boltz-vsynthes 0.0.11__py3-none-any.whl → 0.0.12__py3-none-any.whl

boltz/utils/sdf_to_pre_affinity_npz.py

@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+"""
+boltz-sdf-to-pre-affinity: Convert a docked SDF file (protein-ligand complex) to Boltz pre_affinity_[ligand_id].npz format.
+
+Usage:
+    boltz-sdf-to-pre-affinity --sdf docked_pose.sdf --ligand_id ligand1 --output pre_affinity_ligand1.npz
+
+This command is available after installing boltz with pip.
+"""
+import argparse
+from pathlib import Path
+
+from boltz.data.parse.sdf import parse_sdf
+from boltz.data.types import StructureV2
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Convert SDF to Boltz pre_affinity_*.npz format.")
+    parser.add_argument('--sdf', type=str, required=True, help='Input SDF file (protein-ligand complex)')
+    parser.add_argument('--ligand_id', type=str, required=True, help='Ligand ID (used in output filename)')
+    parser.add_argument('--output', type=str, required=True, help='Output .npz file path')
+    args = parser.parse_args()
+
+    sdf_path = Path(args.sdf)
+    output_path = Path(args.output)
+
+    # Parse the SDF file to StructureV2
+    structure: StructureV2 = parse_sdf(sdf_path)
+
+    # Save as pre_affinity_[ligand_id].npz
+    structure.dump(output_path)
+    print(f"Saved: {output_path}")
+
+if __name__ == "__main__":
+    main() 

{boltz_vsynthes-0.0.11.dist-info → boltz_vsynthes-0.0.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 0.0.11
+Version: 0.0.12
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-0.0.11.dist-info → boltz_vsynthes-0.0.12.dist-info}/RECORD

@@ -108,10 +108,11 @@ 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/sdf_to_pre_affinity_npz.py,sha256=ev0s2pS8NoB-_3BkSjRKk3GMnqjOxTRCH-r9avKYGOg,1212
 boltz/utils/yaml_generator.py,sha256=ermWIG-BE6nNWHFvpEwpk92N9J-YATpGXZGLvD1I2oQ,4012
-boltz_vsynthes-0.0.11.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-0.0.11.dist-info/METADATA,sha256=QXRfzfYl4scRncrhuNJiwV8svTGO8s4MVcwoseF-Vj0,7235
-boltz_vsynthes-0.0.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-0.0.11.dist-info/entry_points.txt,sha256=R_G5TQWoiTDF3a2n7WQfpMLGufFd1lm5tZXVNaczlss,143
-boltz_vsynthes-0.0.11.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-0.0.11.dist-info/RECORD,,
+boltz_vsynthes-0.0.12.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-0.0.12.dist-info/METADATA,sha256=XPcHZExavOK9oz8BaZnp31f-acFOXbCKwmDORbDxaP8,7235
+boltz_vsynthes-0.0.12.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-0.0.12.dist-info/entry_points.txt,sha256=WlXNdHTJF1ahGN-H1QpgMbZm_5SobXY05eiuT8buycw,212
+boltz_vsynthes-0.0.12.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-0.0.12.dist-info/RECORD,,

{boltz_vsynthes-0.0.11.dist-info → boltz_vsynthes-0.0.12.dist-info}/entry_points.txt

@@ -1,4 +1,5 @@
 [console_scripts]
 boltz = boltz.main:cli
 boltz-generate-yaml = boltz.utils.yaml_generator:main
+boltz-sdf-to-pre-affinity = boltz.utils.sdf_to_pre_affinity_npz:main
 boltz-split-sdf = boltz.utils.sdf_splitter:main