@datagrok/bio 2.25.1 → 2.25.2

package/scripts/mol-to-helm.py

@@ -0,0 +1,1279 @@
+#language: python
+#name: molToHelmConverterPy
+#description: Converts molecules to HELM notation based on monomer library
+#input: dataframe moleculesDataframe
+#input: column moleculesColumn {semType: Molecule}
+#input: string libraryJSON
+#output: dataframe result_helm {action:join(moleculesDataframe)} [Sequences, in HELM format]
+molListToProcess = moleculesDataframe[moleculesColumn].tolist()
+import pandas as pd
+import numpy as np
+"""
+Aggregated file combining all modules from the logics folder.
+Generated automatically - do not edit manually.
+"""
+
+# External library imports
+from collections import defaultdict
+from enum import Enum
+from itertools import combinations
+from rdkit import Chem
+from rdkit import RDLogger
+from typing import Dict
+from typing import List
+from typing import Optional
+from typing import Tuple
+import json
+import os
+
+# ============================================================================
+# Content from: fragment_graph.py
+# ============================================================================
+
+from rdkit import Chem
+from typing import Optional, List, Dict, Tuple
+from enum import Enum
+
+
+class LinkageType(Enum):
+    """Types of linkages between fragments"""
+    PEPTIDE = "peptide"
+    DISULFIDE = "disulfide"
+    ESTER = "ester"
+    ETHER = "ether"
+    THIOETHER = "thioether"
+    UNKNOWN = "unknown"
+
+
+class FragmentNode:
+    """Represents a single molecular fragment (amino acid/monomer)"""
+    
+    def __init__(self, fragment_id: int, mol: Chem.Mol):
+        self.id = fragment_id
+        self.mol = mol  # RDKit molecule object
+        self.smiles = Chem.MolToSmiles(mol, canonical=True) if mol else ""
+        self.monomer = None  # Will be filled by matcher - MonomerData object
+        self.is_c_terminal = False
+        self.is_n_terminal = False
+    
+    def __repr__(self):
+        monomer_name = self.monomer.symbol if self.monomer else "Unknown"
+        return f"FragmentNode(id={self.id}, monomer={monomer_name}, smiles={self.smiles[:20]}...)"
+
+
+class FragmentLink:
+    """Represents a connection between two fragments"""
+    
+    def __init__(
+        self, 
+        from_node_id: int, 
+        to_node_id: int,
+        linkage_type: LinkageType,
+        from_atom_idx: Optional[int] = None,
+        to_atom_idx: Optional[int] = None
+    ):
+        self.from_node_id = from_node_id
+        self.to_node_id = to_node_id
+        self.linkage_type = linkage_type
+        self.from_atom_idx = from_atom_idx  # Atom index in from_node's molecule
+        self.to_atom_idx = to_atom_idx      # Atom index in to_node's molecule
+    
+    def __repr__(self):
+        return f"FragmentLink({self.from_node_id} --{self.linkage_type.value}--> {self.to_node_id})"
+
+
+class FragmentGraph:
+    """
+    Graph structure representing a molecule as fragments and their connections.
+    
+    Supports:
+    - Linear peptides (chain of peptide bonds)
+    - Cyclic peptides (peptide bond from last to first)
+    - Disulfide bridges (additional S-S links)
+    - Branched structures (multiple links per fragment)
+    """
+    
+    def __init__(self):
+        self.nodes: Dict[int, FragmentNode] = {}  # node_id -> FragmentNode
+        self.links: List[FragmentLink] = []
+    
+    def add_node(self, node: FragmentNode) -> int:
+        """Add a fragment node to the graph"""
+        self.nodes[node.id] = node
+        return node.id
+    
+    def add_link(self, link: FragmentLink):
+        """Add a linkage between two nodes"""
+        if link.from_node_id not in self.nodes or link.to_node_id not in self.nodes:
+            raise ValueError(f"Cannot add link: nodes {link.from_node_id} or {link.to_node_id} not in graph")
+        self.links.append(link)
+    
+    def get_node(self, node_id: int) -> Optional[FragmentNode]:
+        """Get a node by ID"""
+        return self.nodes.get(node_id)
+    
+    def get_neighbors(self, node_id: int) -> List[Tuple[int, LinkageType]]:
+        """Get all neighbors of a node with their linkage types"""
+        neighbors = []
+        for link in self.links:
+            if link.from_node_id == node_id:
+                neighbors.append((link.to_node_id, link.linkage_type))
+            elif link.to_node_id == node_id:
+                neighbors.append((link.from_node_id, link.linkage_type))
+        return neighbors
+    
+    def get_ordered_nodes(self) -> List[FragmentNode]:
+        """
+        Get nodes in sequential order (for linear/cyclic peptides).
+        For branched structures, returns a depth-first traversal.
+        """
+        if not self.nodes:
+            return []
+        
+        # Find starting node (N-terminal for peptides)
+        start_node_id = None
+        for node_id, node in self.nodes.items():
+            if node.is_n_terminal:
+                start_node_id = node_id
+                break
+        
+        # If no N-terminal found, use first node
+        if start_node_id is None:
+            start_node_id = min(self.nodes.keys())
+        
+        # Traverse the graph
+        ordered = []
+        visited = set()
+        self._traverse_from_node(start_node_id, visited, ordered)
+        
+        return ordered
+    
+    def _traverse_from_node(self, node_id: int, visited: set, ordered: list):
+        """Helper for depth-first traversal"""
+        if node_id in visited:
+            return
+        
+        visited.add(node_id)
+        ordered.append(self.nodes[node_id])
+        
+        # Get peptide bond neighbors first (to maintain chain order)
+        peptide_neighbors = []
+        other_neighbors = []
+        
+        for link in self.links:
+            if link.from_node_id == node_id and link.to_node_id not in visited:
+                if link.linkage_type == LinkageType.PEPTIDE:
+                    peptide_neighbors.append(link.to_node_id)
+                else:
+                    other_neighbors.append(link.to_node_id)
+        
+        # Visit peptide bonds first, then others
+        for neighbor_id in peptide_neighbors + other_neighbors:
+            self._traverse_from_node(neighbor_id, visited, ordered)
+    
+    def get_fragment_sequence(self) -> List[str]:
+        """Get sequence of monomer symbols (for matched fragments)"""
+        ordered_nodes = self.get_ordered_nodes()
+        return [
+            node.monomer.symbol if node.monomer else f"X{node.id}"
+            for node in ordered_nodes
+        ]
+    
+    def __len__(self):
+        return len(self.nodes)
+    
+    def __repr__(self):
+        return f"FragmentGraph(nodes={len(self.nodes)}, links={len(self.links)})"
+    
+    def to_dict(self) -> dict:
+        """Convert graph to dictionary for serialization"""
+        return {
+            "nodes": [
+                {
+                    "id": node.id,
+                    "smiles": node.smiles,
+                    "monomer": node.monomer.symbol if node.monomer else None,
+                    "is_n_terminal": node.is_n_terminal,
+                    "is_c_terminal": node.is_c_terminal
+                }
+                for node in self.nodes.values()
+            ],
+            "links": [
+                {
+                    "from": link.from_node_id,
+                    "to": link.to_node_id,
+                    "type": link.linkage_type.value,
+                    "from_atom": link.from_atom_idx,
+                    "to_atom": link.to_atom_idx
+                }
+                for link in self.links
+            ]
+        }
+
+# ============================================================================
+# Content from: fragment_processor.py
+# ============================================================================
+
+from rdkit import Chem
+
+
+class BondDetector:
+    #GENERALIZATION ITEM: BOND PATTERNS SHOULD BE DERIVED FROM LIBRARY
+    def __init__(self):
+        # True peptide bond: C and N both in backbone (each bonded to carbons)
+        # Alpha carbons can be sp3 (X4) or sp2 (X3) for dehydroamino acids
+        self.peptide_bond = Chem.MolFromSmarts('[C;X3,X4]-[C;X3](=[O;X1])-[N;X3]-[C;X3,X4]')
+        # True disulfide bond: S-S where each S is bonded to carbon (cysteine residues)
+        self.disulfide_bond = Chem.MolFromSmarts('[C;X4]-[S;X2]-[S;X2]-[C;X4]')
+        # Primary amine at N-terminus (can be NH2 or NH3+), alpha-C can be sp3 or sp2
+        self.primary_amine = Chem.MolFromSmarts('[N;H2,H3;X3,X4]-[C;X3,X4]')
+
+    def find_cleavable_bonds(self, mol: Chem.Mol):
+        """
+        Find all cleavable bonds in the molecule.
+        
+        Returns:
+            List of tuples: (atom1_idx, atom2_idx, LinkageType)
+        """
+        try:
+            all_bonds = []
+
+            # Find peptide bonds
+            peptide_bonds = self._find_peptide_bonds(mol)
+            all_bonds.extend([(bond[0], bond[1], LinkageType.PEPTIDE) for bond in peptide_bonds])
+            
+            # Find disulfide bonds
+            disulfide_bonds = self._find_disulfide_bonds(mol)
+            all_bonds.extend([(bond[0], bond[1], LinkageType.DISULFIDE) for bond in disulfide_bonds])
+
+            # Order peptide bonds from N to C (keep disulfide bonds unordered)
+            peptide_only = [(b[0], b[1]) for b in all_bonds if b[2] == LinkageType.PEPTIDE]
+            ordered_peptide = self._order_bonds_from_n_to_c(mol, peptide_only)
+            
+            # Rebuild with types
+            ordered_bonds = [(b[0], b[1], LinkageType.PEPTIDE) for b in ordered_peptide]
+            ordered_bonds.extend([b for b in all_bonds if b[2] != LinkageType.PEPTIDE])
+
+            return ordered_bonds
+
+        except Exception:
+            return []
+
+    def _find_peptide_bonds(self, mol: Chem.Mol):
+        bonds = []
+        try:
+            matches = mol.GetSubstructMatches(self.peptide_bond)
+            for match in matches:
+                if len(match) >= 5:
+                    # Pattern: [C;X3,X4]-[C;X3](=[O;X1])-[N;X3]-[C;X3,X4]
+                    # match[0]=alpha-C (sp2 or sp3), match[1]=carbonyl-C, match[2]=O, match[3]=N, match[4]=next-alpha-C (sp2 or sp3)
+                    c_atom = match[1]  # Carbonyl carbon
+                    n_atom = match[3]  # Nitrogen
+                    bonds.append((c_atom, n_atom))
+        except Exception:
+            pass
+        return bonds
+    
+    def _find_disulfide_bonds(self, mol: Chem.Mol):
+        """Find disulfide bonds (S-S linkages)"""
+        bonds = []
+        try:
+            matches = mol.GetSubstructMatches(self.disulfide_bond)
+            for match in matches:
+                if len(match) >= 4:
+                    # Pattern: [C;X4]-[S;X2]-[S;X2]-[C;X4]
+                    # match[0]=C, match[1]=S, match[2]=S, match[3]=C
+                    s1_atom = match[1]  # First sulfur
+                    s2_atom = match[2]  # Second sulfur
+                    bonds.append((s1_atom, s2_atom))
+        except Exception:
+            pass
+        return bonds
+
+    def _order_bonds_from_n_to_c(self, mol: Chem.Mol, bonds):
+        if not bonds:
+            return bonds
+
+        n_terminal = self._find_n_terminal(mol)
+        if n_terminal is None:
+            return bonds
+
+        ordered = []
+        visited = set()
+        current = n_terminal
+
+        while current is not None and len(ordered) < len(bonds):
+            next_bond = None
+            for bond in bonds:
+                if bond not in visited and bond[1] == current:
+                    next_bond = bond
+                    break
+
+            if next_bond is None:
+                break
+
+            ordered.append(next_bond)
+            visited.add(next_bond)
+            current = next_bond[0]
+
+        for bond in bonds:
+            if bond not in visited:
+                ordered.append(bond)
+
+        return ordered
+
+    def _find_n_terminal(self, mol: Chem.Mol):
+        try:
+            matches = mol.GetSubstructMatches(self.primary_amine)
+            if matches:
+                return matches[0][0]
+
+            max_h = -1
+            n_term = None
+            for atom in mol.GetAtoms():
+                if atom.GetAtomicNum() == 7:
+                    h_count = atom.GetTotalNumHs()
+                    if h_count > max_h:
+                        max_h = h_count
+                        n_term = atom.GetIdx()
+            return n_term
+
+        except Exception:
+            return None
+
+
+class FragmentProcessor:
+    def __init__(self, monomer_library):
+        self.monomer_library = monomer_library
+        self.bond_detector = BondDetector()
+
+    def process_molecule(self, mol: Chem.Mol) -> FragmentGraph:
+        """
+        Process a molecule into a fragment graph.
+        
+        Args:
+            mol: RDKit molecule object
+        
+        Returns:
+            FragmentGraph object containing fragments and their connections
+        """
+        graph = FragmentGraph()
+        # Store original molecule for fragment recovery
+        graph.original_mol = mol
+        
+        try:
+            bonds_to_cleave = self.bond_detector.find_cleavable_bonds(mol)
+
+            if not bonds_to_cleave:
+                # Single fragment (no cleavable bonds)
+                node = FragmentNode(0, mol)
+                node.is_n_terminal = True
+                node.is_c_terminal = True
+                graph.add_node(node)
+                return graph
+
+            # Extract bond info for fragmentation
+            bond_indices = []
+            bond_info = []  # (bond_idx, atom1, atom2, linkage_type)
+            seen_bonds = set()  # Track which bonds we've already added
+            
+            for atom1, atom2, linkage_type in bonds_to_cleave:
+                bond = mol.GetBondBetweenAtoms(atom1, atom2)
+                if bond:
+                    bond_idx = bond.GetIdx()
+                    if bond_idx not in seen_bonds:
+                        bond_indices.append(bond_idx)
+                        bond_info.append((bond_idx, atom1, atom2, linkage_type))
+                        seen_bonds.add(bond_idx)
+                    # Skip duplicate bonds silently
+                # Skip invalid bonds silently
+
+            if not bond_indices:
+                # No valid bonds found
+                node = FragmentNode(0, mol)
+                node.is_n_terminal = True
+                node.is_c_terminal = True
+                graph.add_node(node)
+                return graph
+
+            # Fragment the molecule
+            fragmented_mol = Chem.FragmentOnBonds(mol, bond_indices, addDummies=True)
+            
+            # Get fragments AND their atom mappings separately
+            fragments_tuple = Chem.GetMolFrags(
+                fragmented_mol, 
+                asMols=True, 
+                sanitizeFrags=True
+            )
+            fragments = list(fragments_tuple)
+            
+            # Store bond cleavage info for recovery - we'll use this to selectively re-fragment
+            graph.cleaved_bond_indices = bond_indices
+            graph.bond_info = bond_info
+            print(f"DEBUG: Created {len(fragments)} fragments, cleaved {len(bond_indices)} bonds")
+
+            # Create nodes for each fragment
+            fragment_nodes = []
+            for i, frag in enumerate(fragments):
+                clean_frag = self._clean_fragment(frag)
+                if clean_frag and clean_frag.GetNumAtoms() >= 3:
+                    is_c_terminal = (i == len(fragments) - 1)
+                    is_n_terminal = (i == 0)
+                    # No normalization! Use fragment as-is
+                    node = FragmentNode(i, clean_frag)
+                    node.is_c_terminal = is_c_terminal
+                    node.is_n_terminal = is_n_terminal
+                    graph.add_node(node)
+                    fragment_nodes.append((i, node))
+
+            # Create links between fragments based on cleaved bonds
+            # For sequential peptide bonds
+            peptide_links = [b for b in bond_info if b[3] == LinkageType.PEPTIDE]
+            for i in range(len(fragment_nodes) - 1):
+                from_id, _ = fragment_nodes[i]
+                to_id, _ = fragment_nodes[i + 1]
+                link = FragmentLink(from_id, to_id, LinkageType.PEPTIDE)
+                graph.add_link(link)
+            
+            # Add disulfide bridges (if any)
+            # TODO: Track which fragments contain the S atoms for proper linking
+            disulfide_links = [b for b in bond_info if b[3] == LinkageType.DISULFIDE]
+            # For now, disulfide bonds require more complex atom tracking
+            # This is a placeholder for future enhancement
+
+            return graph
+
+        except Exception as e:
+            # Fallback: single node with original molecule
+            node = FragmentNode(0, mol)
+            node.is_n_terminal = True
+            node.is_c_terminal = True
+            graph.add_node(node)
+            return graph
+
+    def _clean_fragment(self, mol: Chem.Mol):
+        try:
+            mol_copy = Chem.Mol(mol)
+            atoms_to_remove = []
+
+            for atom in mol_copy.GetAtoms():
+                if atom.GetAtomicNum() == 0:
+                    atoms_to_remove.append(atom.GetIdx())
+
+            atoms_to_remove.sort(reverse=True)
+            if atoms_to_remove:
+                emol = Chem.EditableMol(mol_copy)
+                for atom_idx in atoms_to_remove:
+                    emol.RemoveAtom(atom_idx)
+                return emol.GetMol()
+
+            return mol_copy
+
+        except Exception:
+            return None
+
+    def _reconstruct_fragment(self, node_ids: list, graph: FragmentGraph) -> Chem.Mol:
+        """
+        Reconstruct a molecule by combining multiple fragment nodes.
+        Re-fragments the original molecule, excluding bonds between the nodes to merge.
+        """
+        if not node_ids or not hasattr(graph, 'original_mol') or not hasattr(graph, 'cleaved_bond_indices'):
+            return None
+        
+        try:
+            # Sort node IDs to ensure consistent ordering
+            sorted_nodes = sorted(node_ids)
+            
+            # Identify which bonds to exclude (bonds between consecutive merged nodes)
+            bonds_to_exclude = set()
+            for i in range(len(sorted_nodes) - 1):
+                # We want to keep the bond between node i and node i+1
+                # This bond would be at position sorted_nodes[i] in the cleaved_bond_indices
+                if sorted_nodes[i] + 1 == sorted_nodes[i + 1]:
+                    # Consecutive nodes - exclude the bond between them
+                    if sorted_nodes[i] < len(graph.cleaved_bond_indices):
+                        bonds_to_exclude.add(sorted_nodes[i])
+            
+            # Create new bond list excluding the bonds we want to keep
+            new_bond_indices = [
+                bond_idx for i, bond_idx in enumerate(graph.cleaved_bond_indices)
+                if i not in bonds_to_exclude
+            ]
+            
+            print(f"DEBUG reconstruct: Original had {len(graph.cleaved_bond_indices)} cleaved bonds, "
+                  f"excluding {len(bonds_to_exclude)} bonds, new list has {len(new_bond_indices)} bonds")
+            
+            # Re-fragment with the modified bond list
+            if not new_bond_indices:
+                # No bonds to cleave - return whole molecule
+                return graph.original_mol
+            
+            fragmented_mol = Chem.FragmentOnBonds(graph.original_mol, new_bond_indices, addDummies=True)
+            fragments_tuple = Chem.GetMolFrags(fragmented_mol, asMols=True, sanitizeFrags=True)
+            fragments = list(fragments_tuple)
+            
+            # Find which fragment corresponds to our merged nodes
+            # The merged nodes should be at the position of the first node ID in sorted order
+            target_idx = sorted_nodes[0]
+            
+            # Account for excluded bonds shifting fragment indices
+            adjusted_idx = target_idx - sum(1 for excluded_idx in bonds_to_exclude if excluded_idx < target_idx)
+            
+            print(f"DEBUG reconstruct: Got {len(fragments)} fragments after re-fragmentation, "
+                  f"target_idx={target_idx}, adjusted_idx={adjusted_idx}")
+            
+            if adjusted_idx < len(fragments):
+                clean_frag = self._clean_fragment(fragments[adjusted_idx])
+                return clean_frag if clean_frag else fragments[adjusted_idx]
+            
+            return None
+        
+        except Exception as e:
+            print(f"DEBUG reconstruct: Exception: {e}")
+            return None
+
+    def _merge_nodes_in_graph(self, graph: FragmentGraph, nodes_to_merge: list, 
+                              new_node: FragmentNode) -> None:
+        """
+        Remove old nodes, add new merged node, update all links.
+        Preserves terminal flags from edge nodes.
+        """
+        if not nodes_to_merge:
+            return
+        
+        # Sort node IDs to identify edge nodes
+        sorted_nodes = sorted(nodes_to_merge)
+        leftmost = sorted_nodes[0]
+        rightmost = sorted_nodes[-1]
+        
+        # Preserve terminal flags
+        if leftmost in graph.nodes:
+            new_node.is_n_terminal = graph.nodes[leftmost].is_n_terminal
+        if rightmost in graph.nodes:
+            new_node.is_c_terminal = graph.nodes[rightmost].is_c_terminal
+        
+        # Update links: replace references to merged nodes
+        updated_links = []
+        nodes_to_merge_set = set(nodes_to_merge)
+        
+        for link in graph.links:
+            from_in = link.from_node_id in nodes_to_merge_set
+            to_in = link.to_node_id in nodes_to_merge_set
+            
+            # Skip internal links between merged nodes
+            if from_in and to_in:
+                continue
+            
+            # Update link if one end is being merged
+            new_from = new_node.id if from_in else link.from_node_id
+            new_to = new_node.id if to_in else link.to_node_id
+            
+            updated_links.append(FragmentLink(new_from, new_to, link.linkage_type))
+        
+        # Remove old nodes
+        for node_id in nodes_to_merge:
+            if node_id in graph.nodes:
+                del graph.nodes[node_id]
+        
+        # Add new node and update links
+        graph.add_node(new_node)
+        graph.links = updated_links
+
+    def recover_unmatched_fragments(self, graph: FragmentGraph, matcher) -> bool:
+        """
+        Try to recover unmatched fragments by merging with neighbors.
+        Returns True if any merges were successful.
+        """
+        # Identify unmatched nodes
+        unmatched_nodes = []
+        for node_id, node in graph.nodes.items():
+            if node.monomer and node.monomer.symbol.startswith("X"):
+                unmatched_nodes.append(node_id)
+        
+        if not unmatched_nodes:
+            return False
+        
+        print(f"DEBUG: Found {len(unmatched_nodes)} unmatched nodes: {unmatched_nodes}")
+        
+        had_changes = False
+        
+        # Try to recover each unmatched node
+        for node_id in unmatched_nodes:
+            # Check if node still exists (might have been merged already)
+            if node_id not in graph.nodes:
+                continue
+            
+            # Get neighbors
+            neighbors = graph.get_neighbors(node_id)
+            neighbor_ids = [n[0] for n in neighbors]
+            
+            if not neighbor_ids:
+                continue
+            
+            # Separate left and right neighbors (assuming sequential order)
+            left_neighbors = [n for n in neighbor_ids if n < node_id]
+            right_neighbors = [n for n in neighbor_ids if n > node_id]
+            
+            # Try merge combinations: left only, right only, both
+            merge_attempts = []
+            
+            if left_neighbors:
+                merge_attempts.append([left_neighbors[0], node_id])
+            if right_neighbors:
+                merge_attempts.append([node_id, right_neighbors[0]])
+            if left_neighbors and right_neighbors:
+                merge_attempts.append([left_neighbors[0], node_id, right_neighbors[0]])
+            
+            # Try each merge combination
+            for nodes_to_merge in merge_attempts:
+                print(f"DEBUG: Trying to merge nodes {nodes_to_merge}")
+                
+                # Reconstruct combined molecule
+                combined_mol = self._reconstruct_fragment(nodes_to_merge, graph)
+                if not combined_mol:
+                    print(f"DEBUG: Failed to reconstruct molecule for {nodes_to_merge}")
+                    continue
+                
+                print(f"DEBUG: Reconstructed mol with {combined_mol.GetNumAtoms()} atoms")
+                
+                # Count expected connections for this merged fragment
+                # Get all unique neighbors of the merged set
+                all_neighbors = set()
+                for nid in nodes_to_merge:
+                    if nid in graph.nodes:
+                        node_neighbors = graph.get_neighbors(nid)
+                        for neighbor_id, _ in node_neighbors:
+                            if neighbor_id not in nodes_to_merge:
+                                all_neighbors.add(neighbor_id)
+                
+                num_connections = len(all_neighbors)
+                print(f"DEBUG: Expecting {num_connections} connections")
+                
+                # Try to match the combined fragment
+                monomer = matcher.find_exact_match(combined_mol, num_connections)
+                
+                if monomer:
+                    print(f"DEBUG: SUCCESS! Matched to {monomer.symbol}")
+                    # Success! Create new merged node
+                    new_node_id = min(nodes_to_merge)  # Use lowest ID
+                    new_node = FragmentNode(new_node_id, combined_mol)
+                    new_node.monomer = monomer
+                    
+                    # Merge nodes in graph
+                    self._merge_nodes_in_graph(graph, nodes_to_merge, new_node)
+                    
+                    had_changes = True
+                    break  # Stop trying other combinations for this node
+                else:
+                    print(f"DEBUG: No match found for merge {nodes_to_merge}")
+        
+        return had_changes
+
+# ============================================================================
+# Content from: helm_generator.py
+# ============================================================================
+
+class HELMGenerator:
+    """
+    Generates HELM notation from fragment graphs or monomer lists.
+    
+    Supports:
+    - Linear peptides
+    - Cyclic peptides
+    - Disulfide bridges
+    - Custom linkages
+    """
+    
+    def __init__(self):
+        #GENERALIZATION ITEM: POLYMER TYPES SHOULD BE DERIVED FROM LIBRARY
+        self.polymer_types = {
+            "peptide": "PEPTIDE",
+            "rna": "RNA",
+            "dna": "DNA",
+            "chemical": "CHEM"
+        }
+
+    def generate_helm_from_graph(self, graph: FragmentGraph) -> str:
+        """
+        Generate HELM notation from a FragmentGraph.
+        
+        Args:
+            graph: FragmentGraph containing matched monomers and their connections
+        
+        Returns:
+            HELM notation string
+        """
+        if len(graph) == 0:
+            return ""
+        
+        # Get ordered sequence of monomers
+        ordered_nodes = graph.get_ordered_nodes()
+        sequence_symbols = [node.monomer.symbol if node.monomer else "X" for node in ordered_nodes]
+        
+        # Generate linear peptide notation
+        sequence = ".".join(sequence_symbols)
+        
+        # Check for disulfide bridges or other non-peptide bonds
+        has_special_bonds = any(
+            link.linkage_type != LinkageType.PEPTIDE 
+            for link in graph.links
+        )
+        
+        if has_special_bonds:
+            # Add connection notation for disulfide bridges
+            connections = []
+            for link in graph.links:
+                if link.linkage_type == LinkageType.DISULFIDE:
+                    # Format: PEPTIDE1,PEPTIDE1,from_idx:R3-to_idx:R3
+                    connections.append(
+                        f"PEPTIDE1,PEPTIDE1,{link.from_node_id + 1}:R3-{link.to_node_id + 1}:R3"
+                    )
+            
+            if connections:
+                connection_str = "|".join(connections)
+                helm = f"PEPTIDE1{{{sequence}}}${connection_str}$$$V2.0"
+            else:
+                helm = f"PEPTIDE1{{{sequence}}}$$$$"
+        else:
+            helm = f"PEPTIDE1{{{sequence}}}$$$$"
+        
+        return helm
+
+    def generate_helm_notation(self, monomers) -> str:
+        """
+        Legacy method: Generate HELM notation from a list of monomers.
+        Kept for backward compatibility.
+        
+        Args:
+            monomers: List of MonomerData objects
+        
+        Returns:
+            HELM notation string
+        """
+        if not monomers:
+            return ""
+
+        sequence = ".".join([monomer.symbol for monomer in monomers])
+        helm = f"PEPTIDE1{{{sequence}}}$$$$"
+
+        return helm
+
+# ============================================================================
+# Content from: monomer_library.py
+# ============================================================================
+
+from rdkit import Chem
+from rdkit import RDLogger
+from collections import defaultdict
+from itertools import combinations
+import json
+import os
+
+# Suppress RDKit warnings
+RDLogger.DisableLog('rdApp.warning')
+
+class MonomerData:
+    def __init__(self):
+        self.symbol = ""
+        self.name = ""
+        self.mol = None
+        self.smiles = ""  # Original SMILES with R-groups
+        self.r_groups = {}  # R-group label -> cap SMILES
+        self.r_group_count = 0
+        self.capped_smiles_cache = {}  # Cache: frozenset of removed R-groups -> canonical SMILES
+
+    def __repr__(self):
+        return f"Monomer({self.symbol}: {self.name}, R-groups: {self.r_group_count})"
+    
+    def get_capped_smiles_for_removed_rgroups(self, removed_rgroups: frozenset) -> str:
+        """
+        Get canonical SMILES with specific R-groups removed (lazy generation with caching).
+        
+        Args:
+            removed_rgroups: frozenset of R-group labels that were removed (e.g., {'R1', 'R2'})
+        
+        Returns:
+            Canonical SMILES with those R-groups removed, or empty string on error
+            
+        Example:
+            For monomer with R1, R2:
+            - get_capped_smiles_for_removed_rgroups({'R1'}) → SMILES with R1 removed, R2 kept
+            - get_capped_smiles_for_removed_rgroups({'R2'}) → SMILES with R2 removed, R1 kept
+            - get_capped_smiles_for_removed_rgroups({'R1', 'R2'}) → SMILES with both removed
+        """
+        # Check cache first
+        if removed_rgroups in self.capped_smiles_cache:
+            return self.capped_smiles_cache[removed_rgroups]
+        
+        # Generate on demand
+        smiles = self._get_smiles_with_rgroups_removed(removed_rgroups)
+        
+        # Cache for future use
+        self.capped_smiles_cache[removed_rgroups] = smiles
+        
+        return smiles
+    
+    def _get_smiles_with_rgroups_removed(self, removed_rgroups: frozenset) -> str:
+        """
+        Generate canonical SMILES with specific R-groups removed and others capped.
+        
+        Args:
+            removed_rgroups: Set of R-group labels where bonds were broken (e.g., {'R1', 'R2'})
+        
+        Returns:
+            Canonical SMILES string matching fragment structure
+            
+        Logic:
+            - R-groups in removed_rgroups: Remove dummy atom (bond was broken)
+            - R-groups NOT in removed_rgroups: Cap according to library (e.g., OH, H)
+            - Final SMILES has NO [*:X] markers to match fragment SMILES
+        """
+        try:
+            mol_copy = Chem.Mol(self.mol)
+            
+            # Identify which R-groups to cap vs remove
+            kept_rgroups = set(self.r_groups.keys()) - removed_rgroups
+            
+            # Process each R-group
+            # IMPORTANT: SMILES [*:1] uses atom map numbers, not isotopes!
+            dummy_atoms_to_process = []
+            for atom in mol_copy.GetAtoms():
+                if atom.GetAtomicNum() == 0:  # Dummy atom (R-group)
+                    map_num = atom.GetAtomMapNum()
+                    if map_num > 0:
+                        r_label = f"R{map_num}"
+                        if r_label in removed_rgroups:
+                            # Just remove this dummy atom
+                            dummy_atoms_to_process.append((atom.GetIdx(), 'remove', r_label))
+                        elif r_label in kept_rgroups:
+                            # Need to cap this R-group
+                            cap_smiles = self.r_groups.get(r_label, '')
+                            dummy_atoms_to_process.append((atom.GetIdx(), 'cap', cap_smiles))
+            
+            # Apply caps to kept R-groups, remove others
+            # Process in two passes: first cap, then remove
+            # Cap R-groups: Replace [*:X] with the cap group (e.g., H or OH)
+            for atom_idx, action, data in sorted(dummy_atoms_to_process, reverse=True):
+                if action == 'cap':
+                    cap_smiles = data
+                    # For R1 cap '[*:1][H]', we just remove [*:1] (implicit H added)
+                    # For R2 cap 'O[*:2]', we need to add O when removing [*:2]
+                    # Simplified: check if cap has O
+                    if 'O' in cap_smiles and '[*:' in cap_smiles:
+                        # R2-like cap: need to add OH group
+                        # Get the neighbor atom of the dummy
+                        atom = mol_copy.GetAtomWithIdx(atom_idx)
+                        neighbors = atom.GetNeighbors()
+                        if neighbors:
+                            neighbor = neighbors[0]
+                            # Add OH to the neighbor before removing dummy
+                            emol = Chem.EditableMol(mol_copy)
+                            new_o_idx = emol.AddAtom(Chem.Atom(8))  # Oxygen
+                            emol.AddBond(neighbor.GetIdx(), new_o_idx, Chem.BondType.SINGLE)
+                            emol.RemoveAtom(atom_idx)
+                            mol_copy = emol.GetMol()
+                    else:
+                        # R1-like cap: just remove dummy (implicit H)
+                        emol = Chem.EditableMol(mol_copy)
+                        emol.RemoveAtom(atom_idx)
+                        mol_copy = emol.GetMol()
+                elif action == 'remove':
+                    # Just remove the dummy atom
+                    emol = Chem.EditableMol(mol_copy)
+                    emol.RemoveAtom(atom_idx)
+                    mol_copy = emol.GetMol()
+            
+            if mol_copy:
+                # Sanitize to add implicit hydrogens where needed
+                Chem.SanitizeMol(mol_copy)
+                # Generate canonical SMILES without any R-group markers
+                return Chem.MolToSmiles(mol_copy, canonical=True)
+            return ""
+        except Exception as e:
+            return ""
+
+
+class MonomerLibrary:
+    def __init__(self):
+        self.monomers = {}
+        self.smiles_to_monomer = {}
+        self.name_to_monomer = {}
+        self.symbol_to_monomer = {}
+
+    def load_from_helm_json(self, json_path: str) -> None:
+        if not os.path.exists(json_path):
+            return
+
+        try:
+            with open(json_path, 'r', encoding='utf-8') as f:
+                data = json.load(f)
+        except Exception:
+            return
+
+        successful = 0
+        for monomer_dict in data:
+            try:
+                monomer = self._parse_monomer(monomer_dict)
+                if monomer and monomer.mol is not None:
+                    self.monomers[monomer.symbol] = monomer
+                    self.symbol_to_monomer[monomer.symbol] = monomer
+
+                    clean_name = monomer.name.lower().replace(" ", "").replace("-", "").replace("_", "")
+                    self.name_to_monomer[clean_name] = monomer
+
+                    successful += 1
+            except Exception:
+                continue
+
+    def _parse_monomer(self, monomer_dict: dict):
+        # IMPORTANT: Only load PEPTIDE monomers (amino acids)
+        # The library contains RNA, CHEM, etc. with overlapping symbols (A, C, G, T, U)
+        polymer_type = monomer_dict.get('polymerType', '')
+        if polymer_type != 'PEPTIDE':
+            return None
+        
+        monomer = MonomerData()
+        monomer.symbol = monomer_dict.get('symbol', '')
+        monomer.name = monomer_dict.get('name', '')
+
+        if not monomer.symbol:
+            return None
+
+        smiles = monomer_dict.get('smiles', '')
+        molfile = monomer_dict.get('molfile', '')
+
+        if smiles:
+            try:
+                monomer.mol = Chem.MolFromSmiles(smiles)
+                monomer.smiles = smiles
+            except Exception:
+                monomer.mol = None
+
+        if monomer.mol is None and molfile:
+            try:
+                monomer.mol = Chem.MolFromMolBlock(molfile)
+                if monomer.mol:
+                    monomer.smiles = Chem.MolToSmiles(monomer.mol)
+            except Exception:
+                monomer.mol = None
+
+        if monomer.mol is None:
+            return None
+        
+        # Parse R-groups
+        rgroups_list = monomer_dict.get('rgroups', [])
+        for rgroup in rgroups_list:
+            label = rgroup.get('label', '')
+            cap_smiles = rgroup.get('capGroupSMILES', '')
+            if label and cap_smiles:
+                monomer.r_groups[label] = cap_smiles
+        
+        monomer.r_group_count = len(monomer.r_groups)
+
+        return monomer
+
+    def find_monomer_by_fragment_smiles(self, fragment_smiles: str, num_connections: int):
+        """
+        Find monomer by matching fragment SMILES with on-demand R-group removal.
+        
+        Args:
+            fragment_smiles: Canonical SMILES of the fragment  
+            num_connections: Number of connections this fragment has in the graph
+        
+        Returns:
+            MonomerData if match found, None otherwise
+            
+        Logic:
+            - Fragment with N connections → N R-groups were removed during fragmentation
+            - For monomer with M R-groups, try all C(M,N) combinations of which N R-groups were removed
+            - Generate SMILES for each combination on-demand (with caching)
+            
+        Example:
+            Fragment has 1 connection, monomer has R1, R2:
+            - Try removing R1 → check if SMILES matches
+            - Try removing R2 → check if SMILES matches
+        """
+        # Search through all monomers
+        for symbol, monomer in self.monomers.items():
+            # Skip if monomer doesn't have enough R-groups
+            if monomer.r_group_count < num_connections:
+                continue
+            
+            # Generate all combinations of num_connections R-groups that could have been removed
+            r_group_labels = list(monomer.r_groups.keys())
+            
+            # For each combination of R-groups that could have been removed
+            for removed_combo in combinations(r_group_labels, num_connections):
+                removed_set = frozenset(removed_combo)
+                
+                # Generate SMILES with these R-groups removed (lazy, cached)
+                candidate_smiles = monomer.get_capped_smiles_for_removed_rgroups(removed_set)
+                
+                # Check if it matches the fragment
+                if candidate_smiles == fragment_smiles:
+                    return monomer
+        
+        return None
+
+    def find_monomer_by_symbol(self, symbol: str):
+        return self.symbol_to_monomer.get(symbol)
+
+# ============================================================================
+# Content from: monomer_matcher.py
+# ============================================================================
+
+from rdkit import Chem
+
+
+class MonomerMatcher:
+    """
+    Matches molecular fragments to monomers using graph-aware R-group analysis.
+    
+    Revolutionary approach:
+    - No hardcoded mappings
+    - No complex normalization
+    - Direct string comparison of canonical SMILES
+    - Graph topology determines which R-groups are capped
+    """
+    
+    def __init__(self, monomer_library: MonomerLibrary):
+        self.monomer_library = monomer_library
+
+    def find_exact_match(self, fragment: Chem.Mol, num_connections: int = 0):
+        """
+        Find exact match for a fragment based on graph topology.
+        
+        Args:
+            fragment: RDKit molecule object representing a fragment
+            num_connections: Number of connections this fragment has in the graph
+        
+        Returns:
+            MonomerData object if match found, None otherwise
+        """
+        try:
+            # Get canonical SMILES of the fragment
+            frag_smiles = Chem.MolToSmiles(fragment, canonical=True)
+            if not frag_smiles:
+                return None
+
+            # Use the library's new graph-aware matching
+            match = self.monomer_library.find_monomer_by_fragment_smiles(
+                frag_smiles, num_connections
+            )
+            
+            return match
+
+        except Exception:
+            return None
+    
+    def match_graph(self, graph: FragmentGraph):
+        """
+        Match all fragments in a graph to monomers.
+        
+        Args:
+            graph: FragmentGraph with unmatched nodes
+        
+        Returns:
+            Number of successfully matched nodes
+        """
+        matched_count = 0
+        
+        for node_id, node in graph.nodes.items():
+            # Count connections for this node
+            neighbors = graph.get_neighbors(node_id)
+            num_connections = len(neighbors)
+            
+            # Find matching monomer
+            monomer = self.find_exact_match(node.mol, num_connections)
+            
+            if monomer:
+                node.monomer = monomer
+                matched_count += 1
+        
+        return matched_count
+
+# ============================================================================
+# Content from: pipeline.py
+# ============================================================================
+
+from rdkit import Chem
+import os
+import json
+
+# Global variables for caching
+_MONOMER_LIBRARY = None
+_PROCESSOR = None
+_MATCHER = None
+_HELM_GENERATOR = None
+
+
+def _load_monomer_library():
+    global _MONOMER_LIBRARY
+    if _MONOMER_LIBRARY is None:
+        # Define path to library relative to current directory
+        current_dir = os.path.dirname(os.path.abspath(__file__))
+        project_root = os.path.dirname(current_dir)
+        library_path = os.path.join(project_root, "libraries", "HELMCoreLibrary.json")
+
+        if not os.path.exists(library_path):
+            return None
+
+        print("Loading monomer library...")
+        _MONOMER_LIBRARY = MonomerLibrary()
+        _MONOMER_LIBRARY.load_from_helm_json(library_path)
+
+        if not _MONOMER_LIBRARY.monomers:
+            return None
+        
+        print(f"Monomer library loaded: {len(_MONOMER_LIBRARY.monomers)} monomers")
+
+    return _MONOMER_LIBRARY
+
+
+def _get_processors():
+    """
+    Get or create singleton instances of processors.
+    Returns tuple: (processor, matcher, helm_generator)
+    """
+    global _PROCESSOR, _MATCHER, _HELM_GENERATOR
+    
+    if _PROCESSOR is None or _MATCHER is None or _HELM_GENERATOR is None:
+        library = _load_monomer_library()
+        if not library:
+            return None, None, None
+        
+        _PROCESSOR = FragmentProcessor(library)
+        _MATCHER = MonomerMatcher(library)
+        _HELM_GENERATOR = HELMGenerator()
+    
+    return _PROCESSOR, _MATCHER, _HELM_GENERATOR
+
+
+def preload_library():
+    """
+    Preload the monomer library and initialize processors once at the start.
+    Returns True if successful, False otherwise.
+    """
+    library = _load_monomer_library()
+    if library is None:
+        return False
+    
+    # Initialize processors
+    processor, matcher, generator = _get_processors()
+    return processor is not None
+
+
+def convert_molecules_batch(molfiles: list, library_json: str = None) -> list:
+    """
+    Convert a batch of molecules from molfile format to HELM notation.
+    
+    Args:
+        molfiles: List of molfile strings
+        library_json: Optional monomer library as JSON string.
+                     If None, uses default cached library from HELMCoreLibrary.json
+    
+    Returns:
+        List of tuples: (success: bool, helm_notation: str)
+        success is True if molecule was successfully converted, False otherwise
+    """
+    # Determine which library to use
+    if library_json is None:
+        # Use cached global library
+        global _PROCESSOR
+        if _PROCESSOR is None:
+            print("Initializing monomer library and processors...")
+            if not preload_library():
+                print("ERROR: Failed to load monomer library")
+                return [(False, "Library initialization failed") for _ in molfiles]
+            print()
+        
+        # Use shared processor instances
+        processor, matcher, helm_generator = _get_processors()
+        if not processor:
+            return [(False, "") for _ in molfiles]
+    else:
+        # Load custom library from provided JSON string (no caching)
+        try:
+            library_data = json.loads(library_json)
+        except Exception as e:
+            print(f"ERROR: Failed to parse library JSON: {str(e)}")
+            return [(False, "Invalid JSON") for _ in molfiles]
+        
+        print(f"Loading custom library from JSON string...")
+        library = MonomerLibrary()
+        
+        # Parse the library data
+        successful = 0
+        for monomer_dict in library_data:
+            try:
+                monomer = library._parse_monomer(monomer_dict)
+                if monomer and monomer.mol is not None:
+                    library.monomers[monomer.symbol] = monomer
+                    library.symbol_to_monomer[monomer.symbol] = monomer
+                    clean_name = monomer.name.lower().replace(" ", "").replace("-", "").replace("_", "")
+                    library.name_to_monomer[clean_name] = monomer
+                    successful += 1
+            except Exception:
+                continue
+        
+        if not library.monomers:
+            print("ERROR: No monomers loaded from custom library")
+            return [(False, "Library loading failed") for _ in molfiles]
+        
+        print(f"Custom library loaded: {len(library.monomers)} monomers")
+        
+        # Create processor instances for this library
+        processor = FragmentProcessor(library)
+        matcher = MonomerMatcher(library)
+        helm_generator = HELMGenerator()
+    
+    results = []
+    
+    for i in range(len(molfiles)):
+        molfile = molfiles[i]
+        mol = Chem.MolFromMolBlock(molfile)
+        if not mol:
+            results.append((False, ""))
+            continue
+        
+        try:
+            # Process molecule into fragment graph
+            graph = processor.process_molecule(mol)
+            
+            # Match each fragment to a monomer using graph topology
+            unknown_count = 0
+            for node_id, node in graph.nodes.items():
+                # Count connections for this node
+                neighbors = graph.get_neighbors(node_id)
+                num_connections = len(neighbors)
+                
+                # Find matching monomer
+                monomer = matcher.find_exact_match(node.mol, num_connections)
+                if monomer:
+                    node.monomer = monomer
+                else:
+                    unknown_count += 1
+                    mock_monomer = MonomerData()
+                    mock_monomer.symbol = f"X{unknown_count}"
+                    mock_monomer.name = f"Unknown_{unknown_count}"
+                    node.monomer = mock_monomer
+            
+            # Try to recover unmatched fragments by merging with neighbors
+            max_recovery_attempts = 3  # Prevent infinite loops
+            for attempt in range(max_recovery_attempts):
+                had_changes = processor.recover_unmatched_fragments(graph, matcher)
+                if not had_changes:
+                    break
+            
+            if len(graph.nodes) > 0:
+                helm_notation = helm_generator.generate_helm_from_graph(graph)
+                results.append((True, helm_notation))
+            else:
+                results.append((False, ""))
+        except Exception as e:
+            results.append((False, f"Error: {str(e)}"))
+    
+    return results
+
+res_helm_list = convert_molecules_batch(molListToProcess, library_json=libraryJSON)
+result_helm = pd.DataFrame(map(lambda x: x[1], res_helm_list), columns=["regenerated sequences"])