deepmodeling / deepmodeling/Uni-Mol
构象优化评测问题
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- Python
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Description
在构象优化drugs集评测时,使用conf_gen_cal_metrics脚本对评测分子的初始构象生成时,一直跑不出结果,看了具体过程,是先生成M多的初始构象,然后聚类成N类(N为评测构象的2倍),再在每类取一个,共取2N个初始构象,整个初始构象生成过程很耗时,为何要这样操作,这样操作评估效果最好吗?真正在推理过程中,这样操作,会增加推理的时间吧?并且用的target的mol去生成初始构象,为何不是用smiles,这块有点不理解,多谢解答
- Run this command,
mode="gen_data"
nthreads=20 # Num of threads
reference_file="./conformation_generation/drugs/test_data_200.pkl" # Your reference file dir
output_dir="./conformation_generation/drugs" # Generated initial data dir
python ./unimol/utils/conf_gen_cal_metrics.py --mode $mode --nthreads $nthreads --reference-file $reference_file --output-dir $output_dir
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