
+    "PlanarityCalculator",
+    "PlanarityResults",
+    "PositionedAtom",
+    "RmsdCalculator",
+    "RmsdMappedCalculator",
+    "RmsdResults",
+    "SettingConflictError",
+    "ShapeCalculator",
+    "ShapeResults",
+    "TopologyExtractor",
+    "TopologyInfo",
+    "Torsion",
+    "TorsionCalculator",
+    "TorsionInfo",
+    "TorsionResults",
+    "TryCatchOptimizer",
+    "UFFEnergy",
+    "UnitCell",
+    "WrapperNotInstalledError",
+    "XTBEnergy",
+    "XTBExtractor",
+    "XTBResults",
+    "ZMatrix",
     "calculate_angle",
     "calculate_dihedral",
-    "vector_angle",
-    "unit_vector",
-    "is_valid_xtb_solvent",
+    "cap_absolute_value",
+    "functional_groups",
+    "get_approximate_cell_size",
     "get_atom_distance",
+    "get_from_parameters",
+    "get_metal_atoms",
+    "get_torsion_info_angles",
+    "is_valid_xtb_solvent",
+    "mol_from_mae_file",
+    "molecule_analysis",
+    "move_generated_macromodel_files",
+    "unit_vector",
+    "vector_angle",
 ]

src/stko/_internal/molecular/periodic/unitcell.py

@@ -200,10 +200,10 @@ def with_cell_from_cif(self, filename: Path | str) -> Self:
         with filename.open() as f:
             lines = f.readlines()
 
-        for targ in targets:
+        for targ, target_string in targets.items():
             for line in lines:
                 # Avoid running through the rest.
-                if targets[targ] in cell_info:
+                if target_string in cell_info:
                     break
                 splits = line.rstrip().split(" ")
                 if splits[0] == targ:

src/stko/_internal/molecular/subgroup_analysis/subgroup_analyser.py

@@ -222,8 +222,7 @@ def calculate(self, molecule: stk.Molecule) -> dict[str, list[float]]:
         }
 
         fg_results = {}
-        for pot_fg in fg_definitions:
-            fg_cls = fg_definitions[pot_fg]
+        for pot_fg, fg_cls in fg_definitions.items():
             fg_results[pot_fg] = fg_cls.measure(molecule)
 
         return fg_results

src/stko/_internal/optimizers/collapser.py

@@ -570,8 +570,7 @@ def _get_cent_to_lb_vector(
         """Returns dict of long bond atom to bb centroid vectors."""
         position_matrix = mol.get_position_matrix()
         centroid_to_lb_vectors: dict[tuple[int, int], tuple[float]] = {}
-        for bb in bb_centroids:
-            cent = bb_centroids[bb]
+        for bb, cent in bb_centroids.items():
             for b_atom_ids in long_bond_infos:
                 for atom_id in b_atom_ids:
                     (atom_info,) = mol.get_atom_infos(  # type: ignore[attr-defined]
@@ -614,9 +613,7 @@ def _compute_potential(
         long_bond_infos: dict[tuple[int, int], stk.BondInfo],
     ) -> float:
         system_potential = self._compute_non_bonded_potential(mol)
-        for long_bond_ids in long_bond_infos:
-            long_bond = long_bond_infos[long_bond_ids]
-
+        for long_bond in long_bond_infos.values():
             system_potential += self._bond_potential(
                 distance=self._get_bond_length(
                     mol=mol,