ASBase collect

This repo store scripts which can grab web database to h5 databse.

usage

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