goap.pdb not created #13
Comments
|
https://github.com/kiharalab/DOVE#download-code I think you did not follow the instructions here to configure the goap running script correctly? |
|
I have followed the structure line by line, extracted the file, and added best model and goap to my directory. but still I have problem |
|
This function did not execute properly: . Please check here https://github.com/kiharalab/DOVE/blob/master/Input_Preparing/Gen_Goap.py to see which files you are missing. |
|
thanks for your answer. this is a sample of my data: |
|
I got confused about your question. Does our example here https://github.com/kiharalab/DOVE/tree/master/Example/Decoys works for your running? If so, then it would be your input's problem, please compare it against our examples |
|
thank you for your answer. |
|
I think you did not install fortran locally, which may cause the failure of GOAP. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
my main problem is that _goap.pdb files are not created despite I have added all files. I have printed the pwd of 888_goap.pdb file but It is not created while running the code.
Using TensorFlow backend.
/mnt/pixstor/data/fe5vb/negin/dove/dove/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:463: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/mnt/pixstor/data/fe5vb/negin/dove/dove/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:464: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/mnt/pixstor/data/fe5vb/negin/dove/dove/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:465: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/mnt/pixstor/data/fe5vb/negin/dove/dove/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:466: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/mnt/pixstor/data/fe5vb/negin/dove/dove/lib/python3.5/site-packages/tensorflow/python/framework/dtypes.py:467: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/mnt/pixstor/data/fe5vb/negin/dove/DOVE/complex.999888 existed
klkllklklklklklllklklkklklklklklklklklk /mnt/pixstor/data/fe5vb/negin/dove/DOVE/complex.999888/complex.888.pdb
88888888888888888888888888888888888 /mnt/pixstor/data/fe5vb/negin/dove/DOVE/complex.999888/888_goap.pdb
waiting dealing1
./goap: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory
in total, we have 142 residues in receptor, 20 residues in ligand
in the interface 10A cut off, we have 81 residue, 707 atoms in the receptor
in the interface 10A cut off, we have 18 residue, 149 atoms in the ligand
after processing, we only remained 707 atoms in receptor, 149 atoms in ligand
308 atoms actually used in this receptor
/mnt/pixstor/data/fe5vb/negin/dove/DOVE/data_processing/prepare_input.py:360: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
if atom_type=='C' or atom_type=='CA':
/mnt/pixstor/data/fe5vb/negin/dove/DOVE/data_processing/prepare_input.py:366: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
elif atom_type=='N':
/mnt/pixstor/data/fe5vb/negin/dove/DOVE/data_processing/prepare_input.py:372: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
elif atom_type=='O':
386 atoms actually used in this example
C atom 85, N atom 43, O atom 42, other atom 216
in the interface 10A cut off, we have 81 residue, 707 atoms in the receptor
in the interface 10A cut off, we have 18 residue, 149 atoms in the ligand
after processing, we only remained 707 atoms in receptor, 149 atoms in ligand
661 atoms actually used in this receptor
782 atoms actually used in this example
C atom 175, N atom 90, O atom 87, other atom 430
Traceback (most recent call last):
File "main.py", line 67, in
record,input_path=run_pred_single(file_path,random_id,gpu_id)
File "main.py", line 16, in run_pred_single
input_path=Prepare_Input_Singe(file_path,random_id)
File "/mnt/pixstor/data/fe5vb/negin/dove/DOVE/Input_Preparing/Prepare_Input_Single.py", line 57, in Prepare_Input_Singe
rlist, llist = form_goap_list(work_decoy2, rcount)
File "/mnt/pixstor/data/fe5vb/negin/dove/DOVE/data_processing/prepare_goap_input.py", line 14, in form_goap_list
with open(item,'r') as file:
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/pixstor/data/fe5vb/negin/dove/DOVE/complex.999888/888_goap.pdb'
The text was updated successfully, but these errors were encountered: