Scripts: pqr2chimera.py

import sys
try:
        scriptName, pqrFileName = sys.argv
except ValueError:
        raise ValueError("Must supply one argument to script: PQR file name")

f = open(pqrFileName, "r")
pdbOut = open("chimera.pdb", "w")
defattrOut = open("chimera.defattr", "w")
print>>defattrOut, "attribute: charge"
print>>defattrOut, "recipient: atoms"
for line in f:
        if not (line.startswith("ATOM  ") or line.startswith("HETATM")):
                continue
        print>>pdbOut, line[:54]
        
        print>>defattrOut, "\t@/serialNumber=%s\t%s" % (line[6:11].strip(), line[55:62].strip())
f.close()
pdbOut.close()
defattrOut.close()