Comments (9)
if you are using a new dataset, you'd probably have to create them, if you are using a dataset we used in the publication then you can use the molcache files present in the dataset link provided on the README
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Hi, I use the molcache holo4k.molcache2 and take the train_segmentation.py.
The code:
python train_segmentation.py --train_types train_segmentation_data/seg_holo4k_train.types --test_types train_segmentation_data/seg_holo4k_test.types -d tmp_data/holo4k_cavity/holo4k/ --train_recmolcache train_segmentation_data/holo4k.molcache2 --test_recmolcache train_segmentation_data/holo4k.molcache2 -b 8 -o model_saves/seg9 -e 200 -r seg9
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I can't find the directory named 4jpc_1 in the compressed package.
Can you show me your directory structure?
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I think your train recmolcache should be the scpdb recmocache
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I take the scPDB molcache2 and types.
but there still report the error as bellow.
The code:
python train_segmentation.py
--train_types train_segmentation_data/seg_scPDB_train9.types
--test_types train_segmentation_data/seg_scPDB_test9.types
-d data/
--train_recmolcache train_segmentation_data/scPDB_new.molcache2
--test_recmolcache train_segmentation_data/scPDB_new.molcache2
-b 8
-o model_saves/seg9
-e 200
-r seg9
Maybe the package environment is wrong?
or
Some files are missing?
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I have solved this problem by downloading the scPDB original data and set the data_dir.
Thx a lot.
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@fengyuewuya have you re-run data preparation for a custom data? If yes, please help me.
I am trying to use the instruction to prepare data for training a new classifier.
I have stuck in make_types step because I can't find train.txt and test.txt files.
Moreover, I have 4 questions:
- If I want to add several pdb files to the available scPDB dataset, how can I complete it?
- The instruction for preparing data only works for a single pdb file, does it? If not, I need to write a pipeline to wrap up it.
- How to prepare train.txt and test.txt files to run make_types.py?
- Could you please show me which file/folder needed inputting from previous to each step?
I am tried on this pdb.
Thank you very much.
p.s: I have asked in the issue #26.
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Related Issues (20)
- Data Preparation for HOLO4K HOT 3
- How to avoid data leakage? HOT 1
- How to prepare the inputs for training segmentation model? HOT 2
- bary_centers.txt Issue
- Prediction Error
- rank_pockets.py - UserWarning HOT 1
- Training Classifier Problem HOT 1
- Transform part in Train HOT 5
- The number of pocket in types file HOT 3
- .
- predict.py running error HOT 2
- Understanding the Train Dataset for Training Part HOT 2
- Pocket Probability HOT 1
- Channels in training script are different from those in your Supporting Information table s1 HOT 6
- Do not have files for running make_types.py when prerparing custom data for training a new classifier HOT 3
- Training Classifier Dataset HOT 8
- Question about classes HOT 2
- segmentation fault HOT 4
- Full test scripts to reproduce the metrics results in the paper. HOT 6
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