新建
基于Uni-Mol的分子对接
zhougm@dp.tech
推荐镜像 :Uni-Mol:unimol-qsar:v0.5
推荐机型 :c3_m4_1 * NVIDIA T4
赞
2
2
目录
基于Uni-Mol的分子对接
代码
文本
[16]
%%bash
# 选择镜像：unimol-qsar:unimolxxlatest, 机型选择GPU
# 拉取数据、代码和模型权重
rm -rf CASF-2016.tar.gz
rm -rf CASF-2016
rm -rf binding_pose_220908.pt
rm -rf docking.tar.gz
rm -rf docking
wget -nv https://bohrium-example.oss-cn-zhangjiakou.aliyuncs.com/unimol-docking/CASF-2016.tar.gz
wget -nv https://bohrium-example.oss-cn-zhangjiakou.aliyuncs.com/unimol-docking/binding_pose_220908.pt
wget -nv https://bohrium-example.oss-cn-zhangjiakou.aliyuncs.com/unimol-docking/docking.tar.gz
tar --no-same-owner -xzf "CASF-2016.tar.gz"
tar --no-same-owner -xzf "docking.tar.gz"
cd docking
python setup.py install
pip install -q biopandas -i https://pypi.tuna.tsinghua.edu.cn/simple/ --trusted-host pypi.tuna.tsinghua.edu.cn
pip install -q py3Dmol -i https://pypi.tuna.tsinghua.edu.cn/simple/ --trusted-host pypi.tuna.tsinghua.edu.cn
pip install -q ipywidgets -i https://pypi.tuna.tsinghua.edu.cn/simple/ --trusted-host pypi.tuna.tsinghua.edu.cn
2024-04-28 13:31:04 URL:https://bohrium-example.oss-cn-zhangjiakou.aliyuncs.com/unimol-docking/CASF-2016.tar.gz [39434267/39434267] -> "CASF-2016.tar.gz" [1] 2024-04-28 13:31:38 URL:https://bohrium-example.oss-cn-zhangjiakou.aliyuncs.com/unimol-docking/binding_pose_220908.pt [435265981/435265981] -> "binding_pose_220908.pt" [1] 2024-04-28 13:31:38 URL:https://bohrium-example.oss-cn-zhangjiakou.aliyuncs.com/unimol-docking/docking.tar.gz [72258/72258] -> "docking.tar.gz" [1] running install running bdist_egg running egg_info creating unimol_docking.egg-info writing unimol_docking.egg-info/PKG-INFO writing dependency_links to unimol_docking.egg-info/dependency_links.txt writing requirements to unimol_docking.egg-info/requires.txt writing top-level names to unimol_docking.egg-info/top_level.txt writing manifest file 'unimol_docking.egg-info/SOURCES.txt' reading manifest file 'unimol_docking.egg-info/SOURCES.txt' writing manifest file 'unimol_docking.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/unimol_docking copying unimol_docking/infer.py -> build/lib/unimol_docking copying unimol_docking/__init__.py -> build/lib/unimol_docking creating build/lib/unimol_docking/models copying unimol_docking/models/docking_pose.py -> build/lib/unimol_docking/models copying unimol_docking/models/unimol.py -> build/lib/unimol_docking/models copying unimol_docking/models/__init__.py -> build/lib/unimol_docking/models copying unimol_docking/models/transformer_encoder_with_pair.py -> build/lib/unimol_docking/models creating build/lib/unimol_docking/tasks copying unimol_docking/tasks/docking_pose.py -> build/lib/unimol_docking/tasks copying unimol_docking/tasks/unimol.py -> build/lib/unimol_docking/tasks copying unimol_docking/tasks/__init__.py -> build/lib/unimol_docking/tasks creating build/lib/unimol_docking/losses copying unimol_docking/losses/docking_pose.py -> build/lib/unimol_docking/losses copying unimol_docking/losses/unimol.py -> build/lib/unimol_docking/losses copying unimol_docking/losses/__init__.py -> build/lib/unimol_docking/losses copying unimol_docking/losses/cross_entropy.py -> build/lib/unimol_docking/losses copying unimol_docking/losses/reg_loss.py -> build/lib/unimol_docking/losses creating build/lib/unimol_docking/utils copying unimol_docking/utils/docking_utils.py -> build/lib/unimol_docking/utils copying unimol_docking/utils/__init__.py -> build/lib/unimol_docking/utils copying unimol_docking/utils/docking.py -> build/lib/unimol_docking/utils copying unimol_docking/utils/coordinate_model.py -> build/lib/unimol_docking/utils creating build/lib/unimol_docking/data copying unimol_docking/data/data_utils.py -> build/lib/unimol_docking/data copying unimol_docking/data/atom_type_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/distance_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/prepend_and_append_2d_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/mask_points_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/cropping_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/conformer_sample_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/tta_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/normalize_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/__init__.py -> build/lib/unimol_docking/data copying unimol_docking/data/from_str_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/remove_hydrogen_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/key_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/lmdb_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/coord_pad_dataset.py -> build/lib/unimol_docking/data copying unimol_docking/data/add_2d_conformer_dataset.py -> build/lib/unimol_docking/data creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/unimol_docking creating build/bdist.linux-x86_64/egg/unimol_docking/models copying build/lib/unimol_docking/models/docking_pose.py -> build/bdist.linux-x86_64/egg/unimol_docking/models copying build/lib/unimol_docking/models/unimol.py -> build/bdist.linux-x86_64/egg/unimol_docking/models copying build/lib/unimol_docking/models/__init__.py -> build/bdist.linux-x86_64/egg/unimol_docking/models copying build/lib/unimol_docking/models/transformer_encoder_with_pair.py -> build/bdist.linux-x86_64/egg/unimol_docking/models copying build/lib/unimol_docking/infer.py -> build/bdist.linux-x86_64/egg/unimol_docking creating build/bdist.linux-x86_64/egg/unimol_docking/tasks copying build/lib/unimol_docking/tasks/docking_pose.py -> build/bdist.linux-x86_64/egg/unimol_docking/tasks copying build/lib/unimol_docking/tasks/unimol.py -> build/bdist.linux-x86_64/egg/unimol_docking/tasks copying build/lib/unimol_docking/tasks/__init__.py -> build/bdist.linux-x86_64/egg/unimol_docking/tasks creating build/bdist.linux-x86_64/egg/unimol_docking/losses copying build/lib/unimol_docking/losses/docking_pose.py -> build/bdist.linux-x86_64/egg/unimol_docking/losses copying build/lib/unimol_docking/losses/unimol.py -> build/bdist.linux-x86_64/egg/unimol_docking/losses copying build/lib/unimol_docking/losses/__init__.py -> build/bdist.linux-x86_64/egg/unimol_docking/losses copying build/lib/unimol_docking/losses/cross_entropy.py -> build/bdist.linux-x86_64/egg/unimol_docking/losses copying build/lib/unimol_docking/losses/reg_loss.py -> build/bdist.linux-x86_64/egg/unimol_docking/losses copying build/lib/unimol_docking/__init__.py -> build/bdist.linux-x86_64/egg/unimol_docking creating build/bdist.linux-x86_64/egg/unimol_docking/utils copying build/lib/unimol_docking/utils/docking_utils.py -> build/bdist.linux-x86_64/egg/unimol_docking/utils copying build/lib/unimol_docking/utils/__init__.py -> build/bdist.linux-x86_64/egg/unimol_docking/utils copying build/lib/unimol_docking/utils/docking.py -> build/bdist.linux-x86_64/egg/unimol_docking/utils copying build/lib/unimol_docking/utils/coordinate_model.py -> build/bdist.linux-x86_64/egg/unimol_docking/utils creating build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/data_utils.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/atom_type_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/distance_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/prepend_and_append_2d_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/mask_points_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/cropping_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/conformer_sample_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/tta_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/normalize_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/__init__.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/from_str_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/remove_hydrogen_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/key_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/lmdb_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/coord_pad_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data copying build/lib/unimol_docking/data/add_2d_conformer_dataset.py -> build/bdist.linux-x86_64/egg/unimol_docking/data byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/models/docking_pose.py to docking_pose.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/models/unimol.py to unimol.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/models/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/models/transformer_encoder_with_pair.py to transformer_encoder_with_pair.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/infer.py to infer.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/tasks/docking_pose.py to docking_pose.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/tasks/unimol.py to unimol.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/tasks/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/losses/docking_pose.py to docking_pose.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/losses/unimol.py to unimol.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/losses/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/losses/cross_entropy.py to cross_entropy.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/losses/reg_loss.py to reg_loss.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/utils/docking_utils.py to docking_utils.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/utils/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/utils/docking.py to docking.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/utils/coordinate_model.py to coordinate_model.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/data_utils.py to data_utils.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/atom_type_dataset.py to atom_type_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/distance_dataset.py to distance_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/prepend_and_append_2d_dataset.py to prepend_and_append_2d_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/mask_points_dataset.py to mask_points_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/cropping_dataset.py to cropping_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/conformer_sample_dataset.py to conformer_sample_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/tta_dataset.py to tta_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/normalize_dataset.py to normalize_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/__init__.py to __init__.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/from_str_dataset.py to from_str_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/remove_hydrogen_dataset.py to remove_hydrogen_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/key_dataset.py to key_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/lmdb_dataset.py to lmdb_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/coord_pad_dataset.py to coord_pad_dataset.cpython-38.pyc byte-compiling build/bdist.linux-x86_64/egg/unimol_docking/data/add_2d_conformer_dataset.py to add_2d_conformer_dataset.cpython-38.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying unimol_docking.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying unimol_docking.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying unimol_docking.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying unimol_docking.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying unimol_docking.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO /opt/conda/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( /opt/conda/lib/python3.8/site-packages/setuptools/command/easy_install.py:156: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( zip_safe flag not set; analyzing archive contents... unimol_docking.losses.__pycache__.__init__.cpython-38: module references __file__ unimol_docking.tasks.__pycache__.__init__.cpython-38: module references __file__ creating dist creating 'dist/unimol_docking-1.0.0-py3.8.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing unimol_docking-1.0.0-py3.8.egg removing '/opt/conda/lib/python3.8/site-packages/unimol_docking-1.0.0-py3.8.egg' (and everything under it) creating /opt/conda/lib/python3.8/site-packages/unimol_docking-1.0.0-py3.8.egg Extracting unimol_docking-1.0.0-py3.8.egg to /opt/conda/lib/python3.8/site-packages unimol-docking 1.0.0 is already the active version in easy-install.pth Installed /opt/conda/lib/python3.8/site-packages/unimol_docking-1.0.0-py3.8.egg Processing dependencies for unimol-docking==1.0.0 Searching for pandas==1.3.5 Best match: pandas 1.3.5 Adding pandas 1.3.5 to easy-install.pth file Using /opt/conda/lib/python3.8/site-packages Searching for numpy==1.20.3 Best match: numpy 1.20.3 Adding numpy 1.20.3 to easy-install.pth file Installing f2py script to /opt/conda/bin Installing f2py3 script to /opt/conda/bin Installing f2py3.8 script to /opt/conda/bin Using /opt/conda/lib/python3.8/site-packages Searching for pytz==2022.1 Best match: pytz 2022.1 Adding pytz 2022.1 to easy-install.pth file Using /opt/conda/lib/python3.8/site-packages Searching for python-dateutil==2.8.2 Best match: python-dateutil 2.8.2 Adding python-dateutil 2.8.2 to easy-install.pth file Using /opt/conda/lib/python3.8/site-packages Searching for six==1.16.0 Best match: six 1.16.0 Adding six 1.16.0 to easy-install.pth file Using /opt/conda/lib/python3.8/site-packages Finished processing dependencies for unimol-docking==1.0.0 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
代码
文本
[17]
# 载入相关的库
import sys
sys.path.append('/opt/conda/lib/python3.8/site-packages/unimol_docking-1.0.0-py3.8.egg')
from unimol_docking.utils.docking_utils import (
docking_data_pre,
ensemble_iterations,
write_lmdb,
generate_docking_input
)
from tqdm import tqdm
from rdkit import Chem
import subprocess
import py3Dmol
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import pickle
import json
import copy
import os
from ipywidgets import widgets,Layout,HBox,VBox
代码
文本
[4]
# docking函数，传入pdb_id 以及对应的smiles即可
def call_unimol_docking(pdb_id, smiles):
data_path = "./CASF-2016"
seed = 42
results_path = "./results"
os.makedirs(results_path, exist_ok=True)
smiles_list = smiles.split(",")
print("generate predict data...")
write_lmdb(data_path, pdb_id, smiles_list, seed=seed)
print("model inference...")
cmd = ' '.join(['export MKL_SERVICE_FORCE_INTEL=1',
'&&',
'python ./docking/unimol_docking/infer.py',
'--user-dir ./docking/unimol_docking {}'.format(data_path),
'--valid-subset {} --results-path {}'.format(pdb_id, results_path),
'--num-workers 8 --ddp-backend=c10d --batch-size 8 --task docking_pose',
'--loss docking_pose --arch docking_pose --path ./binding_pose_220908.pt',
'--fp16 --fp16-init-scale 4 --fp16-scale-window 256',
'--dist-threshold 8.0 --recycling 3 --log-interval 50 --log-format simple',
])
os.system(cmd)
print("docking ...")
predict_file = os.path.join(results_path, pdb_id + ".out.pkl")
reference_file = os.path.join(data_path, pdb_id + ".lmdb")
generate_docking_input(
predict_file, reference_file, tta_times=10, output_dir=results_path
)
print("visualization ...")
for i, smiles in enumerate(smiles_list[:1]):
print("Docking {}".format(smiles))
input_path = os.path.join(results_path, "{}.{}.pkl".format(pdb_id, i))
ligand_path = os.path.join(results_path, "docking.{}.{}.sdf".format(pdb_id, i))
cmd = "export MKL_THREADING_LAYER=GNU"
cmd += "&& python ./docking/unimol_docking/utils/coordinate_model.py --input {} --output-ligand {}".format(
input_path, ligand_path
)
subprocess.call(cmd, shell=True)
pdb_path = os.path.join(data_path, 'casf2016', pdb_id+'_protein.pdb')
ligand_path = os.path.join(results_path, "docking.{}.{}.sdf".format(pdb_id,0))
gt_ligand_path = os.path.join(data_path,'casf2016',pdb_id+'_ligand.sdf')
view = py3Dmol.view()
view.removeAllModels()
pdb_path = os.path.join(data_path, 'casf2016', pdb_id+'_protein.pdb')
view.addModel(open(pdb_path,'r').read(),format='pdb')
view.setStyle({'cartoon': {'arrows':True, 'tubes':False, 'style':'oval', 'color':'white'}})
view.addSurface(py3Dmol.VDW,{'opacity':0.5,'color':'white'})
view.addModel(open(ligand_path,'r').read(),format='sdf')
ref_m = view.getModel()
ref_m.setStyle({},{'stick':{'colorscheme':'greenCarbon','radius':0.2}})
view.zoomTo(viewer=(100,0))
view.show()
view.removeAllModels()
view.addModel(open(ligand_path,'r').read(),format='sdf')
ref_m = view.getModel()
ref_m.setStyle({},{'stick':{'colorscheme':'greenCarbon','radius':0.2}})
view.addModel(open(gt_ligand_path,'r').read(),format='sdf')
ref_m = view.getModel()
ref_m.setStyle({},{'stick':{'colorscheme':'redCarbon','radius':0.2}})
view.zoomTo(viewer=(100,0))
view.show()
代码
文本
- 目前支持CSAF-2016里面的靶点，默认会选择其对应的分子进行对接；
- 如果想对接其他分子，可以直接修改smiles的输入；
- 如果想对接多个分子，输入smiles，并且用逗号间隔即可；
- 后续会支持更多的场景，包括上传蛋白、辅助筛选口袋、自定义docking；
代码
文本
[5]
data_path = "./CASF-2016"
casf_collect = os.listdir(os.path.join(data_path, "casf2016"))
casf_collect = list(set([item[:4] for item in casf_collect]))
pdb_selector = widgets.SelectMultiple(
options=casf_collect,
value=[np.random.choice(casf_collect)],
row=8,
description='请选择靶点:',
disable=False
)
pdb_label = widgets.Label(value='已选择靶点：')
smiles_label = widgets.Label(value='默认Dock分子: ')
smiles_text = widgets.Text(
description='选择其他分子: ',
layout=Layout(width='36%', height='30px'),
)
submiter = widgets.Button(
description='选择',
button_style='success',
layout=Layout(width='36%', height='30px'),
)
def btn_click(sender):
pdb_id = pdb_selector.value[0]
pdb_label.value='已选择靶点: '+ pdb_selector.value[0]
supp = Chem.SDMolSupplier(os.path.join(data_path, "casf2016", pdb_id + "_ligand.sdf"))
mol = [mol for mol in supp if mol][0]
ori_smiles = Chem.MolToSmiles(mol)
smiles_label.value = '默认Dock分子: '+ori_smiles
submiter.on_click(btn_click)
display(HBox([pdb_selector,
VBox([pdb_label,
smiles_label])]
)
)
display(submiter)
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- 可视化展示的是unimol预测的分子对接效果，上图是unimol预测的分子位置，下图是与真实晶体中的位置进行的比较；
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[6]
### docking ####
### 你可以指定自定义的smiles,传入smiles即可
pdb_id = pdb_selector.value[0]
smiles = smiles_label.value.split(': ')[-1]
call_unimol_docking(pdb_id, smiles)
generate predict data... model inference... Error: mkl-service + Intel(R) MKL: MKL_THREADING_LAYER=INTEL is incompatible with libgomp.so.1 library. Try to import numpy first or set the threading layer accordingly. Set MKL_SERVICE_FORCE_INTEL to force it. 2023-04-11 19:55:12 | INFO | numexpr.utils | Note: NumExpr detected 16 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. 2023-04-11 19:55:12 | INFO | numexpr.utils | NumExpr defaulting to 8 threads. 2023-04-11 19:55:12 | INFO | unimol_docking.inference | loading model(s) from ./binding_pose_220908.pt 2023-04-11 19:55:15 | INFO | unimol_docking.tasks.docking_pose | ligand dictionary: 30 types 2023-04-11 19:55:15 | INFO | unimol_docking.tasks.docking_pose | pocket dictionary: 9 types 2023-04-11 19:55:18 | INFO | unicore.tasks.unicore_task | get EpochBatchIterator for epoch 1 2023-04-11 19:55:20 | INFO | unimol_docking.inference | Done inference! docking ... visualization ... Docking NS(=O)(=O)c1ccccc1F 2weg-NS(=O)(=O)c1ccccc1F-RMSD:22.9571-0.074-0.2547
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