Hi, I'm having trouble running the script reconstruct.py. Could you please help identify the issue?
Command:
python foldtoken/reconstruct.py --path_in foldtoken/pdb/ --path_out foldtoken/pdb/ --level 8
Output:
Traceback (most recent call last):
File "/opt/conda/envs/flash_1/lib/python3.9/site-packages/pytorch_lightning/utilities/parsing.py", line 289, in __getattr__
return self[key]
KeyError: 'k_neighbors'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/data/workspace/FoldToken_open/foldtoken/reconstruct.py", line 38, in <module>
model = load_model(args)
File "/data/workspace/FoldToken_open/foldtoken/reconstruct.py", line 15, in load_model
model = MInterface(**config)
File "/data/workspace/FoldToken_open/foldtoken/model_interface.py", line 28, in __init__
super().__init__()
File "/data/workspace/FoldToken_open/foldtoken/src/interface/model_interface.py", line 13, in __init__
self.load_model()
File "/data/workspace/FoldToken_open/foldtoken/model_interface.py", line 60, in load_model
self.model = PiFold_Model(self.hparams)
File "/data/workspace/FoldToken_open/foldtoken/src/models/FoldToken4.py", line 28, in __init__
self.top_k = args.k_neighbors
File "/opt/conda/envs/flash_1/lib/python3.9/site-packages/pytorch_lightning/utilities/parsing.py", line 291, in __getattr__
raise AttributeError(f'Missing attribute "{key}"') from exp
AttributeError: Missing attribute "k_neighbors"Conda environment:
# packages in environment at /opt/conda/envs/flash:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.0.0 pypi_0 pypi
aiohttp 3.8.5 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
antlr4-python3-runtime 4.9.3 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
async-timeout 4.0.2 pypi_0 pypi
attrs 23.1.0 pypi_0 pypi
bio 1.5.9 pypi_0 pypi
biopython 1.81 pypi_0 pypi
biothings-client 0.3.0 pypi_0 pypi
biotite 0.37.0 pypi_0 pypi
blas 1.0 mkl conda-forge
brotlipy 0.7.0 py39h27cfd23_1003 anaconda
bzip2 1.0.8 h4bc722e_7 conda-forge
ca-certificates 2023.5.7 hbcca054_0 conda-forge
certifi 2023.7.22 py39h06a4308_0 anaconda
cffi 1.15.1 py39h5eee18b_3 anaconda
charset-normalizer 2.0.4 pyhd3eb1b0_0 anaconda
click 8.1.6 pypi_0 pypi
contextlib2 21.6.0 pypi_0 pypi
contourpy 1.2.0 pypi_0 pypi
cryptography 41.0.2 py39h22a60cf_0 anaconda
cuda-cccl 12.6.77 0 nvidia
cuda-cccl_linux-64 12.6.77 0 nvidia
cuda-command-line-tools 11.7.1 0 nvidia
cuda-compiler 12.6.2 0 nvidia
cuda-cudart 11.7.99 0 nvidia
cuda-cudart-dev 11.7.99 0 nvidia
cuda-cuobjdump 12.6.77 0 nvidia
cuda-cupti 11.7.101 0 nvidia
cuda-cuxxfilt 12.6.77 0 nvidia
cuda-documentation 12.4.127 0 nvidia
cuda-driver-dev 12.6.77 0 nvidia
cuda-driver-dev_linux-64 12.6.77 0 nvidia
cuda-gdb 12.6.77 0 nvidia
cuda-libraries 11.7.1 0 nvidia
cuda-libraries-dev 12.6.2 0 nvidia
cuda-memcheck 11.8.86 0 nvidia
cuda-nsight 12.6.77 0 nvidia
cuda-nvcc 11.7.99 0 nvidia/label/cuda-11.7.1
cuda-nvdisasm 12.6.77 0 nvidia
cuda-nvml-dev 12.6.77 2 nvidia
cuda-nvprof 12.6.80 0 nvidia
cuda-nvprune 12.6.77 0 nvidia
cuda-nvrtc 11.7.99 0 nvidia
cuda-nvrtc-dev 11.7.99 0 nvidia
cuda-nvtx 11.7.91 0 nvidia
cuda-nvvp 12.6.80 0 nvidia
cuda-opencl 12.6.77 0 nvidia
cuda-opencl-dev 12.6.77 0 nvidia
cuda-profiler-api 12.6.77 0 nvidia
cuda-runtime 11.7.1 0 nvidia
cuda-sanitizer-api 12.6.77 0 nvidia
cuda-toolkit 11.7.1 0 nvidia/label/cuda-11.7.1
cuda-tools 11.7.1 0 nvidia
cuda-version 12.6 3 nvidia
cuda-visual-tools 12.6.2 0 nvidia
cycler 0.12.1 pypi_0 pypi
dbus 1.13.18 hb2f20db_0 anaconda
deepspeed 0.10.3 pypi_0 pypi
dm-tree 0.1.8 pypi_0 pypi
docker-pycreds 0.4.0 pypi_0 pypi
easydict 1.10 pypi_0 pypi
einops 0.6.1 pypi_0 pypi
expat 2.6.4 h6a678d5_0 anaconda
fair-esm 2.0.0 pypi_0 pypi
ffmpeg 4.3 hf484d3e_0 pytorch
filelock 3.9.0 py39h06a4308_0 anaconda
fontconfig 2.14.1 hef1e5e3_0 anaconda
fonttools 4.47.2 pypi_0 pypi
freetype 2.12.1 h4a9f257_0 anaconda
frozenlist 1.4.0 pypi_0 pypi
fsspec 2023.6.0 pypi_0 pypi
gds-tools 1.7.0.149 0 nvidia
giflib 5.2.1 h5eee18b_3 anaconda
gitdb 4.0.10 pypi_0 pypi
gitpython 3.1.32 pypi_0 pypi
glib 2.78.4 h6a678d5_0 anaconda
glib-tools 2.78.4 h6a678d5_0 anaconda
gmp 6.2.1 h295c915_3 anaconda
gmpy2 2.1.2 py39heeb90bb_0 anaconda
gnutls 3.6.15 he1e5248_0 anaconda
gprofiler-official 1.0.0 pypi_0 pypi
hjson 3.1.0 pypi_0 pypi
huggingface-hub 0.25.1 pypi_0 pypi
icu 58.2 hf484d3e_1000 conda-forge
idna 3.4 py39h06a4308_0 anaconda
imageio 2.35.1 pypi_0 pypi
importlib-resources 6.1.1 pypi_0 pypi
intel-openmp 2023.1.0 hdb19cb5_46306 anaconda
intelpython 2025.0.0 1 https://software.repos.intel.com/python/conda
jinja2 3.1.2 py39h06a4308_0 anaconda
joblib 1.3.1 pypi_0 pypi
jpeg 9e h5eee18b_1 anaconda
kiwisolver 1.4.5 pypi_0 pypi
lame 3.100 h7b6447c_0 anaconda
lazy-loader 0.4 pypi_0 pypi
lcms2 2.12 h3be6417_0 anaconda
ld_impl_linux-64 2.38 h1181459_1 anaconda
lerc 3.0 h295c915_0 anaconda
libcublas 11.10.3.66 0 nvidia
libcublas-dev 11.10.3.66 0 nvidia
libcufft 10.7.2.124 h4fbf590_0 nvidia
libcufft-dev 10.7.2.124 h98a8f43_0 nvidia
libcufile 1.7.0.149 0 nvidia
libcufile-dev 1.7.0.149 0 nvidia
libcurand 10.3.3.53 0 nvidia
libcurand-dev 10.3.3.53 0 nvidia
libcusolver 11.4.0.1 0 nvidia
libcusolver-dev 11.4.0.1 0 nvidia
libcusparse 11.7.4.91 0 nvidia
libcusparse-dev 11.7.4.91 0 nvidia
libdeflate 1.17 h5eee18b_0 anaconda
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libglib 2.78.4 hdc74915_0 anaconda
libgomp 12.2.0 h65d4601_19 conda-forge
libiconv 1.16 h7f8727e_2 anaconda
libidn2 2.3.4 h5eee18b_0 anaconda
libnpp 11.7.4.75 0 nvidia
libnpp-dev 11.7.4.75 0 nvidia
libnsl 2.0.0 h7f98852_0 conda-forge
libnvfatbin 12.6.77 0 nvidia
libnvfatbin-dev 12.6.77 0 nvidia
libnvjitlink 12.6.85 0 nvidia
libnvjitlink-dev 12.6.85 0 nvidia
libnvjpeg 11.8.0.2 0 nvidia
libnvjpeg-dev 11.8.0.2 0 nvidia
libpng 1.6.39 h5eee18b_0 anaconda
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libtasn1 4.19.0 h5eee18b_0 anaconda
libtiff 4.5.0 h6a678d5_2 anaconda
libunistring 0.9.10 h27cfd23_0 anaconda
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp 1.2.4 h11a3e52_1 anaconda
libwebp-base 1.2.4 h5eee18b_1 anaconda
libxcb 1.16 hd590300_0 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.14 h74e7548_0 anaconda
lightning-utilities 0.9.0 pypi_0 pypi
lmdb 1.4.1 pypi_0 pypi
lpips 0.1.4 pypi_0 pypi
lz4-c 1.9.4 h6a678d5_0 anaconda
markupsafe 2.1.1 py39h7f8727e_0 anaconda
matplotlib 3.8.2 pypi_0 pypi
mkl 2023.1.0 h6d00ec8_46342 anaconda
mkl-service 2.4.0 py39h5eee18b_1 anaconda
mkl_fft 1.3.6 py39h417a72b_1 anaconda
mkl_random 1.2.2 py39h417a72b_1 anaconda
ml-collections 0.1.1 pypi_0 pypi
mpc 1.1.0 h10f8cd9_1 anaconda
mpfr 4.0.2 hb69a4c5_1 anaconda
mpmath 1.2.1 py39h06a4308_0 anaconda
msgpack 1.0.5 pypi_0 pypi
multidict 6.0.4 pypi_0 pypi
mygene 3.2.2 pypi_0 pypi
ncurses 6.4 hcb278e6_0 conda-forge
nettle 3.7.3 hbbd107a_1 anaconda
networkx 2.8.4 py39h06a4308_1 anaconda
ninja 1.11.1 pypi_0 pypi
nsight-compute 2024.3.2.3 0 nvidia
nspr 4.35 h27087fc_0 conda-forge
nss 3.89.1 h6a678d5_0 anaconda
numpy 1.25.0 py39h5f9d8c6_0 anaconda
numpy-base 1.25.0 py39hb5e798b_0 anaconda
omegaconf 2.3.0 pypi_0 pypi
opencv-python 4.10.0.84 pypi_0 pypi
opencv-python-headless 4.10.0.84 pypi_0 pypi
openh264 2.1.1 h4ff587b_0 anaconda
openssl 3.1.1 hd590300_1 conda-forge
packaging 23.1 pypi_0 pypi
pandas 2.0.3 pypi_0 pypi
pathtools 0.1.2 pypi_0 pypi
pcre2 10.42 hebb0a14_1 anaconda
pillow 9.4.0 py39h6a678d5_0 anaconda
pip 23.1.2 pyhd8ed1ab_0 conda-forge
platformdirs 3.11.0 pypi_0 pypi
pooch 1.7.0 pypi_0 pypi
protobuf 4.23.4 pypi_0 pypi
psutil 5.9.5 pypi_0 pypi
ptflops 0.7 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
py-cpuinfo 9.0.0 pypi_0 pypi
pycparser 2.21 pyhd3eb1b0_0 anaconda
pydantic 1.10.12 pypi_0 pypi
pyg-lib 0.4.0+pt20cu117 pypi_0 pypi
pyopenssl 23.2.0 py39h06a4308_0 anaconda
pyparsing 3.1.0 pypi_0 pypi
pysocks 1.7.1 py39h06a4308_0 anaconda
python 3.9.17 h955ad1f_0 anaconda
python-dateutil 2.8.2 pypi_0 pypi
python_abi 3.9 2_cp39 conda-forge
pytorch 2.0.1 py3.9_cuda11.7_cudnn8.5.0_0 pytorch
pytorch-cuda 11.7 h778d358_5 pytorch
pytorch-lightning 1.9.0 pypi_0 pypi
pytorch-mutex 1.0 cuda pytorch
pytz 2023.3 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
regex 2023.6.3 pypi_0 pypi
requests 2.29.0 py39h06a4308_0 anaconda
safetensors 0.4.5 pypi_0 pypi
scikit-image 0.24.0 pypi_0 pypi
scikit-learn 1.3.0 pypi_0 pypi
scipy 1.11.1 pypi_0 pypi
seaborn 0.13.1 pypi_0 pypi
sentry-sdk 1.28.1 pypi_0 pypi
sequence-models 1.7.0 pypi_0 pypi
setproctitle 1.3.2 pypi_0 pypi
setuptools 67.7.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
smmap 5.0.0 pypi_0 pypi
sqlite 3.41.2 h5eee18b_0 anaconda
sympy 1.11.1 py39h06a4308_0 anaconda
tbb 2021.8.0 hdb19cb5_0 anaconda
tensorboardx 2.6.2.2 pypi_0 pypi
threadpoolctl 3.2.0 pypi_0 pypi
tifffile 2024.8.30 pypi_0 pypi
tk 8.6.12 h1ccaba5_0 anaconda
tokenizers 0.20.0 pypi_0 pypi
torch-cluster 1.6.1+pt20cu117 pypi_0 pypi
torch-geometric 2.3.1 pypi_0 pypi
torch-scatter 2.1.1+pt20cu117 pypi_0 pypi
torch-sparse 0.6.17+pt20cu117 pypi_0 pypi
torch-spline-conv 1.2.2+pt20cu117 pypi_0 pypi
torchaudio 2.0.2 py39_cu117 pytorch
torcheval 0.0.7 pypi_0 pypi
torchmetrics 1.0.1 pypi_0 pypi
torchtriton 2.0.0 py39 pytorch
torchvision 0.15.2 py39_cu117 pytorch
tqdm 4.65.0 pypi_0 pypi
transformers 4.45.1 pypi_0 pypi
typing_extensions 4.7.1 py39h06a4308_0 anaconda
tzdata 2023.3 pypi_0 pypi
urllib3 1.26.16 py39h06a4308_0 anaconda
wandb 0.15.7 pypi_0 pypi
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xz 5.4.2 h5eee18b_0 anaconda
yacs 0.1.8 pypi_0 pypi
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.2 pypi_0 pypi
zipp 3.17.0 pypi_0 pypi
zlib 1.2.13 h5eee18b_0 anaconda
zstd 1.5.5 hc292b87_0 anaconda
Hi, I'm having trouble running the script
reconstruct.py. Could you please help identify the issue?Command:
Output:
Conda environment: