thuxugang/opus_mut

OPUS-Mut: Studying the Effect of Protein Mutation and protein-protein interaction through Side-Chain Modeling

opus_mut's Issues

rota_model_weight not found

Hi, I have a problem running opus-but. In the end there is a file that it could not be found.
./Mut/models/1/rota_model_weight
Can you help me with this error?

python run_opus_mut.py
2023-12-06 15:57:33.102023: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.10.1
2023-12-06 15:57:52.403166: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set
2023-12-06 15:57:52.404939: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1
2023-12-06 15:57:54.320273: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
pciBusID: 0000:3b:00.0 name: NVIDIA A100-PCIE-80GB computeCapability: 8.0
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.10GiB deviceMemoryBandwidth: 1.76TiB/s
2023-12-06 15:57:54.320312: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.10.1
2023-12-06 15:57:54.332054: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.10
2023-12-06 15:57:54.332163: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.10
2023-12-06 15:57:54.338664: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
2023-12-06 15:57:54.342752: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
2023-12-06 15:57:54.349358: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
2023-12-06 15:57:54.354895: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.10
2023-12-06 15:57:54.368042: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.7
2023-12-06 15:57:54.375938: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
2023-12-06 15:57:54.376622: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2023-12-06 15:57:54.380309: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties:
pciBusID: 0000:3b:00.0 name: NVIDIA A100-PCIE-80GB computeCapability: 8.0
coreClock: 1.41GHz coreCount: 108 deviceMemorySize: 79.10GiB deviceMemoryBandwidth: 1.76TiB/s
2023-12-06 15:57:54.380328: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.10.1
2023-12-06 15:57:54.380343: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublas.so.10
2023-12-06 15:57:54.380349: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcublasLt.so.10
2023-12-06 15:57:54.380356: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcufft.so.10
2023-12-06 15:57:54.380362: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcurand.so.10
2023-12-06 15:57:54.380368: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusolver.so.10
2023-12-06 15:57:54.380374: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcusparse.so.10
2023-12-06 15:57:54.380380: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudnn.so.7
2023-12-06 15:57:54.385658: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1862] Adding visible gpu devices: 0
2023-12-06 15:57:54.385686: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcudart.so.10.1
2023-12-06 16:01:08.277652: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix:
2023-12-06 16:01:08.277714: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] 0
2023-12-06 16:01:08.277731: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1280] 0: N
2023-12-06 16:01:08.291966: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1406] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 75603 MB memory) -> physical GPU (device: 0, name: NVIDIA A100-PCIE-80GB, pci bus id: 0000:3b:00.0, compute capability: 8.0)
2023-12-06 16:01:08.292338: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set
use rota model...
load model: rota4p1
Traceback (most recent call last):
File "/opt/tools/deg/miniforge3/envs/mut/lib/python3.7/site-packages/tensorflow/python/training/py_checkpoint_reader.py", line 95, in NewCheckpointReader
return CheckpointReader(compat.as_bytes(filepattern))
RuntimeError: Unsuccessful TensorSliceReader constructor: Failed to find any matching files for ./Mut/models/1/rota_model_weight

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "run_opus_mut.py", line 23, in
from Mut.inference import run_Mut
File "/DATA/34/CXCR4/OpusMut/Mut/inference.py", line 15, in
from Mut.inference_models import test_infer_step
File "/DATA/34/CXCR4/OpusMut/Mut/inference_models.py", line 30, in
model_rota1.load_model()
File "/DATA/34/CXCR4/OpusMut/Mut/my_model.py", line 85, in load_model
self.load_weights(os.path.join(self.params["save_path"], 'rota_model_weight'))
File "/opt/tools/deg/miniforge3/envs/mut/lib/python3.7/site-packages/tensorflow/python/keras/engine/training.py", line 2199, in load_weights
py_checkpoint_reader.NewCheckpointReader(filepath)
File "/opt/tools/deg/miniforge3/envs/mut/lib/python3.7/site-packages/tensorflow/python/training/py_checkpoint_reader.py", line 99, in NewCheckpointReader
error_translator(e)
File "/opt/tools/deg/miniforge3/envs/mut/lib/python3.7/site-packages/tensorflow/python/training/py_checkpoint_reader.py", line 35, in error_translator
raise errors_impl.NotFoundError(None, None, error_message)
tensorflow.python.framework.errors_impl.NotFoundError: Unsuccessful TensorSliceReader constructor: Failed to find any matching files for ./Mut/models/1/rota_model_weight

IndexError: list index out of range

Hi, I have this problem running opus_mut.
The test works fine, but with my protein I have this problem.
Can you help me?

/opt/tools/deg/opus_mut/Mut/mkdssp/mkdssp CXCR4_Y256M.bb                                                                               
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/opt/tools/deg/miniforge3/envs/mut/lib/python3.7/multiprocessing/pool.py", line 121, in worker
    result = (True, func(*args, **kwds))
  File "/opt/tools/deg/miniforge3/envs/mut/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
    return list(map(*args))
  File "run_opus_mut.py", line 47, in preparation
    make_input(filename, preparation_config)
  File "/opt/tools/deg/opus_mut/Mut/inference_utils.py", line 220, in make_input
    ss8, ss3 = read_ss(ss_path)
  File "/opt/tools/deg/opus_mut/Mut/inference_utils.py", line 190, in read_ss
    ss_result = ss_result[0]
IndexError: list index out of range
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "run_opus_mut.py", line 82, in <module>
    pool.map(preparation, multi_iters)
  File "/opt/tools/deg/miniforge3/envs/mut/lib/python3.7/multiprocessing/pool.py", line 268, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/opt/tools/deg/miniforge3/envs/mut/lib/python3.7/multiprocessing/pool.py", line 657, in get
    raise self._value
IndexError: list index out of range

Error with GPU memory in running model

Hi, I tried to use opus_mut to predict mutation sidechain of protein(86 aa), when finished 3dcnn/csf15/1d_inputs/ss/trr100 and got they in tmp_files, it started running OPUS-Mut, in model1 running, it occupied 23000+M in a 3090(GPU with total 24267M memory) and then failed with gpu in-memory.
The error showed that "no kernel image is available for execution on the device [Op:Tanh]".
If it is convenient, we can exchange emails or wechat.

如何将预测结果转换为pdb格式？

预测结果文件是.mut文件，在一些分子模拟过程中常用pdb文件等，如何转化为pdb文件。.mut文件是你们自创的文件格式吗？

RES X1 X2 X3 X4 RMSD STD

1 P 14.53 -15.65 182.00 182.00 0.04 0.04
2 Q -60.59 -81.55 -5.15 182.00 0.54 0.02
3 I -66.28 168.13 182.00 182.00 0.33 0.02
4 T 55.92 182.00 182.00 182.00 0.05 0.10
5 L -67.94 170.96 182.00 182.00 0.15 0.16
6 W -64.67 108.14 182.00 182.00 0.09 0.08
7 Q -165.80 173.92 -0.02 182.00 0.35 0.20
8 R -101.49 163.83 86.16 178.90 0.75 0.17
9 P 24.46 -26.87 182.00 182.00 0.00 0.00
10 L -65.03 169.07 182.00 182.00 0.09 0.13
11 V -62.36 182.00 182.00 182.00 0.00 0.00
12 T 64.79 182.00 182.00 182.00 0.05 0.10A