rowan-mcp 2.0.0__py3-none-any.whl → 2.0.1__py3-none-any.whl

rowan_mcp/functions/redox_potential.py

@@ -0,0 +1,349 @@
+"""
+Rowan redox potential function for electrochemistry.
+"""
+
+import os
+import logging
+import time
+from typing import Optional
+
+try:
+    import rowan
+except ImportError:
+    rowan = None
+
+# Setup logging
+logger = logging.getLogger(__name__)
+
+
+
+def lookup_molecule_smiles(molecule_name: str) -> str:
+    """Look up canonical SMILES for common molecule names."""
+    # Common molecule SMILES database
+    MOLECULE_SMILES = {
+        # Aromatics
+        "phenol": "Oc1ccccc1",
+        "benzene": "c1ccccc1", 
+        "toluene": "Cc1ccccc1",
+        "aniline": "Nc1ccccc1",
+        "benzoic acid": "O=C(O)c1ccccc1",
+        "pyridine": "c1ccncc1",
+        "furan": "c1ccoc1",
+        "thiophene": "c1ccsc1",
+        "pyrrole": "c1cc[nH]c1",
+        "imidazole": "c1c[nH]cn1",
+        "indole": "c1ccc2c(c1)cc[nH]2",
+        "quinoline": "c1ccc2ncccc2c1",
+        
+        # Aliphatics
+        "methane": "C",
+        "ethane": "CC",
+        "propane": "CCC",
+        "butane": "CCCC",
+        "pentane": "CCCCC",
+        "hexane": "CCCCCC",
+        "heptane": "CCCCCCC",
+        "octane": "CCCCCCCC",
+        "nonane": "CCCCCCCCC",
+        "decane": "CCCCCCCCCC",
+        
+        # Alcohols
+        "methanol": "CO",
+        "ethanol": "CCO",
+        "propanol": "CCCO",
+        "isopropanol": "CC(C)O",
+        "butanol": "CCCCO",
+        "isobutanol": "CC(C)CO",
+        "tert-butanol": "CC(C)(C)O",
+        
+        # Simple molecules
+        "water": "O",
+        "hydrogen peroxide": "OO",
+        "ammonia": "N",
+        "methyl amine": "CN",
+        "ethyl amine": "CCN",
+        "formaldehyde": "C=O",
+        "acetaldehyde": "CC=O",
+        "acetone": "CC(=O)C",
+        "formic acid": "C(=O)O",
+        "acetic acid": "CC(=O)O",
+        "acetamide": "CC(=O)N",
+        "dimethyl sulfoxide": "CS(=O)C",
+        "hydrogen sulfide": "S",
+        "carbon dioxide": "O=C=O",
+        "carbon monoxide": "C#O",
+        
+        # Cyclic compounds
+        "cyclopropane": "C1CC1",
+        "cyclobutane": "C1CCC1",
+        "cyclopentane": "C1CCCC1",
+        "cyclohexane": "C1CCCCC1",
+        "cycloheptane": "C1CCCCCC1",
+        "cyclooctane": "C1CCCCCCC1",
+        
+        # Ethers
+        "diethyl ether": "CCOCC",
+        "tetrahydrofuran": "C1CCOC1",
+        "dioxane": "C1COCCO1",
+        
+        # Halogens
+        "chloroform": "C(Cl)(Cl)Cl",
+        "carbon tetrachloride": "C(Cl)(Cl)(Cl)Cl",
+        "methyl chloride": "CCl",
+        "dichloromethane": "C(Cl)Cl",
+        "fluoromethane": "CF",
+        "bromomethane": "CBr",
+        "iodomethane": "CI",
+        
+        # Sugars
+        "glucose": "C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O",
+        "fructose": "C([C@H]([C@H]([C@@H]([C@H](CO)O)O)O)O)O",
+        "sucrose": "C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@]2([C@H]([C@@H]([C@@H](O2)CO)O)O)CO)O)O)O)O",
+        
+        # Nucleotides
+        "adenine": "c1nc(c2c(n1)ncn2)N",
+        "guanine": "c1nc2c(n1)c(=O)[nH]c(=n2)N",
+        "cytosine": "c1c(nc(=O)[nH]c1=O)N",
+        "thymine": "Cc1c[nH]c(=O)[nH]c1=O",
+        "uracil": "c1c[nH]c(=O)[nH]c1=O",
+        
+        # Amino acids
+        "glycine": "C(C(=O)O)N",
+        "alanine": "C[C@@H](C(=O)O)N",
+        "valine": "CC(C)[C@@H](C(=O)O)N",
+        "leucine": "CC(C)C[C@@H](C(=O)O)N",
+        "isoleucine": "CC[C@H](C)[C@@H](C(=O)O)N",
+        "phenylalanine": "c1ccc(cc1)C[C@@H](C(=O)O)N",
+        "tyrosine": "c1cc(ccc1C[C@@H](C(=O)O)N)O",
+        "tryptophan": "c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N",
+        "serine": "C([C@@H](C(=O)O)N)O",
+        "threonine": "C[C@H]([C@@H](C(=O)O)N)O",
+        "asparagine": "C([C@@H](C(=O)O)N)C(=O)N",
+        "glutamine": "C(CC(=O)N)[C@@H](C(=O)O)N",
+        "aspartic acid": "C([C@@H](C(=O)O)N)C(=O)O",
+        "glutamic acid": "C(CC(=O)O)[C@@H](C(=O)O)N",
+        "lysine": "C(CCN)C[C@@H](C(=O)O)N",
+        "arginine": "C(C[C@@H](C(=O)O)N)CN=C(N)N",
+        "histidine": "c1c([nH]cn1)C[C@@H](C(=O)O)N",
+        "cysteine": "C([C@@H](C(=O)O)N)S",
+        "methionine": "CCSC[C@@H](C(=O)O)N",
+        "proline": "C1C[C@H](NC1)C(=O)O",
+        
+        # Drugs and bioactive molecules
+        "aspirin": "CC(=O)Oc1ccccc1C(=O)O",
+        "caffeine": "Cn1c(=O)c2c(ncn2C)n(C)c1=O",
+        "nicotine": "CN1CCC[C@H]1c2cccnc2",
+        "morphine": "CN1CC[C@]23c4c5ccc(O)c4O[C@H]2[C@@H](O)C=C[C@H]3[C@H]1C5",
+        "codeine": "COc1ccc2c3c1O[C@H]1[C@@H](O)C=C[C@H]4[C@@H]1C[C@@](CC3)(C2)N4C",
+        "glucose": "C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O",
+        "cholesterol": "C[C@H](CCCC(C)C)[C@H]1CC[C@@H]2[C@@H]1CC[C@H]3[C@@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C",
+        "testosterone": "C[C@]12CC[C@H]3[C@H]([C@@H]1CC[C@@H]2O)CCC4=CC(=O)CC[C@]34C",
+        "estradiol": "C[C@]12CC[C@H]3[C@H]([C@@H]1CC[C@@H]2O)CCC4=C3C=CC(=C4)O",
+        
+        # Solvents
+        "dichloromethane": "C(Cl)Cl",
+        "chloroform": "C(Cl)(Cl)Cl",
+        "carbon tetrachloride": "C(Cl)(Cl)(Cl)Cl",
+        "acetonitrile": "CC#N",
+        "dimethylformamide": "CN(C)C=O",
+        "dimethyl sulfoxide": "CS(=O)C",
+        "ethyl acetate": "CCOC(=O)C",
+        "diethyl ether": "CCOCC",
+        "tetrahydrofuran": "C1CCOC1",
+        "1,4-dioxane": "C1COCCO1",
+        "toluene": "Cc1ccccc1",
+        "xylene": "Cc1ccccc1C",
+        "mesitylene": "Cc1cc(C)cc(C)c1",
+        "hexane": "CCCCCC",
+        "heptane": "CCCCCCC",
+        "octane": "CCCCCCCC",
+        "cyclohexane": "C1CCCCC1",
+        "benzene": "c1ccccc1",
+        "nitromethane": "C[N+](=O)[O-]",
+        "acetone": "CC(=O)C",
+        "2-butanone": "CCC(=O)C",
+        "2-propanol": "CC(C)O",
+        "1-butanol": "CCCCO",
+        "2-butanol": "CC(C)CO",
+        "tert-butanol": "CC(C)(C)O",
+        "ethylene glycol": "OCCO",
+        "propylene glycol": "CC(CO)O",
+        "glycerol": "C(C(CO)O)O",
+    }
+    
+    # Try exact match first
+    name_lower = molecule_name.lower().strip()
+    if name_lower in MOLECULE_SMILES:
+        return MOLECULE_SMILES[name_lower]
+    
+    # If not found, return the original input (assume it's already SMILES)
+    return molecule_name
+
+def log_rowan_api_call(workflow_type: str, **kwargs):
+    """Log Rowan API calls with detailed parameters."""
+    
+    try:
+        start_time = time.time()
+        result = rowan.compute(workflow_type=workflow_type, **kwargs)
+        api_time = time.time() - start_time
+        
+        if isinstance(result, dict) and 'uuid' in result:
+            job_status = result.get('status', result.get('object_status', 'Unknown'))
+            status_names = {0: "Queued", 1: "Running", 2: "Completed", 3: "Failed", 4: "Stopped", 5: "Awaiting Queue"}
+            status_text = status_names.get(job_status, f"Unknown ({job_status})")
+        
+        return result
+        
+    except Exception as e:
+        api_time = time.time() - start_time
+        raise e
+
+def rowan_redox_potential(
+    name: str,
+    molecule: str,
+    reduction: bool = True,
+    oxidation: bool = True,
+    mode: str = "rapid",
+    folder_uuid: Optional[str] = None,
+    blocking: bool = True,
+    ping_interval: int = 5
+) -> str:
+    """Predict redox potentials vs. SCE in acetonitrile.
+    
+    Calculates oxidation and reduction potentials for:
+    - Electrochemical reaction design
+    - Battery and energy storage applications
+    - Understanding electron transfer processes
+    
+    **Important**: Only acetonitrile solvent is supported by Rowan's redox workflow.
+    
+    Use this for: Electrochemistry, battery materials, electron transfer studies
+    
+    Args:
+        name: Name for the calculation
+        molecule: Molecule SMILES string or common name (e.g., "phenol", "benzene")
+        reduction: Whether to calculate reduction potential (default: True)
+        oxidation: Whether to calculate oxidation potential (default: True)
+        mode: Calculation accuracy mode - "reckless", "rapid", "careful", "meticulous" (default: "rapid")
+        folder_uuid: Optional folder UUID for organization
+        blocking: Whether to wait for completion (default: True)
+        ping_interval: Check status interval in seconds (default: 5)
+    
+    Returns:
+        Redox potential results vs. SCE in acetonitrile
+    """
+    # Look up SMILES if a common name was provided
+    canonical_smiles = lookup_molecule_smiles(molecule)
+    
+    # Validate mode
+    valid_modes = ["reckless", "rapid", "careful", "meticulous"]
+    mode_lower = mode.lower()
+    if mode_lower not in valid_modes:
+        return f" Invalid mode '{mode}'. Valid modes: {', '.join(valid_modes)}"
+    
+    # At least one type must be selected
+    if not reduction and not oxidation:
+        return f" At least one of 'reduction' or 'oxidation' must be True"
+    
+    logger.info(f"   Name: {name}")
+    logger.info(f"   Input: {molecule}")
+    logger.info(f"   Mode: {mode_lower}")
+    logger.info(f"   Reduction: {reduction}")
+    logger.info(f"   Oxidation: {oxidation}")
+    
+    # Build parameters for Rowan API
+    redox_params = {
+        "name": name,
+        "molecule": canonical_smiles,
+        "reduction": reduction,
+        "oxidation": oxidation,
+        "mode": mode_lower,
+        "solvent": "acetonitrile",  # Required by Rowan
+        "folder_uuid": folder_uuid,
+        "blocking": blocking,
+        "ping_interval": ping_interval
+    }
+    
+    result = log_rowan_api_call(
+        workflow_type="redox_potential",
+        **redox_params
+    )
+    
+    if blocking:
+        status = result.get('status', result.get('object_status', 'Unknown'))
+        
+        if status == 2:  # Completed successfully
+            formatted = f" Redox potential analysis for '{name}' completed successfully!\n\n"
+        elif status == 3:  # Failed
+            formatted = f" Redox potential analysis for '{name}' failed!\n\n"
+        else:
+            formatted = f" Redox potential analysis for '{name}' finished with status {status}\n\n"
+            
+        formatted += f" Molecule: {molecule}\n"
+        formatted += f" SMILES: {canonical_smiles}\n"
+        formatted += f" Job UUID: {result.get('uuid', 'N/A')}\n"
+        formatted += f" Status: {status}\n"
+        formatted += f"⚙ Mode: {mode_lower.title()}\n"
+        formatted += f"Solvent: Acetonitrile\n"
+        
+        # Show which potentials were calculated
+        calc_types = []
+        if reduction:
+            calc_types.append("Reduction")
+        if oxidation:
+            calc_types.append("Oxidation")
+        formatted += f" Calculated: {' + '.join(calc_types)} potential(s)\n"
+        
+        # Try to extract redox potential results
+        if isinstance(result, dict) and 'object_data' in result and result['object_data']:
+            data = result['object_data']
+            
+            if reduction and 'reduction_potential' in data and data['reduction_potential'] is not None:
+                formatted += f" Reduction Potential: {data['reduction_potential']:.3f} V vs. SCE\n"
+            
+            if oxidation and 'oxidation_potential' in data and data['oxidation_potential'] is not None:
+                formatted += f" Oxidation Potential: {data['oxidation_potential']:.3f} V vs. SCE\n"
+            
+            # Legacy support for older format
+            if 'redox_potential' in data and data['redox_potential'] is not None:
+                redox_type = data.get('redox_type', 'unknown')
+                formatted += f" {redox_type.title()} Potential: {data['redox_potential']:.3f} V vs. SCE\n"
+        
+        if status == 2:
+            formatted += f"\n **Results Available:**\n"
+            formatted += f"• Potentials reported vs. SCE (Saturated Calomel Electrode)\n"
+            formatted += f"• Calculated in acetonitrile solvent\n"
+            formatted += f"• Use rowan_workflow_management(action='retrieve', workflow_uuid='{result.get('uuid')}') for detailed data\n"
+        
+        return formatted
+    else:
+        formatted = f" Redox potential analysis for '{name}' submitted!\n\n"
+        formatted += f" Molecule: {molecule}\n"
+        formatted += f" SMILES: {canonical_smiles}\n"
+        formatted += f" Job UUID: {result.get('uuid', 'N/A')}\n"
+        formatted += f" Status: {result.get('status', 'Submitted')}\n"
+        formatted += f"⚙ Mode: {mode_lower.title()}\n"
+        
+        calc_types = []
+        if reduction:
+            calc_types.append("Reduction")
+        if oxidation:
+            calc_types.append("Oxidation")
+        formatted += f" Will calculate: {' + '.join(calc_types)} potential(s)\n"
+        
+        return formatted
+
+def test_rowan_redox_potential():
+    """Test the rowan_redox_potential function."""
+    try:
+        # Test with a simple molecule (non-blocking to avoid long wait)
+        result = rowan_redox_potential("test_redox", "phenol", blocking=False)
+        print(" Redox potential test successful!")
+        print(f"Result length: {len(result)} characters")
+        return True
+    except Exception as e:
+        print(f" Redox potential test failed: {e}")
+        return False
+
+if __name__ == "__main__":
+    test_rowan_redox_potential()