first add

vina_split_and_submit.py

@@ -0,0 +1,66 @@
+import os
+import shutil
+from pathlib import Path
+import sys
+import subprocess
+
+n_splits = int(sys.argv[1]) if len(sys.argv) > 1 else 12   # 默认12份，可传参修改
+src_dir = Path('./ligand/pdbqt')
+dst_root = Path('./ligand')
+
+all_files = sorted(src_dir.glob('*.pdbqt'))
+total = len(all_files)
+if total == 0:
+    raise ValueError("No pdbqt files found in ./ligand/pdbqt")
+
+def split_list_evenly(lst, n):
+    k, m = divmod(len(lst), n)
+    return [lst[i * k + min(i, m):(i + 1) * k + min(i + 1, m)] for i in range(n)]
+
+chunks = split_list_evenly(all_files, n_splits)
+
+for i, files in enumerate(chunks, 1):
+    dst_dir = dst_root / f"pdbqt{i}"
+    dst_dir.mkdir(parents=True, exist_ok=True)
+    for f in files:
+        shutil.copy2(f, dst_dir / f.name)
+
+sh_template = """#!/bin/bash
+#DSUB -n vina_job{idx}
+#DSUB -R 'cpu=32' 
+#DSUB -aa
+#DSUB --label arm
+#DSUB -o vina_docking{idx}_cpu_job_%J.out 
+date
+echo "autodock vina docking task{idx}, version: 1.2.7" 
+cd /share/home/lyzeng24/rdkit_script/vina
+./scripts/batch_docking.sh ./receptor/TrpE_entry_1.pdbqt \\
+                          ./config/TrpE_entry_1.box.txt \\
+                          ./ligand/pdbqt{idx} \\
+                          ./result/poses{idx} \\
+                          ./result/batch_docking{idx}.log ./vina 
+cd ./result/poses{idx} 
+module load mamba
+micromamba run -n vina mk_export.py ./*_out.pdbqt --suffix _converted
+date
+"""
+
+submit_sh_list = []
+for i in range(1, n_splits + 1):
+    sh_content = sh_template.format(idx=i)
+    sh_path = Path(f'./submit_vina{i}.sh')
+    with open(sh_path, 'w') as f:
+        f.write(sh_content)
+    os.chmod(sh_path, 0o755)
+    submit_sh_list.append(sh_path)
+
+print(f"Done! {total} pdbqt files split to {n_splits} folders, {n_splits} shell scripts generated.")
+
+import time
+
+# 自动提交
+for i, sh_path in enumerate(submit_sh_list, 1):
+    print(f"提交: dsub -s {sh_path}")
+    subprocess.run(['dsub', '-s', str(sh_path)])
+    time.sleep(1)  # 每次提交后等待1秒
+