removed `/scratch/xiaobo/129028/xad-8058097.4/working/protonate/xad-protomers-expanded.ism' removed `/scratch/xiaobo/129028/xad-8058097.4/working/protonate/xad-protomers.ism' removed `/scratch/xiaobo/129028/xad-8058097.4/working/protonate/xad-protonated-manual.ism' removed directory: `/scratch/xiaobo/129028/xad-8058097.4/working/protonate' removed `/scratch/xiaobo/129028/xad-8058097.4/working/input-smiles.ism'