Problem to dowload weights and with aromatics/symmetric compounds about flexpose

[tiejundong]

Thanks for your attention to our work.

• You can download parameters here.
• The energy minimization improves the geometric correctness of local structures, e.g., aromatics/symmetric parts. If the local structure is not correct, one may consider the following: 1. enhancing energy minimization (set min_loop=100 or set min_type='LBFGS'). 2. decreasing constraint energy minimizion constant (set min_constraint=0). 3. Failed energy minimization in rare cases (i.e. failed to extract force field parameters in preprocessing). Although minimizing energy can improve local structural correctness, it cannot be expected to be utilized to improve accuracy as mentioned in our article and a recent study (Zhang, Xujun, et al. Nature Computational Science 3.9 (2023): 789-804.), especially for the highly flexible polymer-like ligand you provided, which is more challenging (Wang, Zhe, et al. Physical Chemistry Chemical Physics 18.18 (2016): 12964-12975.).

[xqh19970407]

i got an error, can you help me?

==================== Running FlexPose ====================
2023-12-20 17:51:09,278 ERROR services.py:1363 -- Failed to start the dashboard: Failed to start the dashboard, return code 1
The last 10 lines of /tmp/ray/session_2023-12-20_17-51-06_723181_132336/logs/dashboard.log:
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/aiohttp/client_reqrep.py", line 72, in
import charset_normalizer as chardet # type: ignore[no-redef]
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/init.py", line 24, in
from .api import from_bytes, from_fp, from_path, is_binary
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/api.py", line 5, in
from .cd import (
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/cd.py", line 14, in
from .md import is_suspiciously_successive_range
AttributeError: partially initialized module 'charset_normalizer' has no attribute 'md__mypyc' (most likely due to a circular import)
2023-12-20 17:51:09,278 ERROR services.py:1364 -- Failed to start the dashboard, return code 1
The last 10 lines of /tmp/ray/session_2023-12-20_17-51-06_723181_132336/logs/dashboard.log:
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/aiohttp/client_reqrep.py", line 72, in
import charset_normalizer as chardet # type: ignore[no-redef]
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/init.py", line 24, in
from .api import from_bytes, from_fp, from_path, is_binary
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/api.py", line 5, in
from .cd import (
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/cd.py", line 14, in
from .md import is_suspiciously_successive_range
AttributeError: partially initialized module 'charset_normalizer' has no attribute 'md__mypyc' (most likely due to a circular import)
Traceback (most recent call last):
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/ray/_private/services.py", line 1350, in start_dashboard
raise Exception(err_msg + last_log_str)
Exception: Failed to start the dashboard, return code 1
The last 10 lines of /tmp/ray/session_2023-12-20_17-51-06_723181_132336/logs/dashboard.log:
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/aiohttp/client_reqrep.py", line 72, in
import charset_normalizer as chardet # type: ignore[no-redef]
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/init.py", line 24, in
from .api import from_bytes, from_fp, from_path, is_binary
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/api.py", line 5, in
from .cd import (
File "/home/xiaoqi/miniconda3/envs/diffdock2/lib/python3.8/site-packages/charset_normalizer/cd.py", line 14, in
from .md import is_suspiciously_successive_range
AttributeError: partially initialized module 'charset_normalizer' has no attribute 'md__mypyc' (most likely due to a circular import)
2023-12-20 17:51:09,582 INFO worker.py:1518 -- Started a local Ray instance.
[2023-12-20 17:51:39,874 E 132336 132336] core_worker.cc:149: Failed to register worker 01000000ffffffffffffffffffffffffffffffffffffffffffffffff to Raylet. IOError: [RayletClient] Unable to register worker with raylet. No such file or directory

[tiejundong]

You can try setting prepare_data_with_multi_cpu to False to avoid processing by ray.

Besides, please do not raise irrelevant issues in other people's comments.