Hi Zheng,

Some fingerprints might do this internally but I donít think they (all) expose it. Depending on what you need, signatures may be an option. These capture the circular / layer information of atoms (and molecules). The relevant class is AtomSignature.

J

On 31 Jul 2014, at 22:45, Zheng Shi <zshi3@ualberta.ca> wrote:

Hi, thank you for answering my question.

I have some questions about fingerprint for a molecule. I just wonder if there is any API for calculating fingerprint for every atom in a molecule. I see in the cdk, the API about fingerprint usually takes a molecule as input, so I think this will return a molecule fingerprint. Like the code:
Molecule molecule = new Molecule();
IFingerprinter fingerprinter = new Fingerprinter();
BitSet fingerprint = fingerprinter.getFingerprint(molecule).
But then how to get an atom fingerprint with CDK? Suppose I want to get fingerprint for each atom, including all the paths, like 2-bond, 4-bond, rooted at a specific atom. Are there any APIs can compute atom fingerprint for each atom in a molecule? Thanks.