grid.h

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/**********************************************************************
grid.h - Handle grids of values.
 
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
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.
 
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_GRID_H
#define OB_GRID_H

#include "babelconfig.h"

#if HAVE_IOSTREAM
#include <iostream>
#elif HAVE_IOSTREAM_H
#include <iostream.h>
#endif

#include <algorithm>
#include <vector>
#include <string>

#ifndef OBPolarGrid
#define OBPolarGrid 0x01 /* polar interactions? */
#endif //OBPolarGrid

#ifndef OBLipoGrid
#define OBLipoGrid 0x02 /* lipophilicity? */
#endif //OBLipoGrid

namespace OpenBabel
{

class OBAPI OBProxGrid
{
    int _gridtype;
    int _nxinc,_nyinc,_nzinc,_maxinc;
    double _xmin,_xmax,_ymin,_ymax,_zmin,_zmax,_inc;
    std::vector<std::vector<int> > cell;

public:

    OBProxGrid(int gridtype=0)
    {
        _gridtype=gridtype;
    }
    ~OBProxGrid()
    {}
    void Setup(OBMol &mol,OBMol &box, double cutoff,double resolution = 0.5);
    void Setup(OBMol &mol,OBMol &box, double cutoff,
               std::vector<bool> &use,double resolution = 0.5);
    std::vector<int> *GetProxVector(double,double,double);
    std::vector<int> *GetProxVector(double*);

    bool LipoGrid()
    {
        return((_gridtype&OBLipoGrid) ? true : false);
    }
    bool PolarGrid()
    {
        return(_gridtype&OBPolarGrid);
    }
    void SetGridType(int gridtype)
    {
        _gridtype = gridtype;
    }
    bool PointIsInBox(double x,double y,double z)
    {
        return (x>=_xmin) && (x<=_xmax) &&
               (y>=_ymin) && (y<=_ymax) &&
               (z>=_zmin) && (z<=_zmax);
    }
};

class OBAPI OBFloatGrid
{
protected:
    double *_val;             
    int   *_ival;            
    double _midz,_midx,_midy;   
    int _ydim,_xdim,_zdim;     
    double _spacing,_inv_spa;  
    double _xmin,_xmax,_ymin,_ymax,_zmin,_zmax; 
    double _halfSpace;         

public:

    OBFloatGrid() : _halfSpace(0.0)
    {
        _val=NULL;
        _ival=NULL;
    }
    ~OBFloatGrid()
    {
        if (_ival)
        {
            delete [] _ival;
            _ival = NULL;
        }
        if (_val)
        {
            delete [] _val;
            _val = NULL;
        }
    }
    void Init(OBMol &box,double spacing, double pad= 0.0);
    bool PointIsInBox(double x,double y,double z)
    {
        return (x>=_xmin) && (x<=_xmax) &&
               (y>=_ymin) && (y<=_ymax) &&
               (z>=_zmin) && (z<=_zmax);
    }
    bool PointIsInBox(double *c)
    {
        return (c[0]>=_xmin) && (c[0]<=_xmax) &&
               (c[1]>=_ymin) && (c[1]<=_ymax) &&
               (c[2]>=_zmin) && (c[2]<=_zmax);
    }
    double GetXmin() const    { return(_xmin);    }
    double GetYmin() const    { return(_ymin);    }
    double GetZmin() const    { return(_zmin);    }
    double GetXmax() const    { return(_xmax);    }
    double GetYmax() const    { return(_ymax);    }
    double GetZmax() const    { return(_zmax);    }
    void GetMin(double *a)
    {
        a[0]=_xmin;
        a[1]=_ymin;
        a[2]=_zmin;
    }
    void GetMax(double *a)
    {
        a[0]=_xmax;
        a[1]=_ymax;
        a[2]=_zmax;
    }

    double GetSpacing() const { return(_spacing); }
    void GetSpacing(double &s)
    {
        s=_spacing;
    }
    double GetScale() const   { return(_inv_spa); }
    double GetHalfSpace() const {return(_halfSpace);}
    int GetXdim() const       { return(_xdim);    }
    int GetYdim() const       { return(_ydim);    }
    int GetZdim() const       { return(_zdim);    }
    void GetDim(int *a)
    {
        a[0]=_xdim;
        a[1]=_ydim;
        a[2]=_zdim;
    }
    vector3 GetMidpointVector()
    {
        vector3 v;
        v.Set(_midx,_midy,_midz);
        return(v);
    }
    double *GetVals()    {        return(_val);    }
    void SetVals(double *ptr)    {  _val = ptr;    }
    vector3 Center()
    {
        return vector3(_midx,_midy,_midz);
    }

    friend std::ostream& operator<< ( std::ostream&, const OBFloatGrid& ) ;
    friend std::istream& operator>> ( std::istream&,OBFloatGrid& ) ;

    double Inject(double x,double y,double z);

    void IndexToCoords(int idx, double &x, double &y, double &z);
    void CoordsToIndex(int*,double*);
    int CoordsToIndex(double &x, double &y, double &z);
    double Interpolate(double,double,double);
    double InterpolateDerivatives(double,double,double,double *derivatives);
};

// scoring function used: PLP = Piecewise Linear Potential or ChemScore algorithm
typedef enum { Undefined = -1, PLP, ChemScore } score_t;

class OBAPI OBScoreGrid
{
protected:

    score_t gridtype;
    bool verbose;

public:

    double score;

    OBScoreGrid(void)
    {
        verbose = false;
    }
    virtual ~OBScoreGrid(void)
    {}

    void    SetVerbose(bool v)
    {
        verbose = v;
    }
    void    SetType(score_t type)
    {
        gridtype = type;
    }
    score_t GetType(void)
    {
        return gridtype;
    }

    virtual void   Clear(void)
    { }
    virtual double  Eval(double *)
    {
        return -1;
    }
    virtual double  Eval(OBMol &mol)
    {
        return Eval(mol.GetCoordinates());
    }
    virtual void   Init(OBMol &, OBMol &, std::string &, double)
    {}
    virtual void   Setup(OBMol &)
    {}
    virtual void   Setup(OBMol &, std::vector<int> &)
    {}
    virtual void   Setup(std::vector<int> &)
    {}
    virtual void   Config(std::string)
    {}
    virtual bool   Read(std::string)
    {
        return false;
    }
    virtual bool   Write(std::string)
    {
        return false;
    }
    virtual vector3 Center()
    {
        return VZero;
    }
    virtual vector3 CenterMol(OBMol &)
    {
        return VZero;
    }
};

} // end namespace OpenBabel

#endif // OB_GRID_H

---

This file is part of the documentation for Open Babel, version 2.0.2.

Documentation copyright © 1998-2005, the Open Babel Developers.
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