boltz-vsynthes 1.0.42__py3-none-any.whl → 1.0.44__py3-none-any.whl

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-1.0.42.dist-info → boltz_vsynthes-1.0.44.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.42
+Version: 1.0.44
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.42.dist-info → boltz_vsynthes-1.0.44.dist-info}/RECORD

@@ -108,10 +108,10 @@ boltz/model/potentials/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 boltz/model/potentials/potentials.py,sha256=vev8Vjfs-ML1hyrdv_R8DynG4wSFahJ6nzPWp7CYQqw,17507
 boltz/model/potentials/schedules.py,sha256=m7XJjfuF9uTX3bR9VisXv1rvzJjxiD8PobXRpcBBu1c,968
 boltz/utils/sdf_splitter.py,sha256=ZHn_syOcmm-fDnJ3YEGyGv_vYz2IRzUW7vbbMSU2JBY,2108
-boltz/utils/yaml_generator.py,sha256=0Lg7F5dQRX75_xR8jiFVokSprDmFzsNmhaITI4fHjao,3980
-boltz_vsynthes-1.0.42.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.42.dist-info/METADATA,sha256=IKbpa2PuzcHwROQ7sbRRf2GXL7HmlWzHRg3NUHGrZ58,7171
-boltz_vsynthes-1.0.42.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.42.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.42.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.42.dist-info/RECORD,,
+boltz/utils/yaml_generator.py,sha256=EiF_jX2H9aYfYDP_6AW7avdRRTAh81nusj_t7s8iPK8,3868
+boltz_vsynthes-1.0.44.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.44.dist-info/METADATA,sha256=LiuapPmWR_SnvEuoFiSogDnh57KTAoZmGCEl58frByU,7171
+boltz_vsynthes-1.0.44.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.44.dist-info/entry_points.txt,sha256=R_G5TQWoiTDF3a2n7WQfpMLGufFd1lm5tZXVNaczlss,143
+boltz_vsynthes-1.0.44.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.44.dist-info/RECORD,,

boltz_vsynthes-1.0.44.dist-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+boltz = boltz.main:cli
+boltz-generate-yaml = boltz.utils.yaml_generator:main
+boltz-split-sdf = boltz.utils.sdf_splitter:main

boltz_vsynthes-1.0.42.dist-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-boltz = boltz.main:cli