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kiharalab / DOVE

A Deep-learning based dOcking decoy eValuation mEthod
GNU General Public License v3.0
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crashes on example input #1

Closed quantitative-technologies closed 4 years ago

quantitative-technologies commented 4 years ago

I tried running your code with:

python main.py --mode 0 -F Example/Decoys/complex.1.pdb

However, I receive an error:

/home/james/projects/docking/DOVE/Example/Decoys/complex.1888 created TER 838 ARG A 108

[error] encountered blank atom name TER 1743 SER B 116

[error] encountered blank atom name TER 1002 LEU C 129

[error] encountered blank atom name ENDMDL

[error] encountered blank atom name waiting dealing1 At line 113 of file goap_new.f (unit = 20, file = '/home/james/projects/docking/DOVE/Goap/fort.21_1.61_2') Fortran runtime error: Bad integer for item 1 in list input

Error termination. Backtrace:

0 0x7f0b3de0f7ba

1 0x7f0b3de10365

2 0x7f0b3de10b2d

3 0x7f0b3df7d034

4 0x7f0b3df8032a

5 0x7f0b3df81809

6 0x5603c7f370b4

7 0x5603c7f3b4a2

8 0x7f0b3dac11e2

9 0x5603c7f34ee9

10 0xffffffffffffffff

in total, we have 210 residues in receptor, 122 residues in ligand in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand after processing, we only remained 826 atoms in receptor, 492 atoms in ligand 209 atoms actually used in this receptor /home/james/projects/docking/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': /home/james/projects/docking/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': /home/james/projects/docking/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': 350 atoms actually used in this example C atom 50, N atom 25, O atom 25, other atom 250 in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand after processing, we only remained 826 atoms in receptor, 492 atoms in ligand 690 atoms actually used in this receptor 1139 atoms actually used in this example C atom 175, N atom 89, O atom 89, other atom 786 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 "/home/james/projects/docking/DOVE/Input_Preparing/Prepare_Input_Single.py", line 54, in Prepare_Input_Singe rlist, llist = form_goap_list(work_decoy2, rcount) File "/home/james/projects/docking/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: '/home/james/projects/docking/DOVE/Example/Decoys/complex.1888/888_goap.pdb'

wang3702 commented 4 years ago

Thanks a lot for detailed debug information! I just checked the debug information. I think that's because the file Goap/fort.21_1.61_2 or fort.31_g72_noshift5_new of dove is not successfully cloned by your repo because large files larger than 50MB can't be downloaded. Personally, I suggest you to clone from https://github.rcac.purdue.edu/kiharalab/DOVE to try again, which does not have file size limitations. If that still can't work, please update on this issue. Personally, I can't reproduce your error when I cloned this repo and simply run again.

quantitative-technologies commented 4 years ago

Yes, that was the issue. Thanks.

wang3702 commented 4 years ago

OK. I will close the issue. Thanks a lot for your feedback.

johnnytam100 commented 3 years ago

wang, I met the same problem even I clone by

git clone https://github.com/kiharalab/DOVE.git

Cloning into 'DOVE'...
remote: Enumerating objects: 21, done.
remote: Counting objects: 100% (21/21), done.
remote: Compressing objects: 100% (20/20), done.
remote: Total 352 (delta 4), reused 12 (delta 1), pack-reused 331
Receiving objects: 100% (352/352), 99.81 MiB | 20.68 MiB/s, done.
Resolving deltas: 100% (154/154), done.
Checking out files: 100% (141/141), done.

cd DOVE/

python main.py --mode 0 -F Example/Decoys/complex.1.pdb

2020-10-13 03:34:18.151177: W tensorflow/stream_executor/platform/default/dso_lo                                                                                                                                                                                                                                             ader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcuda                                                                                                                                                                                                                                             rt.so.10.1: cannot open shared object file: No such file or directory; LD_LIBRAR                                                                                                                                                                                                                                             Y_PATH: /home/xtal/PyRosetta.ScientificLinux-r56316.64Bit/rosetta::/home/xtal/ff                                                                                                                                                                                                                                             tw/fftw-2.1.5/local/lib:/home/xtal/mmdb/mmdb-1.21/local/lib
2020-10-13 03:34:18.151226: I tensorflow/stream_executor/cuda/cudart_stub.cc:29]                                                                                                                                                                                                                                              Ignore above cudart dlerror if you do not have a GPU set up on your machine.
/ydcs/cltam/20201021_test_DOVE/DOVE/Example/Decoys/complex.1888 existed
TER     838      ARG A 108

[error] encountered blank atom name
TER    1743      SER B 116

[error] encountered blank atom name
TER    1002      LEU C 129

[error] encountered blank atom name
ENDMDL

[error] encountered blank atom name
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 210 residues in receptor, 122 residues in ligand
in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor
in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand
after processing, we only remained 826 atoms in receptor, 492 atoms in ligand
209 atoms actually used in this receptor
/ydcs/cltam/20201021_test_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':
/ydcs/cltam/20201021_test_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':
/ydcs/cltam/20201021_test_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':
350 atoms actually used in this example
C atom 50, N atom 25, O atom 25, other atom 250
in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor
in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand
after processing, we only remained 826 atoms in receptor, 492 atoms in ligand
690 atoms actually used in this receptor
1139 atoms actually used in this example
C atom 175, N atom 89, O atom 89, other atom 786
Traceback (most recent call last):
  File "main.py", line 67, in <module>
    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 "/ydcs/cltam/20201021_test_DOVE/DOVE/Input_Preparing/Prepare_Input_Single.py", line 54, in Prepare_Input_Singe
    rlist, llist = form_goap_list(work_decoy2, rcount)
  File "/ydcs/cltam/20201021_test_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: '/ydcs/cltam/20201021_test_DOVE/DOVE/Example/Decoys/complex.1888/888_goap.pdb'

May I know is there something wrong with my git clone?

Thank you!

wang3702 commented 3 years ago

Hello, I think that is because you did not download goap dependency script. Maybe because they are large files. Thus, you can follow the instructions here https://github.com/kiharalab/DOVE#download-code.

On Wed, Oct 21, 2020 at 8:01 AM johnnytam100 notifications@github.com wrote:

wang, I met the same problem even I clone by

git clone https://github.com/kiharalab/DOVE.git

Cloning into 'DOVE'... remote: Enumerating objects: 21, done. remote: Counting objects: 100% (21/21), done. remote: Compressing objects: 100% (20/20), done. remote: Total 352 (delta 4), reused 12 (delta 1), pack-reused 331 Receiving objects: 100% (352/352), 99.81 MiB | 20.68 MiB/s, done. Resolving deltas: 100% (154/154), done. Checking out files: 100% (141/141), done.

cd DOVE/

python main.py --mode 0 -F Example/Decoys/complex.1.pdb 2020-10-13 03:34:18.151177: W tensorflow/stream_executor/platform/default/dso_lo ader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcuda rt.so.10.1: cannot open shared object file: No such file or directory; LD_LIBRAR Y_PATH: /home/xtal/PyRosetta.ScientificLinux-r56316.64Bit/rosetta::/home/xtal/ff tw/fftw-2.1.5/local/lib:/home/xtal/mmdb/mmdb-1.21/local/lib 2020-10-13 03:34:18.151226: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. /ydcs/cltam/20201021_test_DOVE/DOVE/Example/Decoys/complex.1888 existed TER 838 ARG A 108

[error] encountered blank atom name TER 1743 SER B 116

[error] encountered blank atom name TER 1002 LEU C 129

[error] encountered blank atom name ENDMDL

[error] encountered blank atom name 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 210 residues in receptor, 122 residues in ligand in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand after processing, we only remained 826 atoms in receptor, 492 atoms in ligand 209 atoms actually used in this receptor /ydcs/cltam/20201021_test_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': /ydcs/cltam/20201021_test_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': /ydcs/cltam/20201021_test_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': 350 atoms actually used in this example C atom 50, N atom 25, O atom 25, other atom 250 in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand after processing, we only remained 826 atoms in receptor, 492 atoms in ligand 690 atoms actually used in this receptor 1139 atoms actually used in this example C atom 175, N atom 89, O atom 89, other atom 786 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 "/ydcs/cltam/20201021_test_DOVE/DOVE/Input_Preparing/Prepare_Input_Single.py", line 54, in Prepare_Input_Singe rlist, llist = form_goap_list(work_decoy2, rcount) File "/ydcs/cltam/20201021_test_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: '/ydcs/cltam/20201021_test_DOVE/DOVE/Example/Decoys/complex.1888/888_goap.pdb'

May I know is there something wrong with my git clone?

Thank you!

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/kiharalab/DOVE/issues/1#issuecomment-713518231, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMD6TMF2CBQVUN4T6CT2DILSL3EP7ANCNFSM4LNY5DDQ .

johnnytam100 commented 3 years ago

Wang, thank you for the reply!

I have now performed the following:

Step1: clone DOVE

git clone https://github.rcac.purdue.edu/kiharalab/DOVE.git

Step2: download model files (due to large size, has to be downloaded separately from git clone)

wget http://kiharalab.org/dove/Large_LFSS.tar.gz
tar zxvf Large_LFSS.tar.gz

Step3: Replace files

rm -rf ./DOVE/Goap/
mv Large_LFS/Goap/ ./DOVE/
rm -rf ./DOVE/Best_Model/*
mv Large_LFS/* ./DOVE/Best_Model/

Then, I tested by:

cd DOVE
python main.py --mode 0 -F Example/Decoys/complex.1.pdb
2020-10-22 12:37:28.134594: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'libcudart.so.10.1'; dlerror: libcudart.so.10.1: cannot open shared object file: No such file or directory
2020-10-22 12:37:28.134766: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
/bwfefs/home/cltam/20200725_pose_prediction_neural_net/step7_benchmark_with_docking_methods/test_DOVE/DOVE_master/DOVE/Example/Decoys/complex.1888 existed
TER     838      ARG A 108

[error] encountered blank atom name
TER    1743      SER B 116

[error] encountered blank atom name
TER    1002      LEU C 129

[error] encountered blank atom name
ENDMDL

[error] encountered blank atom name
waiting dealing1
At line 110 of file goap.f (unit = 20, file = '▒▒▒^')
Fortran runtime error: File '/fort.21_1.61_2' does not exist
in total, we have 210 residues in receptor, 122 residues in ligand
in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor
in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand
after processing, we only remained 826 atoms in receptor, 492 atoms in ligand
209 atoms actually used in this receptor
/bwfefs/home/cltam/20200725_pose_prediction_neural_net/step7_benchmark_with_docking_methods/test_DOVE/DOVE_master/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':
/bwfefs/home/cltam/20200725_pose_prediction_neural_net/step7_benchmark_with_docking_methods/test_DOVE/DOVE_master/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':
/bwfefs/home/cltam/20200725_pose_prediction_neural_net/step7_benchmark_with_docking_methods/test_DOVE/DOVE_master/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':
350 atoms actually used in this example
C atom 50, N atom 25, O atom 25, other atom 250
in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor
in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand
after processing, we only remained 826 atoms in receptor, 492 atoms in ligand
690 atoms actually used in this receptor
1139 atoms actually used in this example
C atom 175, N atom 89, O atom 89, other atom 786
Traceback (most recent call last):
  File "main.py", line 67, in <module>
    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 "/bwfefs/home/cltam/20200725_pose_prediction_neural_net/step7_benchmark_with_docking_methods/test_DOVE/DOVE_master/DOVE/Input_Preparing/Prepare_Input_Single.py", line 54, in Prepare_Input_Singe
    rlist, llist = form_goap_list(work_decoy2, rcount)
  File "/bwfefs/home/cltam/20200725_pose_prediction_neural_net/step7_benchmark_with_docking_methods/test_DOVE/DOVE_master/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: '/bwfefs/home/cltam/20200725_pose_prediction_neural_net/step7_benchmark_with_docking_methods/test_DOVE/DOVE_master/DOVE/Example/Decoys/complex.1888/888_goap.pdb'

The output message changed, but still got the same error at last "FileNotFoundError: [Errno 2] No such file or directory: ..."

Do you have any idea how to proceed in such a case?

Sorry for the disturbance and thanks again!

farz1995 commented 9 months ago

Hello, I have the same issue with trying examples. I also try codes from git clone https://github.com/kiharalab/DOVE.git and download dependencies.

this is my error:

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/data/Dove888 created TER 838 ARG A 108

[error] encountered blank atom name TER 1743 SER B 116

[error] encountered blank atom name TER 1002 LEU C 129

[error] encountered blank atom name ENDMDL

[error] encountered blank atom name TER 838 ARG A 108

[error] encountered blank atom name TER 1743 SER B 116

[error] encountered blank atom name TER 1002 LEU C 129

[error] encountered blank atom name ENDMDL

[error] encountered blank atom name TER 838 ARG A 108

[error] encountered blank atom name TER 1743 SER B 116

[error] encountered blank atom name TER 1002 LEU C 129

[error] encountered blank atom name ENDMDL

[error] encountered blank atom name waiting dealing3 ./goap: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory in total, we have 210 residues in receptor, 122 residues in ligand in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand after processing, we only remained 826 atoms in receptor, 492 atoms in ligand 209 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': 350 atoms actually used in this example C atom 50, N atom 25, O atom 25, other atom 250 in the interface 10A cut off, we have 95 residue, 826 atoms in the receptor in the interface 10A cut off, we have 59 residue, 492 atoms in the ligand after processing, we only remained 826 atoms in receptor, 492 atoms in ligand 690 atoms actually used in this receptor 1139 atoms actually used in this example C atom 175, N atom 89, O atom 89, other atom 786 Traceback (most recent call last): File "main.py", line 76, in final_record,input_path=run_pred_list(file_path,gpu_id) File "main.py", line 33, in run_pred_list input_path = Prepare_Input_List(file_path, random_id) File "/mnt/pixstor/data/fe5vb/negin/dove/DOVE/Input_Preparing/Prepare_Input_List.py", line 75, in Prepare_Input_List 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/data/Dove888/1_goap.pdb' (/mnt/pixstor/data/fe5vb/negin/dove/dove) [fe5vb@hellbender-login DOVE]$ ^C (/mnt/pixstor/data/fe5vb/negin/dove/dove) [fe5vb@hellbender-login DOVE]$ python main.py --mode=0 -F Example/complex.1.pdb --id=888 --gpu=0 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/Example/complex.1888 created cp: cannot stat '/mnt/pixstor/data/fe5vb/negin/dove/DOVE/Example/complex.1.pdb': No such file or directory 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 25, in Prepare_Input_Singe Correct_WrongFormat(work_decoy1) File "/mnt/pixstor/data/fe5vb/negin/dove/DOVE/ops/Correct_WrongFormat.py", line 6, in Correct_WrongFormat with open(pdb_file,'r') as rfile: FileNotFoundError: [Errno 2] No such file or directory: '/mnt/pixstor/data/fe5vb/negin/dove/DOVE/Example/complex.1888/complex.888.pdb'

wang3702 commented 9 months ago

Thank you for your interest in this work. I think this is because you do not have Example/complex.1.pdb on your folder. You have the following error message.

cp: cannot stat '/mnt/pixstor/data/fe5vb/negin/dove/DOVE/Example/complex.1.pdb': No such file or directory

Also, we have an advanced version here https://github.com/kiharalab/GNN_DOVE. Please use this if you still have problems. If you only want to run a few examples, you can also try our server, which I believe is still functional: https://kiharalab.org/dove/

wang3702 commented 9 months ago

@johnnytam100 Sorry I did not see this three years ago. My bad because the issue has been closed. You should also download Goap directory following our instructions.

farz1995 commented 8 months ago

thank you so much for your answer. 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 <module>
    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'