synprepy's Introduction

Retrosynthesis Plan

Python Version

python3.6

Install Requirements

RDKit

# install rdkit
conda install -c conda-forge rdkit
# install pytorch
install from https://pytorch.org/
# install pyg
install from https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html
# install others requirements
cd synprepy #
pip install -r requirements.txt

Prepare Data

Prepare reaction data file with .tsv format

rid	rxn_smi
0	[OH:2][N:3]1[N:4]=[N:5][C:6]2=[C:7]1[CH:8]=[CH:9][CH:10]=[CH:11]2>>[OH:2][N:3]1[N:4]=[N:5][C:6]2=[C:7]1[CH:8]=[CH:9][CH:10]=[CH:11]2
1	[O:13]1[CH2:14][CH2:15][CH2:16][CH2:17]1>>O:13[CH3:17]

write config file (config.json)

{
    "root": "存储反应数据和反应模板数据的文件夹路径",
    "rxn_data_tsv_file_name": "反应数据文件名（该文件必须处于上个设置的root文件夹内）",
    "rid_with_rxn_template_tsv_file_name": "保持默认即可",
    "rxn_centralized_template_tsv_file_name": "保持默认即可",
    "rxn_extended_template_tsv_file_name": "保持默认即可",
    "rid_with_tid_tsv_file_name": "保持默认即可",
    "rxn_centralized_template_selector_config": {
        "root": "存储中心反应模板选择器的相关文件的文件夹",
        "train_rids_file_name": "保持默认即可",
        "test_rids_file_name": "保持默认即可",
        "train_temp_dir_name": "保持默认即可",
        "test_temp_dir_name": "保持默认即可",
        "min_num_covered_rxns_by_rxn_centralized_template": "过滤模板时要求模板的最少覆盖反应数",
        "filter_tids_file_name": "保持默认即可",
        "device": "cpu或者cuda",
        "batch_size": 1000,
        "epoch_num": 200,
        "lr_start": 0.0005,
        "lr_end": 1e-7
    },

  "min_num_covered_rxns_by_rxn_extended_template": 50
}

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