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