obdotnet_circularfingerprint.cs

using System;
using System.Text;
using System.Collections.Generic;
using System.Linq;
using OpenBabel;

namespace OBDotNetExamples
{

    class Program1
    {

        static void Main(string[] args)
        {
            //Set up a translator to Sybyl atom types
            OBTypeTable ttab = new OBTypeTable();
            ttab.SetFromType("INT");
            ttab.SetToType("SYB");

            OBConversion obc = new OBConversion();
            obc.SetInFormat("smi");
            OBMol mol = new OBMol();
            obc.ReadString(mol, "c1(N)ccccc1c(=O)[O-]");

            int maxDepth = 3;

            string atomType;
            
            List<string> fp = new List<string>();
            List<string> fpBlock;

            for(int i = 1; i <= mol.NumAtoms(); i++)
            {
                fpBlock = new List<string>();

                foreach(var pair in mol.AtomsBFSWDepth(i))
                {
                    if(pair.Depth > maxDepth)
                        break;

                    atomType = ttab.Translate(pair.Atom.GetAtomType());
                    
                    fpBlock.Add(string.Format("{0}-{1}",pair.Depth-1,atomType));
                }

                fpBlock.Sort();
                fp.Add(string.Join(";", fpBlock.ToArray()));
            }
            Console.WriteLine(string.Join("\t", fp.ToArray()));
 
        }

    /* output:
      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.ar;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.c
      o2;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
     */
    }



}