MorganFingerprints.h

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//  Created by Greg Landrum, July 2008
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/*! \file MorganFingerprints.h

*/
#ifndef __RD_MORGANFPS_H__
#define __RD_MORGANFPS_H__

#include <vector>
#include <DataStructs/SparseIntVect.h>
#include <boost/cstdint.hpp>

namespace RDKit {
  class ROMol;
  namespace MorganFingerprints {
    const std::string morganFingerprintVersion="0.1.0";
    
    //! returns the Morgan fingerprint for a molecule
    /*!  
      These fingerprints are similar to the well-known ECFP or
      FCFP fingerprints, depending on which invariants are used.
        
      The algorithm used is described in the paper
      D. Rogers, R.D. Brown, M. Hahn J. Biomol. Screen. 10:682-6 (2005)
      and in more detail in an unpublished technical report:
      http://www.ics.uci.edu/~welling/teaching/ICS274Bspring06/David%20Rogers%20-%20ECFP%20Manuscript.doc

      \param mol:    the molecule to be fingerprinted
      \param radius: the number of iterations to grow the fingerprint
      \param invariants : optional pointer to a set of atom invariants to
            be used. By default ECFP-type invariants are used 
            (calculated by getConnectivityInvariants())
      \param fromAtoms : if this is provided, only the atoms in the vector will be
                         used as centers in the fingerprint

      \return a pointer to the fingerprint. The client is
      responsible for calling delete on this.

    */
    SparseIntVect<boost::uint32_t> *
      getFingerprint(const ROMol &mol,
                     unsigned int radius,
                     std::vector<boost::uint32_t> *invariants=0,
                     const std::vector<boost::uint32_t> *fromAtoms=0);

      
    //! returns the connectivity invariants for a molecule
    /*!  

      \param mol:    the molecule to be considered
      \param invariants : used to return the results
      \param includeRingMembership : if set, whether or not the atom is in
                 a ring will be used in the invariant list.
    */
    void getConnectivityInvariants(const ROMol &mol,
                                   std::vector<boost::uint32_t> &invars,
                                   bool includeRingMembership=false);

  } // end of namespace MorganFingerprints
}

#endif