Closed fengyuewuya closed 1 year ago
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
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
The error result:
I can't find the directory named 4jpc_1 in the compressed package. Can you show me your directory structure?
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
The error result:
I can't find the directory named 4jpc_1 in the compressed package. Can you show me your directory structure? ------------------ 原始邮件 ------------------ 发件人: "devalab/DeepPocket" @.>; 发送时间: 2022年11月15日(星期二) 凌晨0:42 @.>; @.**@.>; 主题: Re: [devalab/DeepPocket] lack of gninatypes files (Issue #18)
Closed #18 as completed.
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I think your train recmolcache should be the scpdb recmocache
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
Error report:
Maybe the package environment is wrong? or Some files are missing?
I have solved this problem by downloading the scPDB original data and set the data_dir. Thx a lot.
@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:
I am tried on this pdb.
Thank you very much.
p.s: I have asked in the issue https://github.com/devalab/DeepPocket/issues/26.
I have solved this problem by downloading the scPDB original data and set the data_dir. Thx a lot.
@fengyuewuya could you elaborate on how you fixed this issue? Because I've run into the exact same issue but no fix seems to work.
Hi, I want to use the train_segmentation.py , but it is prompted that the gninatypes file is missing. Can you provide this part of the file? or should I process these files? THX