Move functions.

Author: dcliebschner

mmtbx/ligands/rdkit_utils.py

@@ -18,6 +18,41 @@
   match_mol_indices: Match atom indices of different mols
 """
 
+def get_rdkit_bond_type(cif_order):
+  """
+  Maps CCTBX CIF bond orders to RDKit BondType enum.
+  """
+  if not cif_order: return Chem.BondType.SINGLE
+  order = cif_order.lower()
+  if 'sing' in order: return Chem.BondType.SINGLE
+  if 'doub' in order: return Chem.BondType.DOUBLE
+  if 'trip' in order: return Chem.BondType.TRIPLE
+  if 'deloc' in order or 'arom' in order: return Chem.BondType.AROMATIC
+  return Chem.BondType.SINGLE
+
+def is_amide_bond(mol, bond):
+  """
+  Checks if a bond is a C-N amide bond to prevent cutting peptides.
+  """
+  a1 = bond.GetBeginAtom()
+  a2 = bond.GetEndAtom()
+
+  c_atom, n_atom = None, None
+  if a1.GetSymbol() == 'C' and a2.GetSymbol() == 'N':
+    c_atom, n_atom = a1, a2
+  elif a2.GetSymbol() == 'C' and a1.GetSymbol() == 'N':
+    c_atom, n_atom = a2, a1
+
+  if c_atom is None: return False
+
+  for nbr in c_atom.GetNeighbors():
+    if nbr.GetIdx() == n_atom.GetIdx(): continue
+    if nbr.GetSymbol() == 'O':
+      bond_to_o = mol.GetBondBetweenAtoms(c_atom.GetIdx(), nbr.GetIdx())
+      if bond_to_o is not None and bond_to_o.GetBondType() == Chem.BondType.DOUBLE:
+        return True
+  return False
+
 def get_prop_safe(rd_obj, prop):
   if prop not in rd_obj.GetPropNames(): return False
   return rd_obj.GetProp(prop)

mmtbx/regression/tst_rdkit_utils_fragmentation.py

@@ -6,6 +6,7 @@
 from rdkit import Chem
 from rdkit.Chem import Lipinski, rdmolops
 from scitbx.array_family import flex
+import mmtbx.ligands.rdkit_utils as rdkit_utils
 
 # ------------------------------------------------------------------------------
 
@@ -102,7 +103,7 @@ def run_fragmentation(ligand_isel, model):
         rd_j = name_to_rdkit[atom_2]
         # Check existing to prevent duplicates
         if mol.GetBondBetweenAtoms(rd_i, rd_j) is None:
-          mol.AddBond(rd_i, rd_j, get_rdkit_bond_type(order_str))
+          mol.AddBond(rd_i, rd_j, rdkit_utils.get_rdkit_bond_type(order_str))
 
   # 4. Sanitize (Important for implicit valence calculation)
   try:
@@ -122,7 +123,7 @@ def run_fragmentation(ligand_isel, model):
     if bond is None: continue
 
     # Filter 1: Protect Amides
-    if is_amide_bond(mol, bond): continue
+    if rdkit_utils.is_amide_bond(mol, bond): continue
 
     bidx = bond.GetIdx()
 
@@ -170,41 +171,6 @@ def run_fragmentation(ligand_isel, model):
 
   return cctbx_rigid_components
 
-def get_rdkit_bond_type(cif_order):
-    """
-    Maps CCTBX CIF bond orders to RDKit BondType enum.
-    """
-    if not cif_order: return Chem.BondType.SINGLE
-    order = cif_order.lower()
-    if 'sing' in order: return Chem.BondType.SINGLE
-    if 'doub' in order: return Chem.BondType.DOUBLE
-    if 'trip' in order: return Chem.BondType.TRIPLE
-    if 'deloc' in order or 'arom' in order: return Chem.BondType.AROMATIC
-    return Chem.BondType.SINGLE
-
-def is_amide_bond(mol, bond):
-    """
-    Checks if a bond is a C-N amide bond to prevent cutting peptides.
-    """
-    a1 = bond.GetBeginAtom()
-    a2 = bond.GetEndAtom()
-
-    c_atom, n_atom = None, None
-    if a1.GetSymbol() == 'C' and a2.GetSymbol() == 'N':
-      c_atom, n_atom = a1, a2
-    elif a2.GetSymbol() == 'C' and a1.GetSymbol() == 'N':
-      c_atom, n_atom = a2, a1
-
-    if c_atom is None: return False
-
-    for nbr in c_atom.GetNeighbors():
-      if nbr.GetIdx() == n_atom.GetIdx(): continue
-      if nbr.GetSymbol() == 'O':
-        bond_to_o = mol.GetBondBetweenAtoms(c_atom.GetIdx(), nbr.GetIdx())
-        if bond_to_o is not None and bond_to_o.GetBondType() == Chem.BondType.DOUBLE:
-          return True
-    return False
-
 # ------------------------------------------------------------------------------
 
 pdb_str_01 = '''