rowan-mcp 1.0.2__py3-none-any.whl → 2.0.0__py3-none-any.whl

rowan_mcp/tests/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_mcp/tests/bde.py

@@ -0,0 +1,37 @@
+"""
+Calculate the Bond-Dissociation Energy (BDE) of a molecule using the Rowan API.
+
+| Calculation |   Initial    |    Final     |          Single        | Optimizes  |
+| Mode        | Optimization | Optimization |          Point         | Fragments? |
+|-------------|--------------|--------------|------------------------|------------|
+| Reckless    |              |    GFN-FF    |        GFN2-xTB        |     No     |
+| Rapid       |              |   GFN2-xTB   |        r²SCAN-3c       |     Yes    |
+| Careful     |              |   r²SCAN-3c  |        ωB97X-3c        |     Yes    |
+| Meticulous  |  r²SCAN-3c   |   ωB97X-3c   | ωB97M-D3BJ/def2-TZVPPD |     Yes    |
+
+Rapid is recommended for most work.
+
+See documentation at: https://docs.rowansci.com/science/workflows/bond-dissociation-energy
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.submit_workflow(
+    initial_molecule=Molecule.from_smiles("CCCC"),
+    workflow_type="bde",
+    name="Butane BDE",
+    workflow_data={
+        "mode": "reckless",
+        "all_CH": "true",
+    },
+)
+
+result.wait_for_result()
+result.fetch_latest(in_place=True)
+
+print(result)

rowan_mcp/tests/benchmark_queries.md

@@ -0,0 +1,120 @@
+# Rowan MCP Benchmark Queries
+
+## Tier 1: Single Tool Calls
+
+### Basic Calculation
+1. "Optimize the geometry of water"
+2. "Calculate the energy of methane using GFN2-xTB"
+
+### Conformer Search
+3. "Find the conformers of diethyl ether"
+4. "Search for low-energy conformations of butane"
+
+### pKa
+5. "Calculate the pKa of phenol"
+6. "What's the pKa of acetic acid?"
+
+### Redox Potential
+7. "Calculate the oxidation potential of benzene"
+8. "Find the reduction potential of quinone"
+
+### Solubility
+9. "Predict the solubility of aspirin in water"
+10. "What's the solubility of caffeine in ethanol?"
+
+### Descriptors
+11. "Calculate molecular descriptors for ibuprofen"
+
+### Tautomers
+12. "Find the tautomers of 2-hydroxypyridine"
+
+### Scan
+13. "Perform an angle scan on water from 100 to 110 degrees"
+
+### IRC
+14. "Run an IRC calculation from this transition state: [provide XYZ]"
+
+### Fukui
+15. "Calculate Fukui indices for aniline"
+
+### Docking
+16. "Dock aspirin to CDK2 kinase"
+
+### Protein Cofolding
+17. "Predict the structure of CDK2 with a small molecule ligand"
+
+## Tier 2: Parameter Interpretation
+
+### Basic Calculation with Modes
+18. "Carefully optimize ethanol geometry"
+19. "Run a meticulous energy calculation on benzene"
+
+### Conformer Search with Settings
+20. "Find conformers of cyclohexane using meticulous mode"
+
+### pKa with Specific Sites
+21. "Calculate the pKa of lysine, only looking at nitrogen atoms"
+22. "Find the pKa of phosphoric acid between pH 1 and 14"
+
+### Redox with Both Potentials
+23. "Calculate both oxidation and reduction potentials for ferrocene"
+
+### Solubility with Temperature
+24. "Predict caffeine solubility in water at 25 and 50 degrees Celsius"
+
+### Scan with Custom Parameters
+25. "Scan the C-C bond in ethane from 1.3 to 1.7 Angstroms with 10 points"
+
+### Docking with Options
+26. "Dock ibuprofen to COX-2 without conformational search"
+
+## Tier 3: Batch Operations
+
+### Multiple Molecules
+27. "Calculate pKa values for phenol, p-nitrophenol, and p-methoxyphenol"
+28. "Find conformers for butane, pentane, and hexane"
+29. "Calculate oxidation potentials for benzene, toluene, and xylene"
+
+### Multiple Methods
+30. "Optimize water with GFN2-xTB, UMA, and R2SCAN-3c"
+31. "Calculate ethanol energy using both rapid and careful modes"
+
+### Comparative Analysis
+32. "Compare the solubility of aspirin in water, ethanol, and acetone"
+33. "Screen these three molecules for docking to CDK2: [provide 3 SMILES]"
+
+## Tier 4: Workflow Chaining
+
+### Conformer-Dependent Properties
+34. "Find conformers of p-methoxybenzophenone, then calculate redox potential for the lowest energy conformer"
+35. "Generate conformers of butanol, then calculate pKa for the top 3 structures"
+
+### Optimization to IRC
+36. "Optimize this transition state geometry [XYZ], then run IRC from the result"
+
+### Scan to Property
+37. "Perform a dihedral scan on butane, then calculate the energy of the highest energy point"
+
+### Sequential Docking
+38. "Find conformers of a ligand, then dock the best conformer to CDK2"
+
+## Tier 5: Conditional Logic
+
+### Threshold-Based Analysis
+39. "Screen 5 molecules against CDK2, only run detailed conformer analysis for those with scores better than -8.0"
+40. "Calculate pKa for histidine, if any site has pKa between 6-8, run a conformer search at that pH"
+
+### Outlier Detection
+41. "Find all conformers of cyclohexanol, calculate energies, and recalculate any conformer more than 3 kcal/mol above the minimum with meticulous mode"
+
+### Multi-Stage Screening
+42. "Calculate descriptors for these 10 molecules, identify those with logP > 2, then calculate their pKa values"
+
+### Error Recovery
+43. "Optimize this complex molecule, if it fails with rapid mode, retry with careful mode"
+
+## Notes
+- Queries intentionally use varied phrasing (calculate/find/predict/what's)
+- Mix of SMILES, common names, and descriptive terms
+- Each science tool appears at least once
+- Workflow management tools used implicitly in Tiers 4-5

rowan_mcp/tests/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_mcp/tests/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_mcp/tests/conformers.py

@@ -0,0 +1,31 @@
+"""
+Calculate the conformers of a molecule using the Rowan API.
+
+| Mode                                          | Reckless | Rapid | Careful | Meticulous |
+|-----------------------------------------------|----------|-------|---------|------------|
+| Conformer generation program                  | RDKit    | RDKit | CREST   | CREST      |
+| Level of theory used for conformer generation | MMFF     | MMFF  | GFN-FF  | GFN2-xTB   |
+| CREST Mode                                    |          |       | quick   | normal     |
+| ETKDG number of initial conformers            | 200      | 300   |         |            |
+| Initial energy cutoff (kcal/mol)              | 10       | 15    | 10      | 15         |
+| RMSD similarity cutoff (Å)                    | 0.25     | 0.10  | 0.00    | 0.00       |
+| xTB screening max number of conformers        | 50       | 100   | 150     | 500        |
+| Final energy cutoff (kcal/mol)                | 5        | 5     | 5       | 10         |
+
+Rapid is recommended for most work.
+
+See documentation at: https://docs.rowansci.com/science/workflows/conformers
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.submit_conformer_search_workflow(
+    initial_molecule=Molecule.from_smiles("CCOCC"),
+)
+
+print(result)

rowan_mcp/tests/data.json

@@ -0,0 +1,189 @@
+{
+  "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
+  }
+}