removed `/scratch/xiaobo/56659/xdo-8058088.93/working/protonate/xdo-protomers.ism' removed `/scratch/xiaobo/56659/xdo-8058088.93/working/protonate/xdo-protonated-manual.ism' removed `/scratch/xiaobo/56659/xdo-8058088.93/working/protonate/xdo-protomers-expanded.ism' removed directory: `/scratch/xiaobo/56659/xdo-8058088.93/working/protonate' removed `/scratch/xiaobo/56659/xdo-8058088.93/working/input-smiles.ism'