Closed fengyuewuya closed 1 year ago
Some proteins have more than 1 pocket (albeit under different folder names), the types files ensures that the structures have all the relevant pockets matched
Get, Thx
@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.
Hi, I read the train.types like seg_scPDB_train0.types. The first few lines are as follows: 1 -18.161927039784217 32.606813980669806 85.32244760620364 10mh_1/protein_0.gninatypes 10mh_1/cavity6.mol2 1 -11.51310276710522 28.98620689253697 91.02771812783796 10mh_1/protein_0.gninatypes 10mh_1/cavity6.mol2 1 14.198903210849663 9.972515184884662 25.079490147212237 12gs_1/protein_0.gninatypes 12gs_1/cavity6.mol2 1 6.117556524238361 -2.4037784058248697 32.47945066104617 12gs_1/protein_0.gninatypes 12gs_1/cavity6.mol2
My confusion is that for this PDB 10mh_1 , it seems that there is only one cavity in the source folder "scPDB/10mh_1/", but there are two lines about 10mh_1 in seg_scPDB_train0.types.![image](https://user-images.githubusercontent.com/19147255/201896944-524118b6-6db3-47eb-9ddc-863631ab1840.png)