boltz-vsynthes 1.0.43__tar.gz → 1.0.44__tar.gz

{boltz_vsynthes-1.0.43/src/boltz_vsynthes.egg-info → boltz_vsynthes-1.0.44}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.43
+Version: 1.0.44
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.43 → boltz_vsynthes-1.0.44}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "boltz-vsynthes"
-version = "1.0.43"
+version = "1.0.44"
 requires-python = ">=3.10,<3.13"
 description = "Boltz for VSYNTHES"
 readme = "README.md"

{boltz_vsynthes-1.0.43 → boltz_vsynthes-1.0.44}/src/boltz/utils/yaml_generator.py

@@ -3,39 +3,33 @@ import yaml
 from typing import Optional, Dict, Any
 import string
 
-def get_next_ligand_id(config: Dict[str, Any]) -> str:
+def get_next_ligand_id(config: Dict[str, Any], index: int) -> str:
     """Get the next available ligand ID based on existing IDs in the config.
     
     Parameters
     ----------
     config : Dict[str, Any]
         The configuration dictionary.
+    index : int
+        The index of the current ligand.
         
     Returns
     -------
     str
         The next available ligand ID.
     """
-    # Get all existing IDs
-    existing_ids = set()
+    # Find the base ligand ID from the template
+    base_id = None
     for item in config["sequences"]:
-        for key in item:
-            if "id" in item[key]:
-                existing_ids.add(item[key]["id"])
+        if "ligand" in item:
+            base_id = item["ligand"]["id"]
+            break
     
-    # Find the first available letter
-    for letter in string.ascii_uppercase:
-        if letter not in existing_ids:
-            return letter
+    if base_id is None:
+        raise ValueError("No ligand ID found in template")
     
-    # If we run out of single letters, use AA, AB, etc.
-    for first in string.ascii_uppercase:
-        for second in string.ascii_uppercase:
-            new_id = first + second
-            if new_id not in existing_ids:
-                return new_id
-    
-    raise ValueError("Ran out of available ligand IDs!")
+    # Append the index to the base ID
+    return f"{base_id}{index}"
 
 def generate_yamls_from_sdfs(
     template_yaml: Path,
@@ -75,7 +69,7 @@ def generate_yamls_from_sdfs(
         config = template.copy()
         
         # Get next available ligand ID
-        ligand_id = get_next_ligand_id(config)
+        ligand_id = get_next_ligand_id(config, i + 1)
         
         # Update ligand information
         for item in config["sequences"]:
@@ -92,7 +86,12 @@ def generate_yamls_from_sdfs(
         # Write YAML file
         output_file = output_dir / f"{yaml_prefix}{start_index + i}.yaml"
         with open(output_file, "w") as f:
-            yaml.dump(config, f, default_flow_style=False)
+            yaml.dump(
+                config,
+                f,
+                default_flow_style=False,
+                sort_keys=False,  # Maintain original order
+            )
         
         print(f"Created {output_file} with ligand ID {ligand_id}")
 

{boltz_vsynthes-1.0.43 → boltz_vsynthes-1.0.44/src/boltz_vsynthes.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.43
+Version: 1.0.44
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown