mol-healer 0.1.1__py3-none-any.whl → 0.1.2__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__ = "0.1.2"
 
 __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/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"]
 

{mol_healer-0.1.1.dist-info → mol_healer-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mol-healer
-Version: 0.1.1
+Version: 0.1.2
 Summary: Hit Expansion to Advanced Leads Using Enumerated Reactions
 Author-email: Enes Kelestemur <enesk@email.unc.edu>
 License-Expression: MIT

{mol_healer-0.1.1.dist-info → mol_healer-0.1.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
-healer/__init__.py,sha256=Ig7dSjq3Zf6apKqnRP75xNhSlMLJzaTHNlpzZNbm1XQ,431
-healer/cli.py,sha256=yyBwf9v9mYtXaL3TBxlRCdlxHgIAyB7dQ6CttAnJIKA,16974
+healer/__init__.py,sha256=IfaP1c1xASHEnNquAwE_K-qqWSD2EKla_JHpkkLlcWw,431
+healer/cli.py,sha256=j1gt7UmqpDBvM2in1imIeIWBwzm52SFtlWuKae5aZ9g,17064
 healer/application/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 healer/application/healer.py,sha256=hgUoQuW5FUjRLo5SMynOdAwVww054vK0tgafEDSZp08,45443
 healer/application/optimizers.py,sha256=XoKQQxaZHfFt0N74KHG3CkW7AHoS4KmDzOxvKtjxK4s,2957
@@ -20,13 +20,13 @@ healer/scripts/preprocess_bb_source.py,sha256=uGYW6MF_THW6xHa6PAv89OqaMV3mhba3tv
 healer/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 healer/utils/plotting.py,sha256=ZKuQlsFUDPS7gFpl1izXPhvEawOF9Rs2ktFQNVkpnEI,3914
 healer/utils/rdkit_monkey_patch.py,sha256=1nlnmf6I71rEgvFnUctVzN-xdC_rfCKfU8QeUWp1UoM,2247
-healer/utils/utils.py,sha256=3o02Y75LKUxXTeZkeo8UpT3C775NX--wsvpYTaHawUU,13488
+healer/utils/utils.py,sha256=gER-E_WQ-V10aFhIoTedaQl85gHfbxPabve2uf03XjA,13971
 healer/web/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 healer/web/app.py,sha256=VzgXg5Bfh-2HqGRX_aPINOV9WnU3MlXTfPP-5IClsqo,2022
 healer/web/celery_worker.py,sha256=tBfr1M70gKQBqDC-hbIJYR5BD3Oyrud2QMut90pbx2c,2061
-healer/web/interface.py,sha256=ODjJOdYV06idnYcBiBq_vUZPLwhF5X8FT2NjG80YYQ4,12886
+healer/web/interface.py,sha256=DtwAf-qvLoNuGH1uJOrX9gH7FoGhTkTARjqlTLyBQ_M,12788
 healer/web/models.py,sha256=90pxipzFaaYTGyKs209A4qfsAE5MxSxh8piWZGdPE18,3624
-healer/web/routes.py,sha256=jiqH-T50s-m5lY8jXJibg3ftXGEMo9JVZS0Ko8rU86Y,12412
+healer/web/routes.py,sha256=hNWJUVxqgQvzGOrmGy11q8EISDymHT1bNfvzjiktpj4,12494
 healer/web/static/favicon.ico,sha256=iBN6OD9gAV_xtgnxNyfAIGXjmfn5ZFzGLN0gPvYND5I,90465
 healer/web/static/healer_logo_no_text.png,sha256=eYXkXR90E45MwUeMWByF_3w4sHuPJdNbdewJebiQOQs,1467095
 healer/web/static/index.html,sha256=hRnIsb3ACMzz8hm8nu8oXNey4LanTh9xygMPffmz6TE,459
@@ -86,9 +86,9 @@ healer/web/static/ketcher/static/js/popup.a25226a6.js,sha256=vviCE9qtxlADgp3TRLp
 healer/web/static/ketcher/static/js/popup.a25226a6.js.LICENSE.txt,sha256=u_7whDJJhaQXBb4LS6BSdFTHBUMfMa42Hyg3eJWE71M,2857
 healer/web/static/ketcher/static/js/popup.a25226a6.js.LICENSE.txt:Zone.Identifier,sha256=160oCs1uFqzSg0a2FSaEUR881uUG0ZIhR4m7r4SMOQg,93
 healer/web/static/ketcher/static/js/popup.a25226a6.js:Zone.Identifier,sha256=160oCs1uFqzSg0a2FSaEUR881uUG0ZIhR4m7r4SMOQg,93
-mol_healer-0.1.1.dist-info/licenses/LICENSE,sha256=oxohyDXrpFqI-jDj7P6vVyvmx2VTSS-XmAhJlOM-f-U,1072
-mol_healer-0.1.1.dist-info/METADATA,sha256=Oa8U1tnz8vbOM9btTO7AlDlB2tHS1g1WecGHcreK06w,10498
-mol_healer-0.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-mol_healer-0.1.1.dist-info/entry_points.txt,sha256=s0D-WiNYMo692yK5-_O1_DYxnBdUh6uYqLBCT38IH8o,132
-mol_healer-0.1.1.dist-info/top_level.txt,sha256=Xo-bGDCMbHJvDNZoKXsiFM7NpKo1R0koCUSZ04Ngm0E,7
-mol_healer-0.1.1.dist-info/RECORD,,
+mol_healer-0.1.2.dist-info/licenses/LICENSE,sha256=oxohyDXrpFqI-jDj7P6vVyvmx2VTSS-XmAhJlOM-f-U,1072
+mol_healer-0.1.2.dist-info/METADATA,sha256=Fk_UVeqgZo420cRrz6NYCLdT17gEtnBw2Tz8RZRIG8c,10498
+mol_healer-0.1.2.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+mol_healer-0.1.2.dist-info/entry_points.txt,sha256=s0D-WiNYMo692yK5-_O1_DYxnBdUh6uYqLBCT38IH8o,132
+mol_healer-0.1.2.dist-info/top_level.txt,sha256=Xo-bGDCMbHJvDNZoKXsiFM7NpKo1R0koCUSZ04Ngm0E,7
+mol_healer-0.1.2.dist-info/RECORD,,

{mol_healer-0.1.1.dist-info → mol_healer-0.1.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any