rowan-mcp 1.0.2__py3-none-any.whl → 2.0.1__py3-none-any.whl

rowan_mcp/tests/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_mcp/tests/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_mcp/tests/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)

rowan_mcp/tests/multistage_opt.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)

rowan_mcp/tests/optimization.py

@@ -0,0 +1,21 @@
+"""
+Run an optimization calculation on a molecule using Rowan.
+
+See documentation at: https://docs.rowansci.com/science/quantum-chemistry/geometry-optimization
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+result = rowan.submit_basic_calculation_workflow(
+    initial_molecule=Molecule.from_smiles("O"),
+    method="GFN2-xTB",
+    tasks=["optimize"],
+    engine="xtb",
+    name="Water Optimization",
+)
+
+print(result)

rowan_mcp/tests/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_mcp/tests/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_mcp/tests/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)

rowan_mcp/tests/scan.py

@@ -0,0 +1,28 @@
+"""
+Run an scan calculation on a molecule using Rowan.
+
+See documentation at: https://docs.rowansci.com/science/workflows/scan
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.submit_scan_workflow(
+    initial_molecule=Molecule.from_smiles("O"),
+    name="Water Angle scan",
+    scan_settings={
+        "type": "angle",
+        "atoms": [2, 1, 3],  # 1-indexed
+        "start": 100,
+        "stop": 110,
+        "num": 5,
+    },
+    calculation_method="GFN2-xTB",
+    calculation_engine="xtb",
+)
+
+print(result)

{rowan_mcp-1.0.2.dist-info → rowan_mcp-2.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rowan-mcp
-Version: 1.0.2
+Version: 2.0.1
 Summary: Model Context Protocol server for Rowan computational chemistry platform
 Project-URL: Homepage, https://github.com/k-yenko/rowan-mcp
 Author-email: Katherine Yenko <katherineayenko@gmail.com>
@@ -13,14 +13,15 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.10
+Requires-Python: >=3.11
+Requires-Dist: aiohttp>=3.12.15
 Requires-Dist: fastapi>=0.104.0
-Requires-Dist: fastmcp>=0.2.0
+Requires-Dist: fastmcp>=2.11.3
 Requires-Dist: pubchempy>=1.0.4
 Requires-Dist: pydantic>=2.0.0
 Requires-Dist: python-dotenv>=1.0.0
 Requires-Dist: rdkit>=2025.3.2
-Requires-Dist: rowan-python>=0.1.0
+Requires-Dist: rowan-python>=2.1.1
 Requires-Dist: typing-extensions>=4.0.0
 Requires-Dist: uvicorn>=0.24.0
 Provides-Extra: dev
@@ -32,7 +33,7 @@ Description-Content-Type: text/markdown
 
 # Rowan MCP Server
 
-This project wraps an MCP (Model Context Protocol) around Rowan's tools, making it easy for users to design molecuels and run simulations in natural everyday language. 
+MCP server for making it easy to run Rowan's molecular design and simulation tools.
 
 ---
 
@@ -56,34 +57,25 @@ That's it - no command line setup needed!
 
 Just add this to your MCP configuration and it will automatically install and run:
 
-**Using uvx (simplest):**
+**HTTP/SSE configuration:**
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "uvx",
-      "args": ["--from", "rowan-mcp", "rowan-mcp"],
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
+      "type": "http",
+      "url": "http://127.0.0.1:6276/sse"
     }
   }
 }
 ```
 
-**Using uv run (alternative):**
-```json
-{
-  "mcpServers": {
-    "rowan": {
-      "command": "uv",
-      "args": ["run", "--with", "rowan-mcp", "-m", "rowan_mcp"],
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
-    }
-  }
-}
+Then start the server:
+```bash
+# Set your API key
+export ROWAN_API_KEY="your_api_key_here"
+
+# Start the HTTP server
+uvx --from rowan-mcp rowan-mcp
 ```
 
 ### **Option 2: Manual Installation**
@@ -100,20 +92,24 @@ uv add rowan-mcp
 pip install rowan-mcp
 ```
 
-Then use this configuration:
+Then configure and start:
 ```json
 {
   "mcpServers": {
     "rowan": {
-      "command": "rowan-mcp",
-      "env": {
-        "ROWAN_API_KEY": "your_api_key_here"
-      }
+      "type": "http", 
+      "url": "http://127.0.0.1:6276/sse"
     }
   }
 }
 ```
 
+```bash
+# Set API key and start server
+export ROWAN_API_KEY="your_api_key_here"
+rowan-mcp
+```
+
 ### **Get API Key**
 
 Visit [labs.rowansci.com](https://labs.rowansci.com) → Create account → Generate API key
@@ -134,7 +130,7 @@ Ask the LLM to:
 
 ## **System Requirements**
 
-- **Python 3.10+** (Python 3.11+ recommended)
+- **Python 3.11+** 
 - **Package manager**: [uv](https://docs.astral.sh/uv/) (recommended) or pip
 - **Rowan API key** (free at [labs.rowansci.com](https://labs.rowansci.com))
 - **MCP-compatible client** (Claude Desktop, etc.)
@@ -142,7 +138,8 @@ Ask the LLM to:
 **Development commands** (if you cloned the repo):
 ```bash
 # Run from source
-uv run python -m rowan_mcp --http
+export ROWAN_API_KEY="your_api_key_here"
+uv run python -m rowan_mcp
 ```
 
 ---
@@ -176,7 +173,7 @@ uv run python -m rowan_mcp --http
 
 ## **Requirements**
 
-- Python 3.10+
+- Python 3.11+
 - Rowan API key
 - MCP-compatible AI assistant (Claude Desktop, etc.)
 
@@ -187,19 +184,6 @@ uv run python -m rowan_mcp --http
 
 ---
 
-## **Todo**
-
-- [ ] Remove unnecessary AI spaghetti formatting 🙃
-- [ ] Some complex conformer searches hang on "running"
-- [ ] Edit MCP one-liner context
-- [ ] Transition state finding and IRC
-- [X] `rowan_scan` - Potential energy surfaces
-- [ ] `rowan_docking` - Protein-ligand docking
-- [X] add in h-bond, BDE and macroscopic pka, logD, BBB
-- [ ] Folder listing API bug (returns 500 error) - Rowan side?
-- [ ] Multistage optimization sometimes shows unexpected imaginary frequencies
-- [ ] Some calculations show as finished in logs but not in Rowan UI
-
 ## **Citation**
 
 If you use this MCP tool in your research, please cite the underlying Rowan platform:
@@ -233,3 +217,12 @@ To update the dxt file:
 # Then update the desktop extension
 dxt pack rowan-dxt
 ```
+### MCP inspector
+```bash
+# Start the server first
+export ROWAN_API_KEY="your_api_key_here" 
+uv run python -m rowan_mcp &
+
+# Then inspect
+npx @modelcontextprotocol/inspector http://127.0.0.1:6276/sse
+```        

rowan_mcp-2.0.1.dist-info/RECORD

@@ -0,0 +1,69 @@
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rowan_mcp-1.0.2.dist-info/RECORD

@@ -1,34 +0,0 @@
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