rowan-mcp 1.0.1__py3-none-any.whl → 2.0.0__py3-none-any.whl

rowan_mcp/functions/spin_states.py

@@ -1,747 +0,0 @@
-"""
-Rowan spin states calculation function for MCP tool integration.
-Follows the exact workflow from: https://github.com/rowansci/stjames-public/blob/master/stjames/workflows/spin_states.py
-Implements SpinStatesWorkflow(MoleculeWorkflow) pattern from stjames.
-"""
-
-from typing import Optional, Union, List, Any
-import logging
-import rowan
-from .molecular_converter import convert_to_smiles
-
-logger = logging.getLogger(__name__)
-
-# Mock stjames workflow classes to match their structure
-class Mode:
-    """Mock Mode enum from stjames."""
-    AUTO = "auto"
-    RAPID = "rapid" 
-    CAREFUL = "careful"
-    METICULOUS = "meticulous"
-    RECKLESS = "reckless"
-    MANUAL = "manual"
-
-class Molecule:
-    """Mock Molecule class from stjames."""
-    def __init__(self, smiles: str, charge: int = 0, multiplicity: int = 1):
-        self.smiles = smiles
-        self.charge = charge
-        self.multiplicity = multiplicity
-    
-    def __str__(self):
-        return self.smiles
-
-class MoleculeWorkflow:
-    """
-    Mock MoleculeWorkflow base class from stjames.
-    Base class for Workflows that operate on a single molecule.
-    """
-    def __init__(self, initial_molecule: Union[str, Molecule], mode: str = "auto"):
-        if isinstance(initial_molecule, str):
-            self.initial_molecule = Molecule(initial_molecule)
-        else:
-            self.initial_molecule = initial_molecule
-        
-        # Set mode to RAPID if AUTO is selected (stjames behavior)
-        if mode.lower() == "auto":
-            self.mode = "rapid"
-        else:
-            self.mode = mode.lower()
-    
-    def __repr__(self):
-        return f"<{type(self).__name__} {self.mode.upper()}>"
-
-class SpinStatesWorkflow(MoleculeWorkflow):
-    """
-    Mock SpinStatesWorkflow from stjames that inherits from MoleculeWorkflow.
-    Workflow for computing spin states of molecules.
-    """
-    def __init__(self, initial_molecule: Union[str, Molecule], states: List[int], 
-                 mode: str = "auto", solvent: Optional[str] = None, 
-                 xtb_preopt: bool = False, constraints: Optional[List] = None,
-                 transition_state: bool = False, frequencies: bool = False):
-        super().__init__(initial_molecule, mode)
-        self.states = states
-        self.solvent = solvent
-        self.xtb_preopt = xtb_preopt
-        self.constraints = constraints or []
-        self.transition_state = transition_state
-        self.frequencies = frequencies
-        
-        # Validate states (stjames validation logic)
-        self._validate_states()
-    
-    def _validate_states(self):
-        """Confirm that all spin states are valid (from stjames)."""
-        if not self.states:
-            raise ValueError("Expected at least one spin state.")
-        
-        # Check multiplicities are consistent (all odd or all even)
-        if any((self.states[0] - mult) % 2 for mult in self.states):
-            raise ValueError(f"Inconsistent multiplicities found: {self.states}")
-    
-    def __repr__(self):
-        if self.mode != "manual":
-            return f"<{type(self).__name__} {self.states} {self.mode.upper()}>"
-        return f"<{type(self).__name__} {self.states} {self.mode.upper()}>"
-    
-    def __len__(self):
-        return len(self.states)
-
-
-# Removed old hardcoded conversion function - now using dynamic molecular_converter.py
-
-
-def _generate_3d_coordinates_for_coordination_complex(smiles: str, rdkit_mol):
-    """Generate clean 3D coordinates for coordination complexes."""
-    try:
-        import numpy as np
-        
-        # Get number of atoms
-        num_atoms = rdkit_mol.GetNumAtoms()
-        
-        # Find metal center and ligands
-        metal_idx = None
-        ligand_indices = []
-        
-        for i, atom in enumerate(rdkit_mol.GetAtoms()):
-            atomic_num = atom.GetAtomicNum()
-            if atomic_num in [25, 26, 27, 28, 29, 24, 46]:  # Transition metals
-                metal_idx = i
-            else:
-                ligand_indices.append(i)
-        
-        if metal_idx is None:
-            return None
-        
-        # Initialize coordinates
-        coords = [[0.0, 0.0, 0.0] for _ in range(num_atoms)]
-        
-        # Place metal at origin
-        coords[metal_idx] = [0.0, 0.0, 0.0]
-        
-        # Set appropriate bond length for M-Cl bonds
-        bond_length = 2.4  # Standard M-Cl bond length in Å
-        
-        # Generate geometry based on coordination number
-        num_ligands = len(ligand_indices)
-        
-        if num_ligands == 4:
-            # Square planar for Pd(II) complexes
-            if any(atom.GetAtomicNum() == 46 for atom in rdkit_mol.GetAtoms()):
-                positions = np.array([
-                    [bond_length, 0, 0],
-                    [-bond_length, 0, 0],
-                    [0, bond_length, 0],
-                    [0, -bond_length, 0]
-                ])
-            else:
-                # Tetrahedral for other metals
-                a = bond_length / np.sqrt(3)
-                positions = np.array([
-                    [a, a, a],
-                    [a, -a, -a],
-                    [-a, a, -a],
-                    [-a, -a, a]
-                ])
-        
-        elif num_ligands == 6:
-            # Octahedral geometry
-            positions = np.array([
-                [bond_length, 0, 0],
-                [-bond_length, 0, 0],
-                [0, bond_length, 0],
-                [0, -bond_length, 0],
-                [0, 0, bond_length],
-                [0, 0, -bond_length]
-            ])
-        
-        else:
-            # General spherical distribution
-            angles = np.linspace(0, 2*np.pi, num_ligands, endpoint=False)
-            positions = []
-            for angle in angles:
-                x = bond_length * np.cos(angle)
-                y = bond_length * np.sin(angle)
-                z = 0.0
-                positions.append([x, y, z])
-            positions = np.array(positions)
-        
-        # Assign positions to ligands
-        for i, ligand_idx in enumerate(ligand_indices):
-            if i < len(positions):
-                coords[ligand_idx] = positions[i].tolist()
-        
-        # Validate minimum distances
-        min_distance = float('inf')
-        for i in range(num_atoms):
-            for j in range(i+1, num_atoms):
-                dist = np.linalg.norm(np.array(coords[i]) - np.array(coords[j]))
-                min_distance = min(min_distance, dist)
-        
-        if min_distance > 1.0:  # At least 1.0 Å separation
-            return coords
-        else:
-            return None
-            
-    except Exception as e:
-        logger.warning(f"Coordinate generation failed: {e}")
-        return None
-
-# Removed old complex coordinate generation functions - simplified to single clean function above
-
-def _calculate_molecular_charge(smiles: str) -> int:
-    """Calculate the total molecular charge from SMILES string."""
-    total_charge = 0
-    
-    # Count negative ions
-    if '[Cl-]' in smiles:
-        total_charge -= smiles.count('[Cl-]')
-    if '[F-]' in smiles:
-        total_charge -= smiles.count('[F-]')
-    if '[Br-]' in smiles:
-        total_charge -= smiles.count('[Br-]')
-    if '[I-]' in smiles:
-        total_charge -= smiles.count('[I-]')
-    
-    # Count positive metal ions - common oxidation states
-    positive_ions = {
-        '[Pd+2]': 2, '[Pd+4]': 4,
-        '[Mn+2]': 2, '[Mn+3]': 3, '[Mn+4]': 4, '[Mn+7]': 7,
-        '[Fe+2]': 2, '[Fe+3]': 3,
-        '[Co+2]': 2, '[Co+3]': 3,
-        '[Ni+2]': 2, '[Ni+3]': 3,
-        '[Cu+1]': 1, '[Cu+2]': 2,
-        '[Cr+2]': 2, '[Cr+3]': 3, '[Cr+6]': 6,
-        '[V+2]': 2, '[V+3]': 3, '[V+4]': 4, '[V+5]': 5,
-        '[Ti+2]': 2, '[Ti+3]': 3, '[Ti+4]': 4,
-        '[Zn+2]': 2
-    }
-    
-    for ion, charge in positive_ions.items():
-        if ion in smiles:
-            total_charge += charge * smiles.count(ion)
-    
-    return total_charge
-
-
-def rowan_spin_states(
-    name: str,
-    molecule: str,
-    states: Optional[Union[str, List[int]]] = None,
-    mode: str = "rapid",
-    solvent: Optional[str] = None,
-    xtb_preopt: bool = False,
-    constraints: Optional[str] = None,
-    transition_state: bool = False,
-    frequencies: bool = False,
-    folder_uuid: Optional[str] = None,
-    blocking: bool = False,
-    ping_interval: int = 5
-) -> str:
-    """Calculate electronic spin states for molecular systems.
-    
-    This tool computes and compares different spin multiplicities for a molecule,
-    helping determine the ground state electronic configuration and relative energies
-    of different spin states. Essential for studying transition metals, radicals,
-    and systems with unpaired electrons.
-    
-    Args:
-        name: Name for the spin states calculation
-        molecule: SMILES string of the molecule (e.g., "[Mn+3]", "O=O")
-        states: List of spin multiplicities to calculate (e.g., [1, 3, 5] for singlet, triplet, quintet)
-                Can be provided as comma-separated string "1,3,5" or list [1, 3, 5]
-        mode: Calculation mode ("rapid", "careful", "meticulous", "auto", "reckless", "manual")
-        solvent: Solvent for implicit solvation (e.g., "water", "hexane", "acetonitrile")
-        xtb_preopt: Whether to perform xTB pre-optimization before DFT
-        constraints: Geometric constraints during optimization (advanced feature)
-        transition_state: Whether to optimize for transition state instead of minimum
-        frequencies: Whether to calculate vibrational frequencies
-        folder_uuid: Optional folder UUID to organize the calculation
-        blocking: Whether to wait for completion (default: False to avoid timeouts)
-        ping_interval: Interval in seconds to check calculation status
-        
-    Returns:
-        JSON string with workflow UUID and status (non-blocking) or full results (blocking)
-        
-    Examples:
-        # Manganese atom (stjames-public test example)
-        rowan_spin_states(
-            name="manganese_atom_stjames",
-            molecule="[Mn]",  # Neutral Mn atom
-            states=[2, 4, 6],  # doublet, quartet, sextet
-            mode="rapid",
-            xtb_preopt=True
-        )
-        
-        # Iron atom (stjames-public test example)
-        rowan_spin_states(
-            name="iron_atom_stjames",
-            molecule="[Fe]",  # Neutral Fe atom
-            states=[1, 3, 5],  # singlet, triplet, quintet
-            mode="careful",
-            frequencies=True,
-            xtb_preopt=True
-        )
-        
-        # Manganese hexachloride complex (corrected format)
-        rowan_spin_states(
-            name="mn_hexachloride",
-            molecule="[Cl-].[Cl-].[Cl-].[Cl-].[Cl-].[Cl-].[Mn+2]",
-            states=[2, 4, 6],
-            mode="rapid",
-            solvent="water"
-        )
-    """
-    
-    # Convert input to SMILES format (handles XYZ coordinates, molecular formulas, etc.)
-    original_input = molecule
-    molecule = convert_to_smiles(molecule)
-    
-    # Log the conversion if it happened
-    if molecule != original_input:
-        logger.info(f"Converted input '{original_input}' to SMILES: '{molecule}'")
-    
-    # Check for unsupported formats
-    if molecule.startswith("UNSUPPORTED_"):
-        error_response = {
-            "success": False,
-            "error": f"Unsupported molecular input format: {original_input}",
-            "explanation": {
-                "detected_format": "XYZ coordinates or complex molecular structure",
-                "supported_formats": [
-                    "SMILES strings: '[Mn]', '[Cl-].[Mn+2]'",
-                    "Simple formulas: 'Mn(Cl)6', 'Fe(Cl)6'",
-                    "Common names: 'water', 'methane'"
-                ]
-            },
-            "suggestion": "Please provide the molecule in SMILES format or a supported formula",
-            "name": name
-        }
-        return str(error_response)
-    
-    # First, validate that molecule is actually a molecule (SMILES) and not a PDB file
-    if molecule.lower().endswith('.pdb') or 'pdb' in molecule.lower():
-        error_response = {
-            "success": False,
-            "error": f"Invalid input: '{molecule}' appears to be a PDB file",
-            "correct_usage": {
-                "purpose": "Spin states calculation requires a SMILES molecule string, not a PDB file",
-                "explanation": "This tool calculates electronic spin states for individual molecules",
-                "what_you_provided": "PDB file (protein structure)",
-                "what_is_needed": "SMILES string representing a small molecule"
-            },
-            "examples": {
-                "transition_metals": {
-                    "manganese_atom": "[Mn] (neutral manganese atom)",
-                    "iron_atom": "[Fe] (neutral iron atom)", 
-                    "manganese_complex": "[Cl-].[Cl-].[Cl-].[Cl-].[Cl-].[Cl-].[Mn+2] (MnCl6 complex)"
-                },
-                "organic_molecules": {
-                    "water": "O",
-                    "methane": "C", 
-                    "benzene": "c1ccccc1",
-                    "radical": "c1ccc(cc1)[CH2] (benzyl radical)"
-                }
-            },
-            "stjames_test_examples": {
-                "manganese": "molecule='[Mn]', states=[2,4,6], mode='rapid'",
-                "iron": "molecule='[Fe]', states=[1,3,5], mode='careful'"
-            },
-            "suggestion": "Use a different Rowan tool for protein analysis, or provide a SMILES string for molecular spin states",
-            "name": name,
-            "invalid_input": molecule
-        }
-        return str(error_response)
-    
-    # Check if molecule looks like it needs charge/oxidation state specification
-    needs_charge_info = False
-    molecular_formula = None
-    
-    # Detect if molecule needs proper SMILES formatting
-    # Check for invalid SMILES patterns like [MnCl6]+4 or simple formulas like Mn(Cl)6
-    invalid_patterns = [
-        # Pattern like [MnCl6]+4 where charge is outside brackets
-        (']' in molecule and ('+' in molecule[molecule.rfind(']'):] or '-' in molecule[molecule.rfind(']'):])),
-        # Simple molecular formula without proper charge specification
-        (not any(char in molecule for char in ['[', ']', '+', '-']) and 
-         any(metal in molecule.upper() for metal in ['MN', 'FE', 'CO', 'NI', 'CU', 'CR', 'V', 'TI', 'PD'])),
-        # Invalid complex notation like [MnCl6] without proper ion separation
-        ('[' in molecule and ']' in molecule and 'Cl' in molecule.upper() and 
-         not ('.' in molecule and '[Cl-]' in molecule))
-    ]
-    
-    if any(invalid_patterns) and any(metal in molecule.upper() for metal in ['MN', 'FE', 'CO', 'NI', 'CU', 'CR', 'V', 'TI', 'PD']):
-        needs_charge_info = True
-        molecular_formula = molecule
-    
-    # Ensure we have states - provide intelligent defaults based on electron parity rules
-    if states is None:
-        # Auto-assign reasonable default states based on the molecule and electron count
-        if any(metal in molecule.upper() for metal in ['MN', 'FE', 'CO', 'NI', 'CU', 'CR', 'V', 'TI', 'PD']):
-            # For transition metals, assign states based on electron parity rules
-            # Even electrons (Fe=26, Ni=28, Cr=24, Ti=22, V=23, Zn=30) need ODD multiplicities
-            # Odd electrons (Mn=25, Co=27, Cu=29) need EVEN multiplicities
-            
-            if any(metal in molecule.upper() for metal in ['FE', 'NI', 'CR', 'TI', 'ZN', 'PD']):
-                # Even electron metals → odd multiplicities
-                states_list = [1, 3, 5]  # Singlet, triplet, quintet
-                logger.info(f"Auto-assigned odd multiplicities for even-electron metal: {states_list}")
-            elif any(metal in molecule.upper() for metal in ['MN', 'CO', 'CU', 'V']):
-                # Odd electron metals → even multiplicities  
-                states_list = [2, 4, 6]  # Doublet, quartet, sextet
-                logger.info(f"Auto-assigned even multiplicities for odd-electron metal: {states_list}")
-            else:
-                # Default fallback for other transition metals
-                states_list = [1, 3, 5]  # Conservative choice
-                logger.info(f"Auto-assigned default states for transition metal: {states_list}")
-        else:
-            # For organic molecules, use singlet/triplet (most have even electrons)
-            states_list = [1, 3]  # Singlet, triplet
-            logger.info(f"Auto-assigned default states for organic molecule: {states_list}")
-    
-    # Handle states input - convert to list of integers
-    if states is not None and isinstance(states, str):
-        # Handle special keywords
-        if states.lower() in ['all', 'comprehensive']:
-            states_list = [1, 2, 3, 4, 5, 6]  # All reasonable multiplicities
-        elif states.lower() in ['common', 'typical']:
-            states_list = [2, 4, 6]  # Common for transition metals
-        else:
-            try:
-                # Handle comma-separated string
-                states_list = [int(s.strip()) for s in states.split(',')]
-            except ValueError as e:
-                error_response = {
-                    "success": False,
-                    "error": f"Invalid states format: '{states}'. Expected comma-separated integers, list, or keywords.",
-                    "valid_formats": [
-                        "Comma-separated: '2,4,6' or '1,3,5'",
-                        "List: [2, 4, 6] or [1, 3, 5]", 
-                        "Keywords: 'all' or 'comprehensive' for [1,2,3,4,5,6]",
-                        "Keywords: 'common' or 'typical' for [2,4,6]"
-                    ],
-                    "name": name,
-                    "molecule": molecule
-                }
-                return str(error_response)
-    elif states is not None and isinstance(states, list):
-        try:
-            states_list = [int(s) for s in states]
-        except (ValueError, TypeError) as e:
-            error_response = {
-                "success": False,
-                "error": f"Invalid states list: {states}. All elements must be integers. Error: {e}",
-                "name": name,
-                "molecule": molecule
-            }
-            return str(error_response)
-    elif states is not None:
-        error_response = {
-            "success": False,
-            "error": f"Invalid states type: {type(states)}. Expected string or list.",
-            "name": name,
-            "molecule": molecule
-        }
-        return str(error_response)
-    
-    # Validate states list
-    if not states_list:
-        error_response = {
-            "success": False,
-            "error": "States list cannot be empty. Provide at least one spin multiplicity.",
-            "name": name,
-            "molecule": molecule
-        }
-        return str(error_response)
-    
-    # Validate states are positive
-    for state in states_list:
-        if state <= 0:
-            error_response = {
-                "success": False,
-                "error": f"Invalid spin multiplicity: {state}. Must be positive integer.",
-                "name": name,
-                "molecule": molecule
-            }
-            return str(error_response)
-    
-    # Validate electron parity: even electrons need odd multiplicities, odd electrons need even multiplicities
-    # This prevents impossible electronic configurations
-    try:
-        # Try to estimate electron count from SMILES (basic approach)
-        # For complex molecules, we'll let Rowan handle the detailed validation
-        # But we can catch obvious cases
-        
-        # Check if all states have the same parity (all odd or all even)
-        first_state_parity = states_list[0] % 2
-        mixed_parity = any((state % 2) != first_state_parity for state in states_list)
-        
-        if mixed_parity:
-            error_response = {
-                "success": False,
-                "error": f"Inconsistent spin state parities: {states_list}. All multiplicities must be either odd (1,3,5...) or even (2,4,6...).",
-                "explanation": {
-                    "electron_parity_rule": "Molecules with even electrons need odd multiplicities; molecules with odd electrons need even multiplicities",
-                    "your_states": states_list,
-                    "fix_suggestions": {
-                        "for_even_electrons": "Use odd multiplicities like [1,3,5]",
-                        "for_odd_electrons": "Use even multiplicities like [2,4,6]"
-                    }
-                },
-                "name": name,
-                "molecule": molecule
-            }
-            return str(error_response)
-    except Exception as e:
-        # If electron counting fails, let Rowan handle the validation
-        logger.warning(f"Could not validate electron parity: {e}")
-        pass
-    
-    # Validate mode
-    valid_modes = ["rapid", "careful", "meticulous", "auto", "reckless", "manual"]
-    if mode.lower() not in valid_modes:
-        error_response = {
-            "success": False,
-            "error": f"Invalid mode: {mode}. Valid modes: {valid_modes}",
-            "name": name,
-            "molecule": molecule
-        }
-        return str(error_response)
-    
-    # Create SpinStatesWorkflow instance to validate parameters (stjames pattern)
-    try:
-        spin_workflow = SpinStatesWorkflow(
-            initial_molecule=molecule,
-            states=states_list,
-            mode=mode,
-            solvent=solvent,
-            xtb_preopt=xtb_preopt,
-            constraints=constraints.split(',') if isinstance(constraints, str) else constraints,
-            transition_state=transition_state,
-            frequencies=frequencies
-        )
-        logger.info(f"SpinStatesWorkflow created: {spin_workflow}")
-    except ValueError as e:
-        error_response = {
-            "success": False,
-            "error": f"Invalid workflow parameters: {str(e)}",
-            "name": name,
-            "molecule": molecule,
-            "states": states_list,
-            "validation_error": str(e)
-        }
-        return str(error_response)
-    
-    logger.info(f"Starting spin states calculation: {name}")
-    logger.info(f"Molecule SMILES: {molecule}")
-    logger.info(f"Spin multiplicities: {states_list}")
-    logger.info(f"Mode: {mode}")
-    if solvent:
-        logger.info(f"Solvent: {solvent}")
-    if xtb_preopt:
-        logger.info("xTB pre-optimization: enabled")
-    if frequencies:
-        logger.info("Frequency calculation: enabled")
-    if transition_state:
-        logger.info("Transition state optimization: enabled")
-    
-    # For spin states, we need to provide an initial multiplicity
-    # Use the first state in the list as the starting multiplicity
-    initial_multiplicity = states_list[0]
-    
-    # CRITICAL FIX: Ensure initial_multiplicity follows electron parity rules
-    # Rowan uses initial_multiplicity as the starting point, so it must be valid
-    logger.info(f"Using initial_multiplicity = {initial_multiplicity} for states {states_list}")
-    
-    # Prepare workflow parameters - rowan.compute() wants core params separate from workflow_data
-    workflow_params = {
-        # Core rowan.compute() parameters
-        "molecule": molecule,  # SMILES string
-        "workflow_type": "spin_states",
-        "name": name,
-        "blocking": blocking,
-        "ping_interval": ping_interval,
-        
-        # CRITICAL: Try multiple parameter names for initial multiplicity
-        "multiplicity": initial_multiplicity,  # Most likely parameter name
-        "initial_multiplicity": initial_multiplicity,  # Alternative name
-        "starting_multiplicity": initial_multiplicity,  # Another alternative
-        "states": states_list,  # List of spin multiplicities to calculate
-        "mode": mode.lower(),  # Calculation mode
-    }
-    
-    # Add optional parameters only if provided
-    if folder_uuid:
-        workflow_params["folder_uuid"] = folder_uuid
-    if solvent:
-        workflow_params["solvent"] = solvent
-    if xtb_preopt:
-        workflow_params["xtb_preopt"] = xtb_preopt
-    if transition_state:
-        workflow_params["transition_state"] = transition_state
-    if frequencies:
-        workflow_params["frequencies"] = frequencies
-    
-    # Only add constraints if provided and ensure it's a list
-    if constraints is not None:
-        if isinstance(constraints, str):
-            # Convert string to list (basic parsing)
-            workflow_params["constraints"] = [constraints]
-        elif isinstance(constraints, list):
-            workflow_params["constraints"] = constraints
-        else:
-            workflow_params["constraints"] = [str(constraints)]
-    
-    logger.info("Submitting spin states calculation to Rowan")
-    
-    try:
-        # CRITICAL FIX: Create Molecule object with correct multiplicity instead of string
-        # This ensures Rowan uses the right starting multiplicity
-        try:
-            from stjames.molecule import Molecule as SjamesMolecule
-            from rdkit import Chem
-            
-            # Create molecule with proper multiplicity by constructing atoms directly
-            # Parse SMILES to get atomic numbers and coordinates
-            rdkit_mol = Chem.MolFromSmiles(molecule)
-            if rdkit_mol is None:
-                raise ValueError(f"Invalid SMILES: {molecule}")
-            
-            # Get atoms from RDKit molecule and generate realistic 3D coordinates
-            atoms = []
-            from stjames.molecule import Atom
-            
-            # Generate realistic 3D coordinates using specialized coordination chemistry approach
-            coords_3d = _generate_3d_coordinates_for_coordination_complex(molecule, rdkit_mol)
-            
-            for i, atom in enumerate(rdkit_mol.GetAtoms()):
-                # Create Atom objects with atomic number and realistic 3D positions
-                atoms.append(Atom(
-                    atomic_number=atom.GetAtomicNum(), 
-                    position=coords_3d[i]
-                ))
-            
-            # Calculate total charge from SMILES string
-            total_charge = _calculate_molecular_charge(molecule)
-            
-            logger.info(f"Calculated molecular charge: {total_charge} (from SMILES: {molecule})")
-            
-            # Create Molecule object directly with correct multiplicity and charge
-            molecule_obj = SjamesMolecule(
-                atoms=atoms,
-                charge=total_charge,  # Calculate proper charge from SMILES
-                multiplicity=initial_multiplicity,  # This is the key fix!
-                smiles=molecule  # Keep original SMILES
-            )
-            workflow_params["molecule"] = molecule_obj
-            logger.info(f"Created stjames.Molecule object with multiplicity={initial_multiplicity}")
-        except (ImportError, Exception) as e:
-            # If stjames not available, use string but log the limitation
-            logger.warning(f"stjames.molecule.Molecule creation failed: {e}")
-            logger.warning(f"Rowan may default to multiplicity=1 instead of {initial_multiplicity}")
-        
-        # Submit spin states calculation to Rowan
-        result = rowan.compute(**workflow_params)
-        
-        # Format the response based on blocking mode
-        if result:
-            workflow_uuid = result.get("uuid")
-            status = result.get("object_status", 0)
-            
-            if blocking and status == 2:  # Completed
-                # Extract spin states results for completed blocking calls
-                object_data = result.get("object_data", {})
-                if "spin_states" in object_data:
-                    spin_states_data = object_data["spin_states"]
-                    
-                    # Find ground state (lowest energy)
-                    ground_state = None
-                    min_energy = float('inf')
-                    for state_data in spin_states_data:
-                        energy = state_data.get("energy", float('inf'))
-                        if energy < min_energy:
-                            min_energy = energy
-                            ground_state = state_data.get("multiplicity")
-                    
-                    response = {
-                        "success": True,
-                        "workflow_uuid": workflow_uuid,
-                        "name": name,
-                        "molecule": molecule,
-                        "status": "completed",
-                        "spin_states_results": {
-                            "ground_state_multiplicity": ground_state,
-                            "ground_state_energy": min_energy,
-                            "states_calculated": len(spin_states_data),
-                            "spin_states": spin_states_data
-                        },
-                        "calculation_details": {
-                            "mode": mode,
-                            "solvent": solvent,
-                            "xtb_preopt": xtb_preopt,
-                            "frequencies_calculated": frequencies,
-                            "transition_state": transition_state
-                        },
-                        "runtime_seconds": result.get("elapsed", 0),
-                        "credits_charged": result.get("credits_charged", 0)
-                    }
-                else:
-                    response = {
-                        "success": True,
-                        "workflow_uuid": workflow_uuid,
-                        "name": name,
-                        "molecule": molecule,
-                        "status": "completed", 
-                        "message": "Spin states calculation completed successfully",
-                        "runtime_seconds": result.get("elapsed", 0),
-                        "credits_charged": result.get("credits_charged", 0)
-                    }
-            else:
-                # Non-blocking or still running - return workflow info for tracking
-                status_text = {0: "queued", 1: "running", 2: "completed", 3: "failed"}.get(status, "unknown")
-                response = {
-                    "success": True,
-                    "tracking_id": workflow_uuid,  # Prominent tracking ID
-                    "workflow_uuid": workflow_uuid,  # Keep for backward compatibility
-                    "name": name,
-                    "molecule": molecule,
-                    "status": status_text,
-                    "message": f"Spin states calculation submitted successfully! Use tracking_id to monitor progress.",
-                    "calculation_details": {
-                        "spin_multiplicities": states_list,
-                        "mode": mode,
-                        "solvent": solvent,
-                        "xtb_preopt": xtb_preopt,
-                        "frequencies": frequencies,
-                        "transition_state": transition_state,
-                        "blocking_mode": blocking
-                    },
-                    "progress_tracking": {
-                        "tracking_id": workflow_uuid,
-                        "check_status": f"rowan_workflow_management(action='status', workflow_uuid='{workflow_uuid}')",
-                        "get_results": f"rowan_workflow_management(action='retrieve', workflow_uuid='{workflow_uuid}')"
-                    }
-                }
-        else:
-            response = {
-                "success": False,
-                "error": "No response received from Rowan API",
-                "name": name,
-                "molecule": molecule,
-                "states": states_list
-            }
-            
-        return str(response)
-        
-    except Exception as e:
-        error_response = {
-            "success": False,
-            "error": f"Spin states calculation failed: {str(e)}",
-            "name": name,
-            "molecule": molecule,
-            "states": states_list
-        }
-        logger.error(f"Spin states calculation failed: {str(e)}")
-        return str(error_response)
-