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/********************************************************************** |
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grid.h - Handle grids of values. |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#ifndef OB_GRID_H |
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#define OB_GRID_H |
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|
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#include "config.h" |
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|
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#if HAVE_IOSTREAM |
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#include <iostream> |
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#elif HAVE_IOSTREAM_H |
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#include <iostream.h> |
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#endif |
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|
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#include <algorithm> |
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#include <vector> |
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#include <string> |
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|
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#ifndef OBPolarGrid |
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#define OBPolarGrid 0x01 /* polar interactions? */ |
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#endif //OBPolarGrid |
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|
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#ifndef OBLipoGrid |
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#define OBLipoGrid 0x02 /* lipophilicity? */ |
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#endif //OBLipoGrid |
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|
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namespace OpenBabel |
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{ |
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|
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//! A grid for determining the proximity of a given point to atoms in an OBMol |
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class OBAPI OBProxGrid |
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{ |
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int _gridtype; |
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int _nxinc,_nyinc,_nzinc,_maxinc; |
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double _xmin,_xmax,_ymin,_ymax,_zmin,_zmax,_inc; |
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std::vector<std::vector<int> > cell; |
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|
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public: |
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|
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OBProxGrid(int gridtype=0) |
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{ |
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_gridtype=gridtype; |
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} |
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~OBProxGrid() |
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{} |
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void Setup(OBMol &mol,OBMol &box, double cutoff,double resolution = 0.5); |
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void Setup(OBMol &mol,OBMol &box, double cutoff, |
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std::vector<bool> &use,double resolution = 0.5); |
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std::vector<int> *GetProxVector(double,double,double); |
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std::vector<int> *GetProxVector(double*); |
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|
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bool LipoGrid() |
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{ |
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return((_gridtype&OBLipoGrid) ? true : false); |
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} |
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bool PolarGrid() |
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{ |
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return(_gridtype&OBPolarGrid); |
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} |
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void SetGridType(int gridtype) |
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{ |
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_gridtype = gridtype; |
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} |
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bool PointIsInBox(double x,double y,double z) |
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{ |
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return (x>=_xmin) && (x<=_xmax) && |
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(y>=_ymin) && (y<=_ymax) && |
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(z>=_zmin) && (z<=_zmax); |
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} |
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}; |
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|
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//! Handle floating-point 3D grids (i.e., charge density around an OBMol) |
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class OBAPI OBFloatGrid |
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{ |
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protected: |
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double *_val; //!< doubleing point values |
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int *_ival; //!< for integer values (deprecated) |
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double _midz,_midx,_midy; //!< center of grid in world coordinates |
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int _ydim,_xdim,_zdim; //!< grid dimensions |
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double _spacing,_inv_spa; //!< spacing between grid points and its invers |
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double _xmin,_xmax,_ymin,_ymax,_zmin,_zmax; //!< the min/max values in XYZ axes (i.e., the box) |
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double _halfSpace; //!< half of the grid spacing */ |
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|
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public: |
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|
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OBFloatGrid() : _halfSpace(0.0) |
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{ |
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_val=NULL; |
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_ival=NULL; |
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} |
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~OBFloatGrid() |
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{ |
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if (_ival) |
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{ |
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delete [] _ival; |
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_ival = NULL; |
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} |
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if (_val) |
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{ |
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delete [] _val; |
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_val = NULL; |
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} |
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} |
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//! Initialize the grid using this molecule as a box (plus a padding) |
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//! with the supplied spacing between points |
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void Init(OBMol &box,double spacing, double pad= 0.0); |
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//! \return whether the supplied XYZ coordinates fall within the box |
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bool PointIsInBox(double x,double y,double z) |
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{ |
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return (x>=_xmin) && (x<=_xmax) && |
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(y>=_ymin) && (y<=_ymax) && |
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(z>=_zmin) && (z<=_zmax); |
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} |
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//! \return true if the point falls within the box |
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bool PointIsInBox(double *c) |
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{ |
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return (c[0]>=_xmin) && (c[0]<=_xmax) && |
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(c[1]>=_ymin) && (c[1]<=_ymax) && |
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(c[2]>=_zmin) && (c[2]<=_zmax); |
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} |
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double GetXmin() const { return(_xmin); } |
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double GetYmin() const { return(_ymin); } |
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double GetZmin() const { return(_zmin); } |
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double GetXmax() const { return(_xmax); } |
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double GetYmax() const { return(_ymax); } |
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double GetZmax() const { return(_zmax); } |
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void GetMin(double *a) |
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{ |
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a[0]=_xmin; |
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a[1]=_ymin; |
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a[2]=_zmin; |
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} |
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void GetMax(double *a) |
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{ |
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a[0]=_xmax; |
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a[1]=_ymax; |
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a[2]=_zmax; |
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} |
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|
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double GetSpacing() const { return(_spacing); } |
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void GetSpacing(double &s) |
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{ |
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s=_spacing; |
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} |
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double GetScale() const { return(_inv_spa); } |
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double GetHalfSpace() const {return(_halfSpace);} |
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int GetXdim() const { return(_xdim); } |
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int GetYdim() const { return(_ydim); } |
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int GetZdim() const { return(_zdim); } |
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void GetDim(int *a) |
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{ |
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a[0]=_xdim; |
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a[1]=_ydim; |
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a[2]=_zdim; |
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} |
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vector3 GetMidpointVector() |
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{ |
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vector3 v; |
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v.Set(_midx,_midy,_midz); |
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return(v); |
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} |
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double *GetVals() { return(_val); } |
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void SetVals(double *ptr) { _val = ptr; } |
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vector3 Center() |
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{ |
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return vector3(_midx,_midy,_midz); |
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} |
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|
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friend std::ostream& operator<< ( std::ostream&, const OBFloatGrid& ) ; |
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friend std::istream& operator>> ( std::istream&,OBFloatGrid& ) ; |
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|
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//! \return the value at the given point (rounding as needed) |
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double Inject(double x,double y,double z); |
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|
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void IndexToCoords(int idx, double &x, double &y, double &z); |
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void CoordsToIndex(int*,double*); |
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int CoordsToIndex(double &x, double &y, double &z); |
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//! \return the interpolated value for the given point |
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double Interpolate(double,double,double); |
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//! \return the interpolated value for the given point and set the dx, dy, dz derivatives |
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double InterpolateDerivatives(double,double,double,double *derivatives); |
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}; |
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|
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// scoring function used: PLP = Piecewise Linear Potential or ChemScore algorithm |
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typedef enum { Undefined = -1, PLP, ChemScore } score_t; |
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|
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//! A base class for scoring docking interactions between multiple molecules |
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class OBAPI OBScoreGrid |
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{ |
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protected: |
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|
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score_t gridtype; |
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bool verbose; |
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|
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public: |
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|
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double score; |
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|
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OBScoreGrid(void) |
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{ |
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verbose = false; |
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} |
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virtual ~OBScoreGrid(void) |
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{} |
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|
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void SetVerbose(bool v) |
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{ |
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verbose = v; |
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} |
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void SetType(score_t type) |
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{ |
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gridtype = type; |
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} |
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score_t GetType(void) |
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{ |
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return gridtype; |
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} |
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|
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virtual void Clear(void) |
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{ } |
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virtual double Eval(double *) |
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{ |
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return -1; |
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} |
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virtual double Eval(OBMol &mol) |
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{ |
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return Eval(mol.GetCoordinates()); |
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} |
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virtual void Init(OBMol &, OBMol &, std::string &, double) |
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{} |
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virtual void Setup(OBMol &) |
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{} |
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virtual void Setup(OBMol &, std::vector<int> &) |
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{} |
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virtual void Setup(std::vector<int> &) |
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{} |
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virtual void Config(std::string) |
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{} |
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virtual bool Read(std::string) |
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{ |
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return false; |
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} |
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virtual bool Write(std::string) |
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{ |
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return false; |
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} |
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virtual vector3 Center() |
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{ |
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return VZero; |
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} |
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virtual vector3 CenterMol(OBMol &) |
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{ |
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return VZero; |
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} |
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}; |
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|
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} // end namespace OpenBabel |
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|
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#endif // OB_GRID_H |
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|
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//! \file grid.h |
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//! \brief Handle grids of values. |
