deepfrag2mol's Introduction

DeepFrag2Mol

Converting the molecular fragments generated by DeepFrag[ https://durrantlab.pitt.edu/deepfragmodel/ ] into complete molecules

文档

http://rdkit.chenzhaoqiang.com/mediaManual.html#deepfrag2mol

注意事项：

母核骨架SMILES中的接头原子*，必须放在中括号中。

示例：

   [*]C1=CC=CC=C1

编译后的二进制文件

安装

方法1：源码安装

git clone

cd conda env create -f deepfrag2mol.yaml

conda activate deepfrag2mol

方法2：二进制安装

链接：https://pan.baidu.com/s/10zFsY2mWBxXzQ0Wj9aZk2g?pwd=aj9k 提取码：aj9k

用法：

python deepFrag2mol_CMDgui.py

(base) D:\DeepFrag2mol_v2024>python deepFrag2mol_CMDgui.py

    DeepFrag2Mol: Converting the molecular fragments generated by DeepFrag into complete molecules.
    Usage: deepFrag2mol_CMDgui.py [OPTIONS]

    Options:
    --scaffold TEXT  the SMILES of the molecular scaffold
    --fragfile TEXT  the file  of the molecular fragments generated by DeepFrag
    --help           Show this message and exit.

input scaffold SMILES: [[*]C1=CC=CC=C1]:
input fragment file path and name [deepfrag-scores.csv]:
 89%|███████████████████████████████████████████████████████████████████▋        | 4953/5564 [00:00<00:00, 7662.98it/s][13:19:03] Explicit valence for atom # 1 B, 5, is greater than permitted
error: [Fr]C1=CC=CC=C1 [Cs][BH4]
100%|████████████████████████████████████████████████████████████████████████████| 5564/5564 [00:00<00:00, 7252.01it/s]
Congratulations,You have converted 5564 total fragments to 5563 molecules, The result is saved in file deepfrag-scores_mol.smi

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