rowan-python 2.0.0__tar.gz → 2.0.2__tar.gz

{rowan_python-2.0.0 → rowan_python-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 2.0.0
+Version: 2.0.2
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues

rowan_python-2.0.2/examples/basic_calculation_from_json.py

@@ -0,0 +1,21 @@
+import json
+
+import rowan
+
+# rowan.api_key = ""
+
+with open("examples/data/workflow_example.json") as f:
+    workflow_data = json.load(f)
+
+result = (
+    rowan.submit_workflow(
+        workflow_type="basic_calculation",
+        workflow_data=workflow_data,
+        name="basic calculation from json",
+        initial_molecule=workflow_data["initial_molecule"],
+    )
+    .wait_for_result()
+    .fetch_latest()
+)
+
+print(result)

rowan_python-2.0.2/examples/basic_calculation_with_constraint.py

@@ -0,0 +1,33 @@
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+result = rowan.submit_workflow(
+    initial_molecule=Molecule.from_smiles("CCCC"),
+    workflow_type="basic_calculation",
+    name="Constrained Butane",
+    workflow_data={
+        "engine": "xtb",
+        "settings": {
+            "method": "gfn2_xtb",
+            "tasks": ["optimize"],
+            "mode": "auto",
+            "opt_settings": {
+                "constraints": [
+                    {
+                        "atoms": [4, 3, 2, 1],
+                        "constraint_type": "dihedral",
+                        "value": 0,
+                    },
+                ]
+            },
+        },
+    },
+)
+
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
+print(result)

rowan_python-2.0.2/examples/basic_calculation_with_solvent.py

@@ -0,0 +1,55 @@
+# ruff: noqa
+
+import os
+import sys
+
+from stjames import Molecule, Method
+
+import rowan
+
+# rowan.api_key = ""
+
+
+def compute_energy_with_solvent_correction(molecule: Molecule, method: Method, name: str) -> float:
+    opt = rowan.submit_workflow(
+        initial_molecule=molecule,
+        workflow_type="basic_calculation",
+        name=f"{name} {method} optimization",
+        workflow_data={
+            "settings": {"method": method, "tasks": ["optimize"]},
+            "engine": "omol25",
+        },
+    )
+
+    opt.wait_for_result()
+    opt.fetch_latest(in_place=True)
+
+    calculation_uuid = opt.data["calculation_uuid"]
+    optimized_molecule = rowan.retrieve_calculation_molecules(calculation_uuid)[-1]
+
+    sp = rowan.submit_workflow(
+        initial_molecule=optimized_molecule,
+        workflow_type="basic_calculation",
+        name=f"{name} {method} single point",
+        workflow_data={
+            "settings": {
+                "method": method,
+                "tasks": ["energy"],
+                "solvent_settings": {"solvent": "water", "model": "cpcmx"},
+            },
+            "engine": "omol25",
+        },
+    )
+
+    sp.wait_for_result()
+    sp.fetch_latest(in_place=True)
+
+    calculation_uuid = sp.data["calculation_uuid"]
+    final_molecule = rowan.retrieve_calculation_molecules(calculation_uuid)[0]
+    return final_molecule["energy"]
+
+
+E1 = compute_energy_with_solvent_correction(
+    Molecule.from_smiles("CC(=O)Oc1ccccc1C(=O)O"), Method.OMOL25_CONSERVING_S, "aspirin"
+)
+print(E1)

{rowan_python-2.0.0 → rowan_python-2.0.2}/examples/bde.py

@@ -31,4 +31,7 @@ result = rowan.submit_workflow(
     },
 )
 
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
 print(result)

rowan_python-2.0.2/examples/data/workflow_example.json

@@ -0,0 +1,190 @@
+{
+    "mode": "auto",
+    "engine": "xtb",
+    "messages": [],
+    "settings": {
+      "mode": "rapid",
+      "tasks": [
+        "optimize"
+      ],
+      "method": "gfn2_xtb",
+      "basis_set": null,
+      "corrections": [],
+      "opt_settings": {
+        "max_steps": 250,
+        "constraints": [
+          {
+            "atoms": [
+              4,
+              3,
+              2,
+              1
+            ],
+            "value": 0,
+            "constraint_type": "dihedral"
+          }
+        ],
+        "optimize_cell": false,
+        "energy_threshold": 0.00005,
+        "transition_state": false,
+        "recalc_hess_every": 0,
+        "max_gradient_threshold": 0.005,
+        "rms_gradient_threshold": 0.0035
+      },
+      "scf_settings": {
+        "soscf": false,
+        "max_iters": 250
+      },
+      "level_of_theory": "gfn2_xtb",
+      "compute_settings": {
+        "compute_type_used": null,
+        "requested_compute_type": "cpu"
+      },
+      "solvent_settings": null,
+      "thermochem_settings": {
+        "temperature": 298,
+        "concentration": 0.0408740470708,
+        "scaling_factor": 1,
+        "cutoff_frequency": 100
+      }
+    },
+    "calculation_uuid": "54027970-5efb-42df-8125-c8984d8ca7eb",
+    "initial_molecule": {
+      "cell": null,
+      "atoms": [
+        {
+          "position": [
+            -1.57731622,
+            0.46259034,
+            0.02288227
+          ],
+          "atomic_number": 6
+        },
+        {
+          "position": [
+            -0.55246934,
+            -0.31349805,
+            -0.78986664
+          ],
+          "atomic_number": 6
+        },
+        {
+          "position": [
+            0.65178196,
+            -0.77563238,
+            0.03104792
+          ],
+          "atomic_number": 6
+        },
+        {
+          "position": [
+            1.5013315,
+            0.37070813,
+            0.55769072
+          ],
+          "atomic_number": 6
+        },
+        {
+          "position": [
+            -1.17009891,
+            1.41344062,
+            0.37886292
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            -1.91277475,
+            -0.11690438,
+            0.88874548
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            -2.45332233,
+            0.68757176,
+            -0.59399069
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            -0.21575239,
+            0.30052639,
+            -1.63326648
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            -1.04230601,
+            -1.19688302,
+            -1.21658189
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            0.31558706,
+            -1.39539838,
+            0.87044712
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            1.28031633,
+            -1.41330121,
+            -0.60197473
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            2.39258685,
+            -0.02154188,
+            1.05803044
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            0.95227634,
+            0.97534316,
+            1.28543953
+          ],
+          "atomic_number": 1
+        },
+        {
+          "position": [
+            1.83015992,
+            1.0229789,
+            -0.25746596
+          ],
+          "atomic_number": 1
+        }
+      ],
+      "charge": 0,
+      "dipole": null,
+      "energy": null,
+      "smiles": "CCCC",
+      "stress": null,
+      "elapsed": null,
+      "gradient": null,
+      "velocities": null,
+      "multiplicity": 1,
+      "homo_lumo_gap": null,
+      "scf_completed": null,
+      "scf_iterations": null,
+      "mulliken_charges": null,
+      "calculation_index": null,
+      "vibrational_modes": null,
+      "zero_point_energy": null,
+      "thermal_energy_corr": null,
+      "thermal_enthalpy_corr": null,
+      "mulliken_spin_densities": null,
+      "thermal_free_energy_corr": null
+    }
+  }
+  

rowan_python-2.0.2/examples/macropka.py

@@ -0,0 +1,13 @@
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+result = rowan.submit_macropka_workflow(
+    # oseltamivir
+    initial_smiles="C1CCOC(=O)C1=C[C@@H](OC(CC)CC)[C@H](NC(C)=O)[C@@H]([NH3+])C1CCC1",
+    name="Oseltamivir macropka",
+)
+
+
+print(result)