rowan-python 1.1.13__tar.gz → 2.0.1__tar.gz

{rowan_python-1.1.13 → rowan_python-2.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 1.1.13
+Version: 2.0.1
 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-2.0.1/docs/index.md

@@ -0,0 +1,49 @@
+## Workflow Class and Functions
+::: rowan.workflow
+    handler: python
+    options:
+      show_source: false 
+      show_root_heading: false  
+      show_root_toc_entry: false
+      members_order: source        # show items in the order they appear in code
+      group_by_category: true      # adds “Classes”, “Functions”, … headings -->
+
+## Folder Class and Functions
+::: rowan.folder
+    handler: python
+    options:
+      show_source: false 
+      show_root_heading: false  
+      show_root_toc_entry: false
+      members_order: source        # show items in the order they appear in code
+      group_by_category: true      # adds “Classes”, “Functions”, … headings -->
+
+## User Class and Functions
+::: rowan.user
+    handler: python
+    options:
+      show_source: false 
+      show_root_heading: false  
+      show_root_toc_entry: false
+      members_order: source        # show items in the order they appear in code
+      group_by_category: true      # adds “Classes”, “Functions”, … headings -->
+
+## Protein Class and Functions
+::: rowan.protein
+    handler: python
+    options:
+      show_source: false 
+      show_root_heading: false  
+      show_root_toc_entry: false
+      members_order: source        # show items in the order they appear in code
+      group_by_category: true      # adds “Classes”, “Functions”, … headings -->
+
+## Utilities
+::: rowan.utils
+    handler: python
+    options:
+      show_source: false 
+      show_root_heading: false  
+      show_root_toc_entry: false
+      members_order: source        # show items in the order they appear in code
+      group_by_category: true      # adds “Classes”, “Functions”, … headings -->

rowan_python-2.0.1/docs/rowan_rdkit.md

@@ -0,0 +1,8 @@
+::: rowan.rowan_rdkit
+    handler: python
+    options:
+      show_source: false 
+      show_root_heading: false  
+      show_root_toc_entry: false
+      members_order: source        # show items in the order they appear in code
+      group_by_category: true      # adds “Classes”, “Functions”, … headings -->

rowan_python-2.0.1/docs/stylesheets/colors.css

@@ -0,0 +1,6 @@
+/* Light-mode brand green */
+:root > * {
+  --md-primary-fg-color:        #16a34a;
+  --md-primary-fg-color--light: #c3d3e1; 
+  --md-primary-fg-color--dark:  #74967E; 
+}

rowan_python-2.0.1/examples/PROTAC_solubility.py

@@ -0,0 +1,52 @@
+# ruff: noqa: E501
+
+import rowan
+
+PROTACs = {
+    4564: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCCCCCCN3C=C(CCCOC(=O)NCC4=CC=C(C(=O)NC5=CC=CC=C5N)C=C4)N=N3)C(C)(C)C)C=C2)SC=N1",
+    2438: "CC(=O)N[C@H](C(=O)N1C[C@H](O)C[C@H]1C(=O)NCC1=CC=C(C2=C(C)N=CS2)C=C1OCCCCCCCCCCCC(=O)NC1=CC=C(C(=O)NC2=CC=CC=C2N)C=C1)C(C)(C)C",
+    727: "NC1=CC=CC=C1NC(=O)C1=CC=C(NC(=O)CCCCCNC(=O)COC2=CC=CC3=C2C(=O)N(C2CCC(=O)NC2=O)C3=O)C=C1",
+    728: "NC1=CC=CC=C1NC(=O)C1=CC=C(NC(=O)CCCCCCCCCCCNC(=O)COC2=CC=CC3=C2C(=O)N(C2CCC(=O)NC2=O)C3=O)C=C1",
+    729: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    730: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCCCCCCCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    1843: "O=C(CCCCCCNC(=O)C1=CC=C(NC(=O)COCCOCCNC(=O)COC2=CC=CC3=C2C(=O)N(C2CCC(=O)NC2=O)C3=O)C=C1)NO",
+    2110: "CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)CC1=CC=CC=C1)C(=O)NCCCCCC(=O)NC1=CC=C(NC(=O)CCCCCCC(=O)NO)C=C1",
+    2111: "CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)CC1=CC=CC=C1)C(=O)NCCOCCOCCNC(=O)C1=CC=CC(C(=O)NO)=C1",
+    2112: "CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)CC1=CC=CC=C1)C(=O)NCCOCCOCC(=O)NC1=CC=CC(C(=O)NO)=C1",
+    2419: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCCCCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2420: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCCCCCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2421: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCCCCCCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2422: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCCCCCCCCCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2423: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)COCCCCCCCCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2424: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)CCCCCCCCOCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2425: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)COCCCCCCOCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2426: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)COCCCCCCCCCOCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2427: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)COCCOCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+    2428: "CC1=C(C2=CC=C(CNC(=O)[C@@H]3C[C@@H](O)CN3C(=O)[C@@H](NC(=O)COCCOCCOCC(=O)NC3=CC=C(C(=O)NC4=CC=CC=C4N)C=C3)C(C)(C)C)C=C2)SC=N1",
+}
+
+protac_solubility_folder = rowan.create_folder(name="PROTAC Solubility")
+
+workflows = []
+for id, smiles in PROTACs.items():
+    workflows.append(
+        rowan.submit_solubility_workflow(
+            initial_smiles=smiles,
+            solvents=["CS(=O)C"],
+            temperatures=[293.15],
+            folder_uuid=protac_solubility_folder.uuid,
+            name=f"solubility {id}",
+        )
+    )
+
+
+for workflow in workflows:
+    workflow.wait_for_result()
+    workflow.fetch_latest(in_place=True)
+
+print(
+    [
+        (workflow.name, workflow.data["solubilities"]["CS(=O)C"]["solubilities"])
+        for workflow in workflows
+    ]
+)

rowan_python-2.0.1/examples/basic_calculation_from_json.py

@@ -0,0 +1,20 @@
+import json
+
+import rowan
+
+# rowan.api_key = ""
+
+with open("examples/data/workflow_example.json", "r") 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"],
+)
+
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
+print(result)

rowan_python-2.0.1/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-2.0.1/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-1.1.13 → rowan_python-2.0.1}/examples/bde.py

@@ -14,8 +14,6 @@ Rapid is recommended for most work.
 See documentation at: https://docs.rowansci.com/science/workflows/bond-dissociation-energy
 """
 
-import json
-
 from stjames import Molecule
 
 import rowan
@@ -23,12 +21,17 @@ import rowan
 # rowan.api_key = ""
 
 # Run calculation remotely
-result = rowan.compute(
-    Molecule.from_smiles("CCCC"),
+result = rowan.submit_workflow(
+    initial_molecule=Molecule.from_smiles("CCCC"),
     workflow_type="bde",
     name="Butane BDE",
-    mode="reckless",
-    all_CH=True,
+    workflow_data={
+        "mode": "reckless",
+        "all_CH": "true",
+    },
 )
 
-print(json.dumps(result, indent=4))
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
+print(result)

rowan_python-2.0.1/examples/cofolding_screen.py

@@ -0,0 +1,131 @@
+import rowan
+
+HARTREE_TO_KCALMOL = 627.5096
+
+ligands = [
+    "CCC(C)(C)NC1=NCC2(CCC(=O)C2C)N1",
+    "CCC(C)CN=C1NCC2(CCCOC2)CN1",
+    "CC(C)CCNC1=NCC2CC(COC2=N)O1",
+    "CCC(CC)NC1=NCC2CC(CO)CC12",
+    "CCC(C)CN=C1NC=C2CCC(O)CC2=N1",
+    "CC(C#CC#N)C1=NC=C2C=CC(=O)CN12",
+    "CCC(CCN)C1NCC2=C(CC)SC(O)=C12",
+    "CCC(CC)N=C1NC=C2C=C(F)C=C(N)N12",
+    "CC(C)(C)C(N)C1=NCC2=CC(I)=NC=C2O1",
+    "CCC(CC)NC1=NCC2CC(N1)C(C)CN2",
+    "CCCC(C)N=C1NCC2CCNC2(C)CO1",
+    "CC(C)CC(N)C1NCC2=CC(N)=C(Br)N=C12",
+    "CC(C)C(CN)C1=NC=C2C=CN(C)C2=C1Br",
+    "CC(CC#C)NC1=NCC2=C(C)N(C)C=C2O1",
+    "CCCC(C)(N)C1=NCC2=CC(N)=CC=C2O1",
+    "CCCCC(N)C1=NC=C2C=CN(C)C(C)=C12",
+    "CCC(CC)N=C1NCC2CC(N)CCCN12",
+    "CC(C)C(C)(N)C1=NC=C2C=CNC(=N)C2=N1",
+    "CC(C)(CC#N)C1=NCC2CCN=COC2O1",
+    "C#CCC(C#N)C1=NC=C2C=CNN=C12",
+    "CCCCCNC1=NCC2=C(C)NN=C2N1",
+    "CCCCC(N)C1=NC=C2C(C)=NOC2=C1Br",
+    "CCCCCNC1=NCC2(CC#N)OCC1O2",
+    "CC(C)CCNC1=NC=C2CC(=N)OCCN12",
+    "CCCC(C#N)C1N(C)C2=C(C=NS2)C1=O",
+    "CCC(CC#N)C1=NCC2=C(CO1)OC(=N)S2",
+    "CCC(CCN)C1=NCC2=C(CO1)SC=N2",
+    "CCC(C(C)N)C1NCC2CCOC1C2(C)C",
+    "CC(C)(C)CNC1=NCC2CCOC1(O2)C#C",
+    "CCCCCN=C1N(C)C2CCOC2C1(C)C",
+    "CC(C)CCN=C1NCC2(CCOC2O1)C#C",
+    "CC(C)C(C#N)C1NCC2=CC(O)=C(Br)N=C12",
+    "CCC(C(C)N)C1(N)CC2CC(OC)C1C2C",
+    "CC(C)(C)CN=C1NC=C2CC(O)CC2O1",
+    "CCC(C)(C#N)C1=NC=C2CC(=O)C(C=O)N12",
+    "CCCC(C)NC1=NCC2(CCOC=N2)CC1",
+    "CCCC(C)N=C1N=CC2=CC(=O)N=C2C1=N",
+    "CC(C)C(C#N)C1=NC=C2C=C(O)OC2=C1N",
+    "CCCC(CN=C1NCC2=C(C)SC=C12)C=O",
+    "CC(C)(C)CN=C1NCC2=CNC3=C2C1=CN3",
+    "CCCCC(N)C1=NC=C2CNCC2=C1I",
+    "CC(CC#C)NC1=NCC2=C(NC(=C2)C#C)N1",
+    "CCC#CCN=C1NCC2=CNC=C2N1",
+    "CCCC(C#N)C1N(C)C2=C(NC=C2)OC1=O",
+    "CC(C)(C)CN=C1NC=C2C=NC=C2SC1=N",
+    "CC(C)C(C#N)C1NCC2=CN=C(C=C12)C#N",
+    "CC(C)C(C#N)C1(N)CC2CN(C)CC2C1C",
+    "CCC(C)(C)N=C1NCC2=C(NC(C)=C2)C1O",
+    "CC(C)C(C)NC1=NCC2CNC(C)C(C2)C1",
+    "CCC(C)CN=C1NCC2C(N)C(C)C(C)C12",
+    "CCC(C)(C#N)C1=NC=C2CNC(C)C(C)N12",
+    "CC(C)C(C#N)C1NCC2=C(N=C(C)N2)C1C",
+    "CCC(C)(C)NC1=NCC2=C(N=C(C)N2)C1C",
+    "CCC(C)(C)N=C1N=CC2=CN(C)N=C2N1C",
+    "CC(C)CCN=C1NC=C2C=NC(=NN12)C#C",
+    "CC(C)C(CN=C1NCC2(CN=CO2)O1)C#N",
+    "CCC(CC)N=C1N(C)C2=C(NC(=O)S2)C1=O",
+    "CCCC(C#N)C1NCC2=C(N=CS2)S1(=O)=O",
+    "CCC(C)(C)NC1=NCC2=CNN=C2C(=N)N1",
+    "CC(C)CCN=C1NC=C2C(N)=NC(C)=C2S1",
+    "CCC(C)(C)NC1=NC=C2C(=N)N=CNC2=N1",
+    "CCC(CC)N=C1N(C)C2=C(NN=N2)C1=NO",
+    "CCC(C)(C)NC1=NCC2=CN=NN2CCC1",
+    "CCC(C)CN=C1N=CC2=CNN=NC2=N1",
+    "CCC(CCN)C1=NC=C2C(N)=NSC2=N1",
+    "CCC(C)(CN)C1NCC2=C(N)OC=C2C1C",
+    "CC(C)(CCN)C1=NC=C2C(=N)SN=C2C=N1",
+    "CC(C)(C)CNC1=NC=C2C(=N)SN=C2O1",
+    "CCC(C)C(N)C1=NCC2=C(O1)C=CC(=N)S2",
+    "CCCCCN=C1NCC2=C(O1)N=C(S2)C#N",
+    "CCC(C)(CNC1=NCC2=C(O1)SC=N2)C=O",
+    "CC#CC(CN)C1=NCC2=C(O1)SN=C2C",
+    "CCCC(C#N)C1NCC2COC1(C2)C(C)=O",
+    "CC(C)(C)C(N)C1(N)CC2COC1C(C)(C)C2",
+    "CCCC(C#N)C1NCC2COC1(C)CN2C",
+    "CCC(C)(C)N=C1N(C)C2COC1(C)OC2C",
+    "CC(C)CCN=C1NCC2=C(OC1=N)N=NN2",
+    "CCC(CC#N)(C1NCC2=COC=C12)N(C)C",
+    "CCCC(C)(N)C1NCC2=C(OC=C12)N(C)C",
+    "CC(C)(C)CNC1=NCC2=C(OCC1)N=CS2",
+    "CC#CCCN=C1NCC2=COC=C2C=C1",
+    "CCCCCNC1=NC=C2C(OCC2(C)O)=C1",
+    "CCC(C)(C#N)C1N(C)C2=COC=C2N=C1N",
+    "CCC(C)(C)N=C1NCC2(C)OC(CC12)=NC",
+    "CCC(C)(CN)C1NCC2C(O)CCC1C2C",
+    "CCCC(C)NC1=NCC2COCC(C1)C2C",
+    "CC(C)C(C)NC1=NCC2COCCC2(C)O1",
+    "CC(C)CC(N)C1=NC=C2COC(C)C(C)N12",
+    "CCC(C)(C)NC1=NCC2COC(C)(O1)C2N",
+    "CCCC(C)(N)C1=NC=C2COCCOC2=N1",
+    "CCCC(C)N=C1N(C)C2=COC(N)=C2C1=O",
+    "CCCCCNC1=NCC2(C)OC=NCCC12",
+    "CCC(C(C)N)C1=NC=C2COC(N)=NC2=C1",
+    "CCCC(C)NC1=NCC2(C)OC(=O)OC2O1",
+    "CCCCC(N)C1NCC2=CON=C2C1C#C",
+    "CC(C)C(C)N=C1NCC2=C(O)N(C)C=C2O1",
+    "CCCC(C)N=C1N=CC2=C(O)N(C)C=CN12",
+    "CC(C)C(C#N)C1=NC=C2C(O)=NSC2=C1O",
+    "CCC(CC)N=C1NCC2=C(O)SC(=N)N=C12",
+    "CC(C)C(CN)C1NCC2=C(SC=C2C)C1C",
+]
+
+workflows = []
+results = {}
+cofolding_result_folder = rowan.create_folder(name="Cofolding results")
+
+for ligand in ligands:
+    workflow = rowan.submit_protein_cofolding_workflow(
+        initial_protein_sequences=[
+            "MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL"
+        ],
+        initial_smiles_list=[ligand],
+        ligand_binding_affinity_index=0,
+        name=f"Cofolding {ligand}",
+        folder_uuid=cofolding_result_folder.uuid,
+    )
+    workflows.append(workflow)
+
+for workflow in workflows:
+    workflow.wait_for_result()
+    workflow.fetch_latest(in_place=True)
+
+for workflow in workflows:
+    results[workflow.name] = workflow.data["affinity_score"]["probability_binary"]
+
+print(results)

rowan_python-2.0.1/examples/conformer_dependent_redox.py

@@ -0,0 +1,37 @@
+import stjames
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+conformer_dependent_redox_folder = rowan.create_folder(name="Conformer dependent redox results")
+
+result = rowan.submit_conformer_search_workflow(
+    initial_molecule=Molecule.from_smiles("CC(C)Cc1ccc(C(=O)c2ccc(O)cc2)cc1"),
+    folder_uuid=conformer_dependent_redox_folder.uuid,
+)
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
+redox_potential_workflows = []
+
+for conformer in result.data["conformer_uuids"][:10]:
+    uuid = conformer[0]
+    molecule = rowan.retrieve_calculation_molecules(uuid)[0]
+    stjames_molecule = stjames.Molecule.model_validate(molecule)
+    redox_potential_workflows.append(
+        rowan.submit_redox_potential_workflow(
+            stjames_molecule,
+            reduction=True,
+            oxidization=True,
+            folder_uuid=conformer_dependent_redox_folder.uuid,
+        )
+    )
+
+for workflow in redox_potential_workflows:
+    workflow.wait_for_result()
+    workflow.fetch_latest(in_place=True)
+
+
+print([workflow.data["redox_potential"] for workflow in redox_potential_workflows])

{rowan_python-1.1.13 → rowan_python-2.0.1}/examples/conformers.py

@@ -17,8 +17,6 @@ Rapid is recommended for most work.
 See documentation at: https://docs.rowansci.com/science/workflows/conformers
 """
 
-import json
-
 from stjames import Molecule
 
 import rowan
@@ -26,11 +24,8 @@ import rowan
 # rowan.api_key = ""
 
 # Run calculation remotely
-result = rowan.compute(
-    Molecule.from_smiles("CCOCC"),
-    workflow_type="conformers",
-    name="Diethyl ether conformers",
-    mode="reckless",
+result = rowan.submit_conformer_search_workflow(
+    initial_molecule=Molecule.from_smiles("CCOCC"),
 )
 
-print(json.dumps(result, indent=4))
+print(result)

rowan_python-2.0.1/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
+    }
+  }
+