rowan-python 1.1.13__tar.gz → 2.0.0__tar.gz

{rowan_python-1.1.13 → rowan_python-2.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 1.1.13
+Version: 2.0.0
 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-2.0.0/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-2.0.0/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-2.0.0/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-2.0.0/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-1.1.13 → rowan_python-2.0.0}/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 +21,14 @@ 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))
+print(result)

rowan_python-2.0.0/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-2.0.0/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-2.0.0}/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-2.0.0/examples/docking_screen.py

@@ -0,0 +1,157 @@
+import time
+
+import stjames
+
+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 = {}
+
+docking_result_folder = rowan.create_folder(name="Docking results")
+
+
+protein = rowan.create_protein_from_pdb_id("CDK2", "1HCK")
+
+protein.sanitize()
+time.sleep(60)
+protein.refresh()
+
+for ligand in ligands:
+    workflow = rowan.submit_docking_workflow(
+        protein.uuid,
+        pocket=[[103.55, 100.59, 82.99], [27.76, 32.67, 48.79]],
+        initial_molecule=stjames.Molecule.from_smiles(ligand),
+        folder_uuid=docking_result_folder.uuid,
+        name=f"Docking {ligand}",
+    )
+    workflows.append(workflow)
+
+
+for workflow in workflows:
+    workflow.wait_for_result()
+    workflow.fetch_latest(in_place=True)
+
+lowest_conformer_energy = 0
+for workflow in workflows:
+    conformers = workflow.data["conformers"]
+    for conformer in conformers:
+        energy = rowan.retrieve_calculation_molecules(
+            conformer[0] if isinstance(conformer, list) else conformer
+        )[0]["energy"]
+        lowest_conformer_energy = min(lowest_conformer_energy, energy)
+
+    sorted_scores = sorted(workflow.data["scores"], key=lambda x: float(x["score"]))
+    for score in sorted_scores:
+        pose_energy = rowan.retrieve_calculation_molecules(score["pose"])[0]["energy"]
+        strain = (pose_energy - lowest_conformer_energy) * HARTREE_TO_KCALMOL
+        if score["posebusters_valid"] and strain < 4:
+            results[workflow.name] = score
+            break
+
+print(results)

rowan_python-2.0.0/examples/irc.py

@@ -0,0 +1,24 @@
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+result = rowan.submit_irc_workflow(
+    initial_molecule=Molecule.from_xyz_lines(
+        """7
+SMILES `N=C([O-])[OH2+]`
+N    -0.15519741  -1.36979175  -0.20679433
+C     1.11565384  -1.23943631  -0.14797646
+O     2.17614993  -1.72950370  -0.04017850
+H    -0.55869366  -2.29559315  -0.23834737
+O     1.02571386   0.42871733  -0.27925360
+H    -0.09029954  -0.04166676  -0.31495768
+H     1.26740151   0.88347299   0.53620841
+""".splitlines()
+    ),
+    name="HNCO + H₂O - IRC",
+    preopt=False,
+)
+
+print(result)

rowan_python-2.0.0/examples/multistage_opt.py

@@ -0,0 +1,18 @@
+import stjames
+
+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_workflow(
+    initial_molecule=stjames.Molecule.from_smiles("C1CCC1"),  # cyclobutane
+    workflow_type="multistage_opt",
+    name="Multistage optimization cyclobutane",
+    workflow_data={
+        "mode": "reckless",
+    },
+)
+
+
+print(result)

{rowan_python-1.1.13 → rowan_python-2.0.0}/examples/optimization.py

@@ -4,24 +4,18 @@ Run an optimization calculation on a molecule using Rowan.
 See documentation at: https://docs.rowansci.com/science/quantum-chemistry/geometry-optimization
 """
 
-import json
-
 from stjames import Molecule
 
 import rowan
 
 # rowan.api_key = ""
 
-# Run calculation remotely
-result = rowan.compute(
-    Molecule.from_smiles("O"),
-    workflow_type="basic_calculation",
-    name="Water Optimization",
-    settings={
-        "method": "GFN2-xTB",
-        "tasks": ["optimize"],
-    },
+result = rowan.submit_basic_calculation_workflow(
+    initial_molecule=Molecule.from_smiles("O"),
+    method="GFN2-xTB",
+    tasks=["optimize"],
     engine="xtb",
+    name="Water Optimization",
 )
 
-print(json.dumps(result, indent=4))
+print(result)

rowan_python-2.0.0/examples/phenol_pka.py

@@ -0,0 +1,36 @@
+import stjames
+
+import rowan
+
+phenols_to_compute = {
+    "p-nitrophenol": "Oc1ccc(N(=O)=O)cc1",
+    "p-(trifluoromethyl)phenol": "Oc1ccc(C(F)(F)F)cc1",
+    "methyl p-hydroxybenzoate": "COC(=O)c1ccc(O)cc1",
+    "p-fluorophenol": "Oc1ccc(F)cc1",
+    "p-chlorophenol": "Oc1ccc(Cl)cc1",
+    "phenol": "Oc1ccccc1",
+    "p-cresol": "Oc1ccc(C)cc1",
+    "p-methoxyphenol": "COc1ccc(O)cc1",
+    "p-(dimethylamino)phenol": "CN(C)c1ccc(O)cc1",
+}
+
+pka_folder = rowan.create_folder(name="phenol pKa results")
+
+workflows = []
+for name, smiles in phenols_to_compute.items():
+    stjames_molecule = stjames.Molecule.from_smiles(smiles)
+    workflows.append(
+        rowan.submit_pka_workflow(
+            stjames_molecule,
+            name=f"pKa {name}",
+            folder_uuid=pka_folder.uuid,
+            deprotonate_elements=[8],
+        )
+    )
+
+
+for workflow in workflows:
+    workflow.wait_for_result()
+    workflow.fetch_latest(in_place=True)
+
+print([(workflow.name, workflow.data["conjugate_bases"][0]["pka"]) for workflow in workflows])

{rowan_python-1.1.13 → rowan_python-2.0.0}/examples/pka.py

@@ -13,18 +13,10 @@ import rowan
 
 # rowan.api_key = ""
 
-# Run calculation remotely
-result = rowan.compute(
-    Molecule.from_smiles("n1ccccc1"),
-    workflow_type="pka",
-    name="Pyridine pKa",
+result = rowan.submit_pka_workflow(
+    initial_molecule=Molecule.from_smiles("n1ccccc1"),
     mode="reckless",
+    name="Pyridine pKa",
 )
 
-logfile = result["object_logfile"]
-strongest_base = result["object_data"]["strongest_base"]
-
-print(f"""\
-{logfile}
-
-pKa of conjugate acid: {strongest_base:.2f}""")
+print(result)

rowan_python-2.0.0/examples/protein_cofolding.py

@@ -0,0 +1,17 @@
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.submit_protein_cofolding_workflow(
+    initial_protein_sequences=[
+        "ASKGTSHEAGIVCRITKPALLVLNHETAKVIQTAFQRASYPDITGEKAMMLLGQVKYGLHNIQISHLSIASSQVELVEAKSIDVSIQDVSVVFKGTLKYGYTTAWWLGIDQSIDFEIDSAIDLQINTQLTADSGRVRTDAPDCYLSFHKLLLHLQGEREPGWIKQLFTNFISFTLKLVLKGQICKEINVISNIMADFVQTRAASILSDGDIGVDISLTGDPVITASYLESHHKGHFIYKDVSEDLPLPTFSPTLLGDSRMLYFWFSERVFHSLAKVAFQDGRLMLSLMGDEFKAVLETWGFNTNQEIFQEVVGGFPSQAQVTVHCLKMPKISCQNKGVVVDSSVMVKFLFPRPDQQHSVAYTFEEDIVTTVQASYSKKKLFLSLLDFQITPKTVSNLTESSSESIQSFLQSMITAVGIPEVMSRLEVVFTALMNSKGVSLFDIINPEIITRDGFLLLQMDFGFPEHLLVDFLQSLS"
+    ],
+    initial_smiles_list=[
+        "CCOC(=O)N1c2ccc(C(F)(F)F)cc2[C@@H](N(Cc2cc(C(F)(F)F)cc(C(F)(F)F)c2)C(=O)OC)C[C@H]1CC"
+    ],
+    ligand_binding_affinity_index=0,
+    name="Torcetrapib Cofolding",
+)
+
+print(result)