Test MDTraj on PDB

test_mdtraj_on_pdb.py

import os
import mdtraj as md
import gzip
import tempfile
import glob

directories = glob.glob("./all_pdb/*")
for directory in directories:
    filenames = glob.glob("%s/*.gz" % directory)
    for filename in filenames:
        gfile = gzip.open(filename, 'rb')
        pdb_filename = tempfile.mktemp(suffix=".pdb")
        fout = open(pdb_filename, 'w')
        fout.write(gfile.read())
        fout.close()
        try:
            t = md.load_pdb(pdb_filename)
            top, bonds = t.top.to_dataframe()
        except Exception as e:
            print(e)
            print(filename)