first add

scripts/batch_prepare_ligands.sh

@@ -0,0 +1,83 @@
+#!/bin/bash
+
+# 并行批量准备配体脚本（带日志记录 + GNU parallel）
+# 用法: ./batch_prepare_ligands_parallel.sh input_sdf_dir output_pdbqt_dir [log_file] [max_jobs]
+
+if [ $# -lt 2 ] || [ $# -gt 4 ]; then
+    echo "用法: $0 <输入SDF目录> <输出PDBQT目录> [日志文件] [并发数]"
+    exit 1
+fi
+
+INPUT_DIR="$1"
+OUTPUT_DIR="$2"
+LOG_FILE="${3:-batch_prepare_ligands_parallel.log}"
+MAX_JOBS="${4:-4}"  # 默认4并发
+
+# 创建输出目录和日志文件
+mkdir -p "$OUTPUT_DIR"
+mkdir -p "$(dirname "$LOG_FILE")"
+
+# 初始化日志文件
+echo "=== 并行批量配体准备日志 ===" > "$LOG_FILE"
+echo "开始时间: $(date)" >> "$LOG_FILE"
+echo "输入目录: $INPUT_DIR" >> "$LOG_FILE"
+echo "输出目录: $OUTPUT_DIR" >> "$LOG_FILE"
+echo "最大并发数: $MAX_JOBS" >> "$LOG_FILE"
+echo "================================" >> "$LOG_FILE"
+
+export OUTPUT_DIR LOG_FILE
+
+# 单个任务的处理逻辑，写成函数供parallel调用
+process_ligand() {
+    sdf_file="$1"
+    basename=$(basename "$sdf_file" .sdf)
+    output_file="$OUTPUT_DIR/${basename}.pdbqt"
+    error_file=$(mktemp)
+
+    if mk_prepare_ligand.py -i "$sdf_file" -o "$output_file" 2>"$error_file"; then
+        echo "[SUCCESS] $(date): $basename -> $output_file" >> "$LOG_FILE"
+        rm -f "$error_file"
+        echo "SUCCESS $sdf_file"
+    else
+        {
+            echo "[FAILED] $(date): $basename"
+            echo "  输入文件: $sdf_file"
+            echo "  预期输出: $output_file"
+            echo "  错误信息:"
+            if [ -s "$error_file" ]; then
+                sed 's/^/    /' "$error_file"
+            else
+                echo "    未捕获到具体错误信息"
+            fi
+            echo ""
+        } >> "$LOG_FILE"
+        rm -f "$error_file"
+        echo "FAILED $sdf_file"
+    fi
+}
+
+export -f process_ligand
+
+echo "开始并行批量准备配体..."
+echo "输入目录: $INPUT_DIR"
+echo "输出目录: $OUTPUT_DIR"
+echo "日志文件: $LOG_FILE"
+echo "最大并发数: $MAX_JOBS"
+
+# 用 parallel 调度
+results=$(find "$INPUT_DIR" -maxdepth 1 -name '*.sdf' | parallel -j "$MAX_JOBS" process_ligand {})
+
+count=$(echo "$results" | grep -c '^SUCCESS ')
+failed=$(echo "$results" | grep -c '^FAILED ')
+
+# 汇总统计
+echo "================================" >> "$LOG_FILE"
+echo "结束时间: $(date)" >> "$LOG_FILE"
+echo "成功处理: $count 个配体" >> "$LOG_FILE"
+echo "失败: $failed 个配体" >> "$LOG_FILE"
+
+echo "批量准备完成!"
+echo "成功处理: $count 个配体"
+echo "失败: $failed 个配体"
+echo "详细日志请查看: $LOG_FILE"
+