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cannot generate hdf5 for some complexes

See original GitHub issue

code and data: /projects/0/deeprank/BM5/issue147

Create new database ./1ZM4.hdf5

Start creating HDF5 database: ./1ZM4.hdf5 Creating database : 0%| | 0/1 [00:00<?, ?it/s, mol=1ZM4_ranair-it0_9812.pdb] Processing PDB file: ./decoys/1ZM4/1ZM4_ranair-it0_9812.pdb /home/lixue1/tools/pdb2sql/pdb2sql/pdb2sqlcore.py:194: UserWarning: Missing chainID and set it with segID warnings.warn(“Missing chainID and set it with segID”) Traceback (most recent call last): File “hdf5_generate.py”, line 47, in <module> database.create_database(prog_bar=True) File “/nfs/home6/lixue1/deeprank/deeprank/generate/DataGenerator.py”, line 439, in create_database self._rotate_feature(molgrp, axis, angle, mol_center) File “/nfs/home6/lixue1/deeprank/deeprank/generate/DataGenerator.py”, line 1581, in _rotate_feature xyz = data[:, 1:4] IndexError: too many indices for array Creating database : 0%| | 0/1 [00:12<?, ?it/s, mol=1ZM4_ranair-it0_9812.pdb]

Issue Analytics

State:
Created 3 years ago
Comments:17 (17 by maintainers)

Top GitHub Comments

1reaction

NicoRenaudcommented, Apr 14, 2020

I think we will always find some PDB for which the data generation will fail. We should try to cover most cases but covering them all is unrealistic (especially with the amount of hours we have left 😦 )

Maybe we should add a best practice for the data quality, i.e. a description of how to prepare data for DeepRank to be able to exploit them.

0reactions

LilySnowcommented, Apr 17, 2020

Perfect 😃 I will regenerate the data then.

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