MolPrint2D format (mpd)

An implementation of the circular fingerprint MolPrint2D

MolPrint2D is an atom-environment fingerprint developed by Bender et al [bmg2004] which has been used in QSAR studies and for measuring molecular similarity.

The format of the output is as follows:

[Molec_name]\t[atomtype];[layer]-[frequency]-[neighbour_type];

Example for the SMILES string CC(=O)Cl:

acid chloride   1;1-1-2;2-1-9;2-1-15;   2;1-1-1;1-1-9;1-1-15;
                9;1-1-2;2-1-1;2-1-15;   15;1-1-2;2-1-1;2-1-9;

[bmg2004]

Andreas Bender, Hamse Y. Mussa, and Robert C. Glen. Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naive Bayesian Classifier. J. Chem. Inf. Comput. Sci. 2004, 44, 170-178. [Link]

Note

This is a write-only format.

Write Options

-n

prefix molecule names with name of file

-c

use XML style separators instead

-i

use IDX atom types of babel internal