Calculate circular fingerprints with Pybel II

OpenBabel 2.2.0 came out a little while ago with a lot of new features. One of the new features is a breadth-first iterator over a molecule that returns the current depth as well as the current atom (OBMolAtomBFSIter). Nice. Because now it's a doddle to write a Python script to create circular fingerprints.

The script below creates a circular fingerprint for the example molecule in Bender et al., JCICS, 2004, 44, 170 as follows:

D:\>python25 fp.py
0-C.ar;1-C.ar;1-C.ar;1-N.pl3;2-C.2;2-C.ar;2-C.ar        0
-N.pl3;1-C.ar;2-C.ar;2-C.ar     0-C.ar;1-C.ar;1-C.ar;2
-C.ar;2-C.ar;2-N.pl3    0-C.ar;1-C.ar;1-C.ar;2-C.ar;2
-C.ar   0-C.ar;1-C.ar;1-C.ar;2-C.ar;2-C.ar      0-C.ar;1-
C.ar;1-C.ar;2-C.2;2-C.ar;2-C.ar 0-C.ar;1-C.2;1-C.a
r;1-C.ar;2-C.ar;2-C.ar;2-N.pl3;2-O.co2;2-O.co2  0-C
.2;1-C.ar;1-O.co2;1-O.co2;2-C.ar;2-C.ar 0-O.co2;1-
C.2;2-C.ar;2-O.co2      0-O.co2;1-C.2;2-C.ar;2-O.co2

Here's the script, which is considerably shorter than the original one.:

import pybel

# Set up a translator to Sybyl atom types
ttab = pybel.ob.OBTypeTable()
ttab.SetFromType("INT")
ttab.SetToType("SYB")

if __name__ == "__main__":
    D = 3 # default max depth
    mol = pybel.readstring("smi", "c1(N)ccccc1c(=O)[O-]")

    fp = []
    for i in range(len(mol.atoms)):
        ans = []
        for atom, depth in pybel.ob.OBMolAtomBFSIter(mol.OBMol, i + 1):
            if depth > D: break
            atomtype = ttab.Translate(atom.GetType())
            ans.append("%d-%s" % (depth - 1, atomtype))
        fp.append(";".join(sorted(ans)))
    print "\t".join(fp)