spectrophore.h

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/**********************************************************************
Spectrophore.h - Spectrophore(TM) calculator.
                 Declarations of OBSpectrophore

Copyright (C) 2005-2010 by Silicos NV

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

The algorithm in this software has been covered by patent WO2009146735.
However, Silicos NV and the inventors of the above mentioned patent assure
that no patent infringment claims will be issued against individuals or
institutions that use this software under the GNU General Public License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/


#ifndef OB_SPECTROPHORE_H
#define OB_SPECTROPHORE_H

#include <openbabel/babelconfig.h>
#include <vector>

#define MIN(x, y) (((x) < (y)) ? (x) : (y))
#define MAX(x, y) (((x) > (y)) ? (x) : (y))
#define N_PROPERTIES 4



namespace OpenBabel
{
  class OBMol;

   class OBAPI OBSpectrophore
   {
      public:

         enum AccuracyOption {AngStepSize1,
                              AngStepSize2,
                              AngStepSize5,
                              AngStepSize10,
                              AngStepSize15,
                              AngStepSize20,
                              AngStepSize30,
                              AngStepSize36,
                              AngStepSize45,
                              AngStepSize60};

         enum NormalizationOption {NoNormalization,
                                   NormalizationTowardsZeroMean,
                                   NormalizationTowardsUnitStd,
                                   NormalizationTowardsZeroMeanAndUnitStd};

         enum StereoOption {NoStereoSpecificProbes,
                            UniqueStereoSpecificProbes,
                            MirrorStereoSpecificProbes,
                            AllStereoSpecificProbes};


         OBSpectrophore(void);

         OBSpectrophore(const OBSpectrophore& sphore);

         virtual ~OBSpectrophore(void);

         OBSpectrophore& operator=(const OBSpectrophore& sphore);

         void SetResolution(const double r = 3.0);

         void SetAccuracy(const AccuracyOption a = AngStepSize20);

         void SetStereo(const StereoOption s = NoStereoSpecificProbes);

         void SetNormalization(const NormalizationOption n = NoNormalization);

         AccuracyOption GetAccuracy(void) const;

         double GetResolution(void) const;

         StereoOption GetStereo(void) const;

         NormalizationOption GetNormalization(void) const;

         std::vector<double> GetSpectrophore(OpenBabel::OBMol* mol);


      protected:

         double               _resolution;
         AccuracyOption       _accuracy;
         StereoOption         _stereoFlag;
         NormalizationOption  _normalization;
         std::vector<int>     _rotationStepList;
         unsigned int         _nAtoms;
         double**             _property;
         double*              _radii;
         double**             _oricoor;
         double**             _coor;
         unsigned int         _beginProbe;
         unsigned int         _endProbe;
         unsigned int         _numberOfProbes;
         std::vector<double>  _spectro;
         struct
         {
            int value[12];
         }                    _probe[48];
         struct
         {
            double x;
            double y;
            double z;
            double v[N_PROPERTIES];
         }                    _boxPoint[12];

         void _getMoleculeData(OpenBabel::OBMol*);
         void _orient(void);
         void _getBox(double**);
         void _setBox(void);
         void _getEnergies(double**, double*);
         void _initiateSpectrophore(double*, double*);
         void _rotateX(double**, double**, const double, const double);
         void _rotateY(double**, double**, const double, const double);
         void _rotateZ(double**, double**, const double, const double);
         void _updateSpectrophore(double*, double*);
         void _calculateProperties(OpenBabel::OBMol*);
         void _solveMatrix(double**, double*, unsigned int);
         void _luDecompose(double**, std::vector<int>&, unsigned int);
         void _luSolve(double**, std::vector<int>&, double*, unsigned int);
         void _swapRows(double*, unsigned int, unsigned int);
         void _swapRows(double**, unsigned int, unsigned int, unsigned int);

   };

} // end namespace OpenBabel


#endif   //OB_SPECTROPHORE_H