Builder.h

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//
//  Copyright (C) 2004-2006 Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#ifndef _RD_UFFBUILDER_H_
#define _RD_UFFBUILDER_H_

#include <vector>
#include <string>
#include <boost/shared_array.hpp>

namespace ForceFields {
  class ForceField;
  namespace UFF {
    class AtomicParams;
  }
}

namespace RDKit {
  class ROMol;
  namespace UFF {
    typedef std::vector<const ForceFields::UFF::AtomicParams *> AtomicParamVect;

    //! Builds and returns a UFF force field for a molecule
    /*!
      
      \param mol        the molecule to use
      \param vdwThresh  the threshold to be used in adding van der Waals terms
                        to the force field. Any non-bonded contact whose current
                        distance is greater than \c vdwThresh * the minimum value
                        for that contact will not be included.
      \param confId     the optional conformer id, if this isn't provided, the molecule's
                        default confId will be used.
      \param ignoreInterfragInteractions if true, nonbonded terms will not be added between
                                         fragments

      \return the new force field. The client is responsible for free'ing this.
    */
    ForceFields::ForceField *constructForceField(ROMol &mol,
                                                 double vdwThresh=100.0,
                                                 int confId=-1,
                                                 bool ignoreInterfragInteractions=true);

    //! Builds and returns a UFF force field for a molecule
    /*!
      
      \param mol        the molecule to use
      \param params     a vector with pointers to the ForceFields::UFF::AtomicParams
                        structures to be used
      \param vdwThresh  the threshold to be used in adding van der Waals terms
                        to the force field. Any non-bonded contact whose current
                        distance is greater than \c vdwThresh * the minimum value
                        for that contact will not be included.
      \param confId     the optional conformer id, if this isn't provided, the molecule's
                        default confId will be used.
      \param ignoreInterfragInteractions if true, nonbonded terms will not be added between
                                         fragments
    
      \return the new force field. The client is responsible for free'ing this.
    */
    ForceFields::ForceField *constructForceField(ROMol &mol,
                                                 const AtomicParamVect &params,
                                                 double vdwThresh=100.0,
                                                 int confId=-1,
                                                 bool ignoreInterfragInteractions=true);

    namespace Tools {
      // these functions are primarily exposed so they can be tested.
      void addBonds(const ROMol &mol,const AtomicParamVect &params,
                    ForceFields::ForceField *field);
      boost::shared_array<int> buildNeighborMatrix(const ROMol &mol);
      void addAngles(const ROMol &mol,const AtomicParamVect &params,
                     ForceFields::ForceField *field,boost::shared_array<int> neighborMatrix);
      void addNonbonded(const ROMol &mol,int confId, const AtomicParamVect &params,
                        ForceFields::ForceField *field,boost::shared_array<int> neighborMatrix,
                        double vdwThresh=100.0,bool ignoreInterfragInteractions=true);
      void addTorsions(const ROMol &mol,const AtomicParamVect &params,
                       ForceFields::ForceField *field,
                       std::string torsionBondSmarts="[!$(*#*)&!D1]~[!$(*#*)&!D1]");
      //void addInversions(const ROMol &mol,const AtomicParamVect &params,
      //ForceFields::ForceField *field);
    }
  }
}


#endif