sync torsion tree update from nashtools (#43)

dptech-corp · Sep 26, 2023 · 8b4181b · 8b4181b
1 parent 84f3e88
commit 8b4181b
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Showing 2 changed files with 16 additions and 2 deletions.
diff --git a/unidock_tools/unidock_tools/ligand_prepare/rotatable_bond.py b/unidock_tools/unidock_tools/ligand_prepare/rotatable_bond.py
@@ -8,8 +8,10 @@ def __init__(self,
                  max_breaks=4):
 
         self.rotatable_bond_smarts = '[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]'
+        self.amide_bond_smarts = '[C&$(C=O)]-[N&$(NC=O);v3;H1,H2;0]'
         self.conjugate_bond_smarts = '*=*[*]=,#,:[*]'
         self.rotatable_bond_pattern = Chem.MolFromSmarts(self.rotatable_bond_smarts)
+        self.amide_bond_pattern = Chem.MolFromSmarts(self.amide_bond_smarts)
         self.conjugate_bond_pattern = Chem.MolFromSmarts(self.conjugate_bond_smarts)
 
         self.min_macrocycle_size = min_macrocycle_size
@@ -19,4 +21,13 @@ def __init__(self,
 
     def identify_rotatable_bonds(self, mol):
         default_rotatable_bond_info_list = list(mol.GetSubstructMatches(self.rotatable_bond_pattern))
+        amide_rotatable_bond_info_list = list(mol.GetSubstructMatches(self.amide_bond_pattern))
+
+        for amide_rotatable_bond_info in amide_rotatable_bond_info_list:
+            amide_rotatable_bond_info_reversed = tuple(reversed(amide_rotatable_bond_info))
+            if amide_rotatable_bond_info in default_rotatable_bond_info_list:
+                default_rotatable_bond_info_list.remove(amide_rotatable_bond_info)
+            elif amide_rotatable_bond_info_reversed in default_rotatable_bond_info_list:
+                default_rotatable_bond_info_list.remove(amide_rotatable_bond_info_reversed)
+
         return default_rotatable_bond_info_list
diff --git a/unidock_tools/unidock_tools/ligand_prepare/topology_builder.py b/unidock_tools/unidock_tools/ligand_prepare/topology_builder.py
@@ -55,8 +55,11 @@ def build_molecular_graph(self):
             if bond_info in rotatable_bond_info_list or bond_info_reversed in rotatable_bond_info_list:
                 rotatable_bond_idx_list.append(bond.GetIdx())
 
-        splitted_mol = FragmentOnBonds(mol, rotatable_bond_idx_list, addDummies=False)
-        splitted_mol_list = list(GetMolFrags(splitted_mol, asMols=True, sanitizeFrags=False))
+        if len(rotatable_bond_idx_list) != 0:
+            splitted_mol = FragmentOnBonds(mol, rotatable_bond_idx_list, addDummies=False)
+            splitted_mol_list = list(GetMolFrags(splitted_mol, asMols=True, sanitizeFrags=False))
+        else:
+            splitted_mol_list = [mol]
 
         num_fragments = len(splitted_mol_list)