Closed drorhunvural closed 1 year ago
1 represents the class, yes i believe the protein_0.gninatypes file should be enough though Im not sure if it will provide an error (semantic or syntax) in the code
Hello @drorhunvural 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.
My question is simple, but I believe it will be useful for everyone to understand the paper better.
The following code block needs to be run to train the classification
python train.py -m model.py --train_types scPDB_train0.types --test_types scPDB_test0.types -i 200000 --train_recmolcache scPDB_new.molcache2 --test_recmolcache scPDB_new.molcache2 -r val0 -o /model_saves/val9 --base_lr 0.001 --solver Adam
Here is an example line of the train and test files as follows
1 50.69633356250253 -8.818796255105756 9.213237190116068 2bel_4/protein_0.gninatypes 2bel_4/cavity6.mol2
I have two questions.
First, what does the number 1 in the first part represent?
My second question is that does the last part of the dataset need to be in the train and test files? (Las part means:
2bel_4/cavity6.mol2
) If I delete the2bel_4/cavity6.mol2
in the last part, will the train part work or do I need themol2
files too? Isn't just the gninatype enough (2bel_4/protein_0.gninatypes
)?