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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
  1. parser html resource and store them to h5py database
python parser_asbase.py
  1. extract infomation from h5 database and construct it to 3D molecule files
mkdir pdbs
mkdir xyzs
python extract_3D.py
  1. transfer 3D file to gaussian input

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

geninput input.xyz
  1. batch computation by PBS or SLURM
qsub xxxx

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