Pafnucy

tar zxf openbabel-3.1.1.tar.bz2
cd openbabel-3.1.1
mkdir build
cd build/
cmake ..
make
sudo make install

obabel --help

conda install -c openbabel openbabel

self.NAMED_PROPS = ['hyb', 'heavydegree', 'heterodegree', 'partialcharge']

self.NAMED_PROPS = ['hyb', 'heavyvalence', 'heterovalence', 'partialcharge']

import os
from mindsponge import PipeLine
from openbabel import pybel

# 小分子为mol2文件，蛋白质为pdb文件或mol2文件
pocket_path = {YOUR_POCKET_PATH}
ligand_path = {YOUR_LIGAND_PATH}
raw_data = [pocket_path, ligand_path]
pipe = PipeLine(name = "pafnucy")
pipe.set_device_id(0)
pipe.initialize("config")
pipe.model.from_pretrained()
result = pipe.predict(raw_data)
print(result)

from mindsponge import PipeLine
pipe = PipeLine(name = "pafnucy")
pipe.set_device_id(0)
pipe.initialize("config")
pipe.train({YOUR_DATA_PATH}, num_epochs = 1)

@article{10.1093/bioinformatics/bty374,
    author = {Stepniewska-Dziubinska, Marta M and Zielenkiewicz, Piotr and Siedlecki, Pawel},
    title = "{Development and evaluation of a deep learning model for protein–ligand binding affinity prediction}",
    journal = {Bioinformatics},
    volume = {34},
    number = {21},
    pages = {3666-3674},
    year = {2018},
    month = {05},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/bty374},
    url = {https://doi.org/10.1093/bioinformatics/bty374},
}