Merge pull request #21 from wsprague-nu/dev

Version 0.5.5a1

doranet/modules/post_processing/post_processing.py

@@ -27,7 +27,7 @@
 import rdkit.Chem.rdmolfiles
 import rdkit.Chem.rdmolops
 from PIL import Image, ImageChops, ImageDraw, ImageFont
-from pypdf import PdfMerger, PdfReader
+from pypdf import PdfReader, PdfWriter
 from rdkit import Chem
 from rdkit.Chem import Descriptors, Draw
 from rdkit.Chem.rdMolDescriptors import CalcMolFormula
@@ -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:
@@ -2869,7 +2870,7 @@ def pathway_visualization(
 
     print("Finished with pages, writing to pdf")
     pages.sort()  # [(page_number, object)]
-    merger = PdfMerger()
+    merger = PdfWriter()
     for page in pages:
         merger.append(PdfReader(page[1]))
 

doranet/modules/synthetic/Reaction_Smarts_Forward.py

@@ -1310,6 +1310,13 @@ class OperatorSmarts:
         kekulize_flag=True,
     ),
     # Ester Hydrogenation
+    # Ketenes #############################################
+    OperatorSmarts(
+        "[2+2] Cycloaddition",
+        "[C+0:1]=[C+0:2]=[O+0:3].[C!$(*(=O)=O)!$(*-O)+0:4]=[O,N;+0:5]>>[*:1]1[*:2](=[*:3])[*:5][*:4]1",
+        (1, 1),
+        (1,),
+    ),
     # Benzene and Derivatives #############################################
     # Benzene Hydrogenation
     OperatorSmarts(
@@ -2181,6 +2188,20 @@ class OperatorSmarts:
         (1, 2),
         (1,),
     ),
+    # Amines Dehydrogenation to Nitriles    doi/10.1021/jacs.4c00493
+    OperatorSmarts(
+        "Amines Dehydrogenation to Nitriles",
+        "[C+0;H2,H3:1]-[N+0H2:2]>>[*:1]#[*:2].[H][H]",
+        (1,),
+        (1, 2),
+    ),
+    # Amines Oxidative Dehydrogenation to Nitriles
+    OperatorSmarts(
+        "Amines Oxidative Dehydrogenation to Nitriles",
+        "[C+0;H2,H3:1]-[N+0H2:2].[O+0:3]=[O+0]>>[*:1]#[*:2].[*:3]",
+        (1, 1),
+        (1, 2),
+    ),
     # Nitrile Hydrogenation to Aldehydes
     OperatorSmarts(
         "Nitrile Hydrogenation to Aldehydes",

doranet/modules/synthetic/Reaction_Smarts_Retro.py

@@ -1370,6 +1370,15 @@ class OperatorSmarts:
         kekulize_flag=True,
     ),
     # Ester Hydrogenation
+    # Ketenes #############################################
+    OperatorSmarts(
+        "[2+2] Cycloaddition",
+        "[C+0:1]1[C+0:2](=[O+0:3])[O,N;+0:5][C!$(*(-O)-O)+0:4]1>>[*:1]=[*:2]=[*:3].[*:4]=[*:5]",
+        (1,),
+        (1, 1),
+        ring_issue=True,
+        Retro_Not_Aromatic=True,
+    ),
     # Benzene and Derivatives #############################################
     # Benzene Hydrogenation
     OperatorSmarts(
@@ -2283,6 +2292,20 @@ class OperatorSmarts:
         (1,),
         (1, 2),
     ),
+    # Amines Dehydrogenation to Nitriles
+    OperatorSmarts(
+        "Amines Dehydrogenation to Nitriles",
+        "[C+0:1]#[N+0:2].[H][H]>>[*:1][*:2]",
+        (1, 2),
+        (1,),
+    ),
+    # Amines Oxidative Dehydrogenation to Nitriles
+    OperatorSmarts(
+        "Amines Oxidative Dehydrogenation to Nitriles",
+        "[C+0:1]#[N+0:2].[O+0H2:3]>>[*:1][*:2].[*:3]=[O]",
+        (1, 2),
+        (1, 1),
+    ),
     # Nitrile Hydrogenation to Aldehydes
     OperatorSmarts(
         "Nitrile Hydrogenation to Aldehydes",

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,

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = 'doranet'
-version = '0.5.3a9'
+version = '0.5.5a1'
 authors = [
     { name='William Sprague', email='[email protected]' },
     { name='Quan Zhang', email='[email protected]' },