mol-healer 0.1.0__tar.gz → 0.1.2__tar.gz

{mol_healer-0.1.0/mol_healer.egg-info → mol_healer-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mol-healer
-Version: 0.1.0
+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-0.1.0 → mol_healer-0.1.2}/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__ = "0.1.0"
+__version__ = "0.1.2"
 
 __all__ = [
     "MoleculeHEALER",

{mol_healer-0.1.0 → mol_healer-0.1.2}/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')
     

{mol_healer-0.1.0 → mol_healer-0.1.2}/healer/domain/bb_repository.py

@@ -3,6 +3,7 @@
 """
 from __future__ import annotations
 
+import os
 import logging
 from dataclasses import dataclass, field
 from pathlib import Path
@@ -19,7 +20,7 @@ logger = logging.getLogger(__name__)
 
 _HEALER_PKG = Path(__file__).parent.parent
 _DATA_DIR = _HEALER_PKG / "data"
-_BB_DIR = _DATA_DIR / "buildingblocks"
+_BB_DIR = Path(os.getenv("HEALER_DATA_DIR", str(_DATA_DIR / "buildingblocks")))
 
 BB_PATHS: Dict[str, str] = {
     "US_stock": str(_BB_DIR / "Enamine_Rush-Delivery_Building_Blocks-US" / "*_processed.sdf"),

{mol_healer-0.1.0 → mol_healer-0.1.2}/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.

{mol_healer-0.1.0 → mol_healer-0.1.2}/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:

{mol_healer-0.1.0 → mol_healer-0.1.2}/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-0.1.0 → mol_healer-0.1.2/mol_healer.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mol-healer
-Version: 0.1.0
+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-0.1.0 → mol_healer-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "mol-healer"
-version = "0.1.0"
+version = "0.1.2"
 description = "Hit Expansion to Advanced Leads Using Enumerated Reactions"
 readme = "README.md"
 license = "MIT"