Fixed atom economy for bio pathways

wsprague-nu · Sep 17, 2024 · e994f2d · e994f2d
1 parent 3f32f75
commit e994f2d
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Showing 2 changed files with 10 additions and 5 deletions.
diff --git a/doranet/modules/post_processing/post_processing.py b/doranet/modules/post_processing/post_processing.py
@@ -1651,7 +1651,7 @@ def path_eco(
             for (
                 i
             ) in left_dict:  # find idx for a intermediate molecule to produce
-                if i not in starters:
+                if i not in starters | set(has_bio):
                     popkey = i
                     break
             # num_mol = left_dict.pop(popkey)
@@ -1700,7 +1700,7 @@ def path_eco(
 
             key_list = list()
             for key in left_dict:  # balance left and right dict
-                if key not in starters and key in right_dict:
+                if key not in starters | set(has_bio) and key in right_dict:
                     key_list.append(key)
             for key in key_list:
                 if left_dict[key] == right_dict[key]:
@@ -1717,7 +1717,8 @@ def path_eco(
 
             done_flag = True
             for key in left_dict:
-                if key not in starters:  # check if left only contain starters
+                if key not in starters | set(has_bio):
+                    # check if left only contain starters
                     done_flag = False
             if done_flag is True or timecount == timeout:
                 repeat_flag = False
@@ -1772,7 +1773,7 @@ def path_eco(
 
         print("Min_eco", min_eco)
         print("Max_eco", max_eco)
-        # print("none_eco", none_eco)
+        print("None_eco", none_eco)
         diff_eco = max_eco - min_eco
         for i in eco_list:
             if diff_eco != 0:

diff --git a/doranet/modules/synthetic/generate_network.py b/doranet/modules/synthetic/generate_network.py
@@ -488,7 +488,10 @@ def generate_network(
     for smarts in smarts_list:
         if smarts.kekulize_flag is False:
             network.add_op(
-                engine.op.rdkit(smarts.smarts),
+                engine.op.rdkit(
+                    smarts.smarts,
+                    drop_errors=True,
+                ),
                 meta={
                     "name": smarts.name,
                     "reactants_stoi": smarts.reactants_stoi,
@@ -508,6 +511,7 @@ def generate_network(
                 engine.op.rdkit(
                     smarts.smarts,
                     kekulize=True,
+                    drop_errors=True,
                 ),
                 meta={
                     "name": smarts.name,