This repo store scripts which can grab web database to h5 databse.
- Prerequisites:
- h5py
- rdkit
- numpy
- bs4
- requests
- requests
- download data from web ASBase
python get_pages.py
- parser html resource and store them to h5py database
python parser_asbase.py
- extract infomation from h5 database and construct it to 3D molecule files
mkdir pdbs
mkdir xyzs
python extract_3D.py
- transfer 3D file to gaussian input
call geninput, a shell script which convert .xyz to gaussian input .gjf
geninput input.xyz
- batch computation by PBS or SLURM
qsub xxxx