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rdk / p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

Home Page:https://rdk.github.io/p2rank/

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File path in *.ds file

JinyuanSun opened this issue · comments

commented

Hi,
It seems the file name in *.ds file does not support an absolute path like /home/user/dataset/*.pdb.
I have a .ds file:

/home/jsun/gpse_v2/test/structure_dataset/A0A1Q8LK65_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/W7ISS8_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A5EDZ7_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A0A3G7HEQ2_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A0A6J4VWF3_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A0A1R4K1N1_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A0A7W8E001_AF.pdb

and in the error log:

[INFO] Console - ----------------------------------------------------------------------------------------------
[INFO] Console -  P2Rank 2.4
[INFO] Console - ----------------------------------------------------------------------------------------------
[INFO] Console - 
[INFO] Main - loading default config from [/home/jsun/gpse_v2/p2rank_2.4/config/default.groovy]
[INFO] Main - looking for dataset in dataset_base_dir [/home/jsun/gpse_v2/GPSE/filtered.ds]...
[INFO] Dataset - loading dataset [/home/jsun/gpse_v2/GPSE/filtered.ds]
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A7W8E001_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/W7ISS8_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A1Q8LK65_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A5EDZ7_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A1M4DY30_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A447WAH0_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A1R4K1N1_AF.pdb

How can I modify the setting to avoid this? Thanks a lot! 🙏

commented

Thanks for the bug report. This is a bug and unfortunately there is no workaround or setting that would fix it.

It fill be fixed in the next release. It's already fixed in develop branch so you can make your own build.

commented

Fix will be included in the next release.

commented

Fix released in 2.4.1