ASBase collect

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

usage

• Prerequisites:
  • h5py
  • rdkit
  • numpy
  • bs4
  • requests
  • requests

1. download data from web ASBase

python get_pages.py

2. parser html resource and store them to h5py database

python parser_asbase.py

3. extract infomation from h5 database and construct it to 3D molecule files

mkdir pdbs
mkdir xyzs
python extract_3D.py

4. transfer 3D file to gaussian input

call geninput, a shell script which convert .xyz to gaussian input .gjf

geninput input.xyz

5. batch computation by PBS or SLURM

qsub xxxx