mol-healer 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

healer/__init__.py

@@ -3,7 +3,7 @@
 from healer.application.healer import MoleculeHEALER, SiteHEALER, FragmentHEALER
 from healer.domain.bb_repository import get_repository, clear_repository_cache, BB_PATHS
 
-__version__ = "0.1.1"
+__version__ = "0.1.3"
 
 __all__ = [
     "MoleculeHEALER",

healer/cli.py

@@ -374,7 +374,8 @@ def add_common_args(parser: argparse.ArgumentParser) -> None:
     parser.add_argument('--bb-source', default='US_stock',
                         help='Building block source: US_stock, EU_stock, Global_stock, or path')
     parser.add_argument('--reactions', default='all',
-                        help='Comma-separated reaction tags or "all" (default: all)')
+                        help=f'Comma-separated reaction tags or "all" (default: all). '
+                             f'Available tags: {", ".join(utils.get_reaction_tags())}')
     parser.add_argument('--shuffle', action='store_true',
                         help='Shuffle building block order')
     

healer/data/reactions/reaction_tags.txt

@@ -0,0 +1,116 @@
+4-hydroxyquinoline
+Barton-Zard
+Biginelli
+Bischler-Mohlau
+Buchwald-Hartwig
+C-C
+C-C bond formation
+C-N
+C-N bond formation
+C-O
+C-O bond formation
+C-S
+C-S bond formation
+CO insertion
+Castro-Stephens
+Chan-Lam
+Claisen
+Conrad-Limpach
+Curtius Rearrangement
+Erlenmeyer-Plochl
+Feist-Benary
+Fischer
+Friedel-Crafts
+Friedlander
+Goldberg
+Guareshi-Thorpe
+Hantzsch
+Heck
+Knorr
+Krohnke
+Mitsunobu
+N-arylation
+Negishi
+Niementowski
+O-arylation
+Paal-Knorr
+Pechmann
+Pictet-Spengler
+S-arylation
+Sonagashira
+Stille
+Suzuki
+Ullman
+Ullmann
+Williamson
+acetylene
+acylation
+alkylation
+alkyne
+all
+amide
+amide coupling
+amination
+amine
+aminothiophene
+arylation
+azlactone
+azole
+benzimidazole
+benzofuran
+benzothiazole
+benzothiophene
+benzoxazole
+beta-ketoester
+biaryl
+biginelli
+boronate
+boronic acid
+boronic ester
+carbamate
+carbamates
+chromanone
+click
+condensation
+coumarin
+cross coupling
+cyclization
+diaryl amine
+diketone
+diyne
+ester
+esterification
+ether
+etherification
+flavone
+furan
+heterocycle
+heterocycle formation
+imidazole
+indole
+organostannane
+oxadiazole
+oxazole
+phthalazinone
+pyrazole
+pyridine
+pyridone
+pyrimidine
+pyrimidinedione
+pyrimidone
+pyrrole
+quinazoline
+quinazolinone
+quinoline
+reductive amination
+spiro-chromanone
+sulfonamide
+tetrazole
+thiazole
+thioether
+thiophene
+thiourea
+triazole
+trifluoroborate
+urea
+ureas

healer/utils/utils.py

@@ -6,6 +6,7 @@ import os
 import sys
 import json
 import base64
+from pathlib import Path
 from typing import List, Union, Tuple
 from itertools import chain
 
@@ -92,6 +93,21 @@ def read_cxsmiles_file(file_path: str, header: bool=True) -> list[str]:
 
     return smiles_list
 
+def get_reaction_tags() -> list[str]:
+    '''
+        Retrieves available reaction tags from the reaction_tags.txt file.
+
+        Returns:
+            list of reaction tags as strings.
+    '''
+    healer_pkg = Path(__file__).parent.parent
+    reaction_tags_path = healer_pkg / 'data' / 'reactions' / 'reaction_tags.txt'
+    
+    with open(reaction_tags_path, 'r') as file:
+        tags = [line.strip() for line in file if line.strip()]
+    
+    return tags
+
 def load_reactions_from_json(file_path: str) -> list[ReactionTemplate21]:
     '''
         Loads reactions from a json file.

healer/web/interface.py

@@ -340,12 +340,10 @@ def format_enumeration_results(results: List[Dict[str, Any]], app_type: str) ->
                     if result.get(url_key):
                         display_result[url_key] = result[url_key]
         elif app_type == 'site':
-            if bb_keys and result.get(bb_keys[0]):
-                display_result['BB'] = result[bb_keys[0]]
-                if result.get('URL'):
-                    display_result['URL'] = result['URL']
-                elif result.get('URL1'):
-                    display_result['URL'] = result['URL1']
+            if bb_keys and result.get(bb_keys[1]):
+                display_result['BB'] = result[bb_keys[1]]
+                if result.get('URL2'):
+                    display_result['URL'] = result['URL2']
         
         rxn_keys = [k for k in result.keys() if k.startswith('Reaction') and k.endswith('_name')]
         if rxn_keys:

healer/web/routes.py

@@ -248,6 +248,7 @@ async def get_reaction_tags():
         reaction_tags_path = healer_pkg / 'data' / 'reactions' / 'reaction_tags.txt'
         
         if not reaction_tags_path.exists():
+            print("Warning: reaction_tags.txt not found, returning default tags")
             return ["amide coupling", "amide", "C-N bond formation", "C-N",
                     "alkylation", "N-arylation", "azole", "amination"]