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tim |
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/********************************************************************** |
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grid.cpp - Handle grids of values. |
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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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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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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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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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#include "mol.hpp" |
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#include "grid.hpp" |
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using namespace std; |
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namespace OpenBabel |
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{ |
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void OBProxGrid::Setup(OBMol &mol,OBMol &box,double cutoff,double res) |
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{ |
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OBAtom *atom; |
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vector<OBNodeBase*>::iterator i; |
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for (atom = box.BeginAtom(i);atom;atom = box.NextAtom(i)) |
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if (atom->GetIdx() == 1) |
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{ |
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_xmin = atom->GetX(); |
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_xmax = atom->GetX(); |
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_ymin = atom->GetY(); |
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_ymax = atom->GetY(); |
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_zmin = atom->GetZ(); |
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_zmax = atom->GetZ(); |
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} |
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else |
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{ |
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if (atom->GetX() < _xmin) |
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_xmin = atom->GetX(); |
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if (atom->GetX() > _xmax) |
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_xmax = atom->GetX(); |
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if (atom->GetY() < _ymin) |
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_ymin = atom->GetY(); |
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if (atom->GetY() > _ymax) |
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_ymax = atom->GetY(); |
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if (atom->GetZ() < _zmin) |
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_zmin = atom->GetZ(); |
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if (atom->GetZ() > _zmax) |
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_zmax = atom->GetZ(); |
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} |
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_inc = res; // 1/2 angstrom resolution |
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_nxinc = (int) floor((_xmax - _xmin)/0.5); |
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_nyinc = (int) floor((_ymax - _ymin)/0.5); |
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_nzinc = (int) floor((_zmax - _zmin)/0.5); |
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_maxinc = _nxinc*_nyinc*_nzinc; |
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int j,size = _nxinc*_nyinc*_nzinc; |
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cell.resize(size); |
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for (unsigned int num = 0; num < cell.size(); num++) |
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cell[num].resize(0); |
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cutoff *= cutoff; //don't do sqrts |
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int k,l,m; |
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double x,y,z,dx_2,dy_2; |
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double *c = mol.GetCoordinates(); |
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size = mol.NumAtoms()*3; |
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for (atom = mol.BeginAtom(i),j=0;atom;atom = mol.NextAtom(i),j+=3) |
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if (PointIsInBox(c[j],c[j+1],c[j+2])) |
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for (x = _xmin+(_inc/2.0),k=0;k < _nxinc;x+=_inc,k++) |
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if ((dx_2 = SQUARE(c[j]-x)) < cutoff) |
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for (y = _ymin+(_inc/2.0),l=0;l < _nyinc;y+=_inc,l++) |
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if ((dx_2+(dy_2 = SQUARE(c[j+1]-y))) < cutoff) |
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for (z = _zmin+(_inc/2.0),m=0;m < _nzinc;z+=_inc,m++) |
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if ((dx_2+dy_2+SQUARE(c[j+2]-z)) < cutoff) |
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cell[(k*_nyinc*_nzinc)+(l*_nzinc)+m].push_back(atom->GetIdx()); |
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_inc = 1/_inc; |
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} |
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void OBProxGrid::Setup(OBMol &mol,OBMol &box,double cutoff,vector<bool> &use, |
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double res) |
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{ |
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OBAtom *atom; |
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vector<OBNodeBase*>::iterator i; |
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for (atom = box.BeginAtom(i);atom;atom = box.NextAtom(i)) |
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if (atom->GetIdx() == 1) |
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{ |
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_xmin = atom->GetX(); |
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_xmax = atom->GetX(); |
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_ymin = atom->GetY(); |
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_ymax = atom->GetY(); |
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_zmin = atom->GetZ(); |
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_zmax = atom->GetZ(); |
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} |
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else |
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{ |
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if (atom->GetX() < _xmin) |
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_xmin = atom->GetX(); |
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if (atom->GetX() > _xmax) |
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_xmax = atom->GetX(); |
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if (atom->GetY() < _ymin) |
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_ymin = atom->GetY(); |
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if (atom->GetY() > _ymax) |
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_ymax = atom->GetY(); |
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if (atom->GetZ() < _zmin) |
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_zmin = atom->GetZ(); |
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if (atom->GetZ() > _zmax) |
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_zmax = atom->GetZ(); |
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} |
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_inc = res; // 1/2 angstrom resolution |
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_nxinc = (int) floor((_xmax - _xmin)/0.5); |
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_nyinc = (int) floor((_ymax - _ymin)/0.5); |
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_nzinc = (int) floor((_zmax - _zmin)/0.5); |
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_maxinc = _nxinc*_nyinc*_nzinc; |
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int j,size = _nxinc*_nyinc*_nzinc; |
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cell.resize(size); |
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cutoff *= cutoff; //don't do sqrts |
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int k,l,m; |
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double x,y,z,dx_2,dy_2; |
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double *c = mol.GetCoordinates(); |
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size = mol.NumAtoms()*3; |
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for (atom = mol.BeginAtom(i),j=0;atom;atom = mol.NextAtom(i),j+=3) |
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if (use[atom->GetIdx()]) |
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if (PointIsInBox(c[j],c[j+1],c[j+2])) |
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for (x = _xmin+(_inc/2.0),k=0;k < _nxinc;x+=_inc,k++) |
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if ((dx_2 = SQUARE(c[j]-x)) < cutoff) |
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for (y = _ymin+(_inc/2.0),l=0;l < _nyinc;y+=_inc,l++) |
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if ((dx_2+(dy_2 = SQUARE(c[j+1]-y))) < cutoff) |
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for (z = _zmin+(_inc/2.0),m=0;m < _nzinc;z+=_inc,m++) |
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if ((dx_2+dy_2+SQUARE(c[j+2]-z)) < cutoff) |
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cell[(k*_nyinc*_nzinc)+(l*_nzinc)+m].push_back(atom->GetIdx()); |
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_inc = 1/_inc; |
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} |
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vector<int> *OBProxGrid::GetProxVector(double x,double y,double z) |
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{ |
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if (x < _xmin || x > _xmax) |
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return(NULL); |
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if (y < _ymin || y > _ymax) |
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return(NULL); |
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if (z < _zmin || z > _zmax) |
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return(NULL); |
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x -= _xmin; |
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y -= _ymin; |
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z -= _zmin; |
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int i,j,k,idx; |
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i = (int) (x*_inc); |
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j = (int) (y*_inc); |
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k = (int) (z*_inc); |
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idx = (i*_nyinc*_nzinc)+(j*_nzinc)+k; |
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if (idx >= _maxinc) |
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return(NULL); |
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return(&cell[idx]); |
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} |
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vector<int> *OBProxGrid::GetProxVector(double *c) |
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{ |
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double x,y,z; |
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x = c[0]; |
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y = c[1]; |
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z = c[2]; |
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return( GetProxVector(x, y, z) ); |
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} |
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void OBFloatGrid::Init(OBMol &box,double spacing, double pad) |
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{ |
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OBAtom *atom; |
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vector<OBNodeBase*>::iterator i; |
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for (atom = box.BeginAtom(i);atom;atom = box.NextAtom(i)) |
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if (atom->GetIdx() == 1) |
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{ |
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_xmin = atom->GetX(); |
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_xmax = atom->GetX(); |
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_ymin = atom->GetY(); |
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_ymax = atom->GetY(); |
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_zmin = atom->GetZ(); |
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_zmax = atom->GetZ(); |
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} |
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else |
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{ |
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if (atom->GetX() < _xmin) |
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_xmin = atom->GetX(); |
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if (atom->GetX() > _xmax) |
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_xmax = atom->GetX(); |
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if (atom->GetY() < _ymin) |
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_ymin = atom->GetY(); |
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if (atom->GetY() > _ymax) |
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_ymax = atom->GetY(); |
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if (atom->GetZ() < _zmin) |
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_zmin = atom->GetZ(); |
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if (atom->GetZ() > _zmax) |
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_zmax = atom->GetZ(); |
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} |
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_xmin -= pad; |
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_xmax += pad; |
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_ymin -= pad; |
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_ymax += pad; |
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_zmin -= pad; |
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_zmax += pad; |
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double midx,midy,midz; |
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int xdim,ydim,zdim; |
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midx=0.5*(_xmax+_xmin); |
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midy=0.5*(_ymax+_ymin); |
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midz=0.5*(_zmax+_zmin); |
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xdim=3+(int) ((_xmax-_xmin)/spacing); |
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ydim=3+(int) ((_ymax-_ymin)/spacing); |
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zdim=3+(int) ((_zmax-_zmin)/spacing); |
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/* store in Grid */ |
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_midx=midx; |
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_midy=midy; |
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_midz=midz; |
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_xdim=xdim; |
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_ydim=ydim; |
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_zdim=zdim; |
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_spacing=spacing; |
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_halfSpace= _spacing/2.0; |
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_inv_spa=1.0/spacing; |
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_val=NULL; |
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_ival=NULL; |
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int size = _xdim*_ydim*_zdim; |
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_val = new double [size]; |
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memset(_val,'\0',sizeof(double)*size); |
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//return(true); |
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} |
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double OBFloatGrid::Inject(double x,double y,double z) |
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{ |
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if((x<=_xmin)||(x>=_xmax)) |
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return(0.0); |
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if((y<=_ymin)||(y>=_ymax)) |
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return(0.0); |
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if((z<=_zmin)||(z>=_zmax)) |
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return(0.0); |
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int gx=(int)((x-_xmin)*_inv_spa); |
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int gy=(int)((y-_ymin)*_inv_spa); |
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int gz=(int)((z-_zmin)*_inv_spa); |
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return(_val[(gz*_ydim*_xdim)+(gy*_xdim)+gx]); |
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} |
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void OBFloatGrid::IndexToCoords(int idx, double &x, double &y, double &z) |
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{ |
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long int grid_x,grid_y,grid_z; |
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grid_x = idx % (int)_xdim; |
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grid_z = (int)(idx /(_xdim * _ydim)); |
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grid_y = (int)((idx - (grid_z * _xdim * _ydim))/_xdim); |
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x = ((double)grid_x * _spacing + _xmin) + this->_halfSpace; |
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y = ((double)grid_y * _spacing + _ymin) + this->_halfSpace; |
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z = ((double)grid_z * _spacing + _zmin) + this->_halfSpace; |
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} |
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int OBFloatGrid::CoordsToIndex(double &x, double &y, double &z) |
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{ |
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int gx=(int)((x-_xmin)*_inv_spa); |
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int gy=(int)((y-_ymin)*_inv_spa); |
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int gz=(int)((z-_zmin)*_inv_spa); |
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return((gz*_ydim*_xdim)+(gy*_xdim)+gx); |
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} |
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void OBFloatGrid::CoordsToIndex(int *idx,double *c) |
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{ |
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idx[0]=(int)((c[0]-_xmin)*_inv_spa); |
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idx[1]=(int)((c[1]-_ymin)*_inv_spa); |
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idx[2]=(int)((c[2]-_zmin)*_inv_spa); |
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} |
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double OBFloatGrid::Interpolate(double x,double y,double z) |
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{ |
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int n,igx,igy,igz; |
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double xydim; |
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double gx,gy,gz,fgx,fgy,fgz; |
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double ax,ay,az,bx,by,bz; |
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double AyA,ByA,AyB,ByB,Az,Bz; |
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if((x<=_xmin)||(x>=_xmax)) |
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return(0.0); |
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if((y<=_ymin)||(y>=_ymax)) |
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return(0.0); |
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if((z<=_zmin)||(z>=_zmax)) |
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return(0.0); |
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xydim = _xdim*_ydim; |
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/* calculate grid voxel and fractional offsets */ |
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gx=(x-_xmin-_halfSpace)*_inv_spa; |
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if (gx<0) |
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gx=0; |
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igx=(int)gx; |
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fgx=gx-(double)igx; |
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gy=(y-_ymin-_halfSpace)*_inv_spa; |
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if (gy<0) |
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gy=0; |
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igy=(int) gy; |
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fgy= gy - (double) igy; |
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gz=(z-_zmin-_halfSpace)*_inv_spa; |
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if (gz<0) |
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gz=0; |
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igz=(int) gz; |
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fgz= gz - (double) igz; |
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n=(int)(igx+ _xdim*igy + xydim*igz); |
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/* calculate linear weightings */ |
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ax=1.0-fgx; |
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bx=fgx; |
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ay=1.0-fgy; |
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by=fgy; |
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az=1.0-fgz; |
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bz=fgz; |
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/* calculate interpolated value */ |
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AyA=ax*_val[n ]+bx*_val[(int)(n+1) ]; |
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ByA=ax*_val[n+_xdim]+bx*_val[(int)(n+1+_xdim) ]; |
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Az=ay*AyA+by*ByA; |
| 347 |
|
|
|
| 348 |
|
|
AyB=ax*_val[(int)(n +xydim)]+bx*_val[(int)(n+1 +xydim)]; |
| 349 |
|
|
ByB=ax*_val[(int)(n+_xdim+xydim)]+bx*_val[(int)(n+1+_xdim+xydim)]; |
| 350 |
|
|
Bz=ay*AyB+by*ByB; |
| 351 |
|
|
|
| 352 |
|
|
return(az*Az+bz*Bz); |
| 353 |
|
|
} |
| 354 |
|
|
|
| 355 |
|
|
|
| 356 |
|
|
double OBFloatGrid::InterpolateDerivatives(double x,double y,double z,double *derivatives) |
| 357 |
|
|
{ |
| 358 |
|
|
int n,igx,igy,igz; |
| 359 |
|
|
double xydim; |
| 360 |
|
|
double gx,gy,gz,fgx,fgy,fgz; |
| 361 |
|
|
double ax,ay,az,bx,by,bz; |
| 362 |
|
|
double AyA,ByA,AyB,ByB,Az,Bz; |
| 363 |
|
|
double energy,fx,fy,fz; |
| 364 |
|
|
|
| 365 |
|
|
if((x<=_xmin)||(x>=_xmax)) |
| 366 |
|
|
return(0.0); |
| 367 |
|
|
if((y<=_ymin)||(y>=_ymax)) |
| 368 |
|
|
return(0.0); |
| 369 |
|
|
if((z<=_zmin)||(z>=_zmax)) |
| 370 |
|
|
return(0.0); |
| 371 |
|
|
|
| 372 |
|
|
xydim = _xdim*_ydim; |
| 373 |
|
|
|
| 374 |
|
|
/* calculate grid voxel and fractional offsets */ |
| 375 |
|
|
gx=(x-_xmin-_halfSpace)*_inv_spa; |
| 376 |
|
|
if (gx<0) |
| 377 |
|
|
gx=0; |
| 378 |
|
|
igx=(int)gx; |
| 379 |
|
|
fgx=gx-(double)igx; |
| 380 |
|
|
gy=(y-_ymin-_halfSpace)*_inv_spa; |
| 381 |
|
|
if (gy<0) |
| 382 |
|
|
gy=0; |
| 383 |
|
|
igy=(int) gy; |
| 384 |
|
|
fgy= gy - (double) igy; |
| 385 |
|
|
gz=(z-_zmin-_halfSpace)*_inv_spa; |
| 386 |
|
|
if (gz<0) |
| 387 |
|
|
gz=0; |
| 388 |
|
|
igz=(int) gz; |
| 389 |
|
|
fgz= gz - (double) igz; |
| 390 |
|
|
|
| 391 |
|
|
n=(int)(igx+ _xdim*igy + xydim*igz); |
| 392 |
|
|
/* calculate linear weightings */ |
| 393 |
|
|
ax=1.0-fgx; |
| 394 |
|
|
bx=fgx; |
| 395 |
|
|
ay=1.0-fgy; |
| 396 |
|
|
by=fgy; |
| 397 |
|
|
az=1.0-fgz; |
| 398 |
|
|
bz=fgz; |
| 399 |
|
|
|
| 400 |
|
|
/* calculate interpolated value */ |
| 401 |
|
|
AyA=ax*_val[n ]+bx*_val[(int)(n+1) ]; |
| 402 |
|
|
ByA=ax*_val[n+_xdim]+bx*_val[(int)(n+1+_xdim) ]; |
| 403 |
|
|
|
| 404 |
|
|
Az=ay*AyA+by*ByA; |
| 405 |
|
|
|
| 406 |
|
|
AyB=ax*_val[(int)(n +xydim)]+bx*_val[(int)(n+1 +xydim)]; |
| 407 |
|
|
ByB=ax*_val[(int)(n+_xdim+xydim)]+bx*_val[(int)(n+1+_xdim+xydim)]; |
| 408 |
|
|
Bz=ay*AyB+by*ByB; |
| 409 |
|
|
|
| 410 |
|
|
energy = az*Az+bz*Bz; |
| 411 |
|
|
|
| 412 |
|
|
//calculate derivatives |
| 413 |
|
|
|
| 414 |
|
|
fz=-Az+Bz; |
| 415 |
|
|
|
| 416 |
|
|
Az=-AyA+ByA; |
| 417 |
|
|
Bz=-AyB+ByB; |
| 418 |
|
|
|
| 419 |
|
|
fy=az*Az+bz*Bz; |
| 420 |
|
|
|
| 421 |
|
|
AyA=-_val[n ]+_val[(int)(n+1) ]; |
| 422 |
|
|
ByA=-_val[n+_xdim ]+_val[(int)(n+1+_xdim)]; |
| 423 |
|
|
|
| 424 |
|
|
Az=ay*AyA+by*ByA; |
| 425 |
|
|
|
| 426 |
|
|
AyB=-_val[(int)(n +xydim)]+_val[(int)(n+1 +xydim)]; |
| 427 |
|
|
ByB=-_val[(int)(n+_xdim+xydim)]+_val[(int)(n+1+_xdim+xydim)]; |
| 428 |
|
|
|
| 429 |
|
|
Bz=ay*AyB+by*ByB; |
| 430 |
|
|
|
| 431 |
|
|
fx=az*Az+bz*Bz; |
| 432 |
|
|
|
| 433 |
|
|
derivatives[0] += fx; |
| 434 |
|
|
derivatives[1] += fy; |
| 435 |
|
|
derivatives[2] += fz; |
| 436 |
|
|
|
| 437 |
|
|
return(energy); |
| 438 |
|
|
|
| 439 |
|
|
} |
| 440 |
|
|
|
| 441 |
|
|
|
| 442 |
|
|
ostream& operator<< ( ostream &os, const OBFloatGrid& fg) |
| 443 |
|
|
{ |
| 444 |
|
|
os.write((const char*)&fg._xmin,sizeof(double)); |
| 445 |
|
|
os.write((const char*)&fg._xmax,sizeof(double)); |
| 446 |
|
|
os.write((const char*)&fg._ymin,sizeof(double)); |
| 447 |
|
|
os.write((const char*)&fg._ymax,sizeof(double)); |
| 448 |
|
|
os.write((const char*)&fg._zmin,sizeof(double)); |
| 449 |
|
|
os.write((const char*)&fg._zmax,sizeof(double)); |
| 450 |
|
|
|
| 451 |
|
|
os.write((const char*)&fg._midx,sizeof(double)); |
| 452 |
|
|
os.write((const char*)&fg._midy,sizeof(double)); |
| 453 |
|
|
os.write((const char*)&fg._midz,sizeof(double)); |
| 454 |
|
|
os.write((const char*)&fg._inv_spa,sizeof(double)); |
| 455 |
|
|
os.write((const char*)&fg._spacing,sizeof(double)); |
| 456 |
|
|
os.write((const char*)&fg._xdim,sizeof(int)); |
| 457 |
|
|
os.write((const char*)&fg._ydim,sizeof(int)); |
| 458 |
|
|
os.write((const char*)&fg._zdim,sizeof(int)); |
| 459 |
|
|
os.write((const char*)&fg._val[0], |
| 460 |
|
|
(sizeof(double)*(fg._xdim*fg._ydim*fg._zdim))); |
| 461 |
|
|
|
| 462 |
|
|
return(os); |
| 463 |
|
|
} |
| 464 |
|
|
|
| 465 |
|
|
istream& operator>> ( istream &is,OBFloatGrid& fg) |
| 466 |
|
|
{ |
| 467 |
|
|
is.read((char*)&fg._xmin,sizeof(double)); |
| 468 |
|
|
is.read((char*)&fg._xmax,sizeof(double)); |
| 469 |
|
|
is.read((char*)&fg._ymin,sizeof(double)); |
| 470 |
|
|
is.read((char*)&fg._ymax,sizeof(double)); |
| 471 |
|
|
is.read((char*)&fg._zmin,sizeof(double)); |
| 472 |
|
|
is.read((char*)&fg._zmax,sizeof(double)); |
| 473 |
|
|
|
| 474 |
|
|
is.read((char*)&fg._midx,sizeof(double)); |
| 475 |
|
|
is.read((char*)&fg._midy,sizeof(double)); |
| 476 |
|
|
is.read((char*)&fg._midz,sizeof(double)); |
| 477 |
|
|
is.read((char*)&fg._inv_spa,sizeof(double)); |
| 478 |
|
|
is.read((char*)&fg._spacing,sizeof(double)); |
| 479 |
|
|
is.read((char*)&fg._xdim,sizeof(int)); |
| 480 |
|
|
is.read((char*)&fg._ydim,sizeof(int)); |
| 481 |
|
|
is.read((char*)&fg._zdim,sizeof(int)); |
| 482 |
|
|
int size = fg._xdim*fg._ydim*fg._zdim; |
| 483 |
|
|
fg._val = new double [size]; |
| 484 |
|
|
size *= (int) sizeof(double); |
| 485 |
|
|
|
| 486 |
|
|
is.read((char*)&fg._val[0],size); |
| 487 |
|
|
fg._halfSpace= fg._spacing/2.0; |
| 488 |
|
|
|
| 489 |
|
|
return(is); |
| 490 |
|
|
} |
| 491 |
|
|
|
| 492 |
|
|
#ifdef FOO |
| 493 |
|
|
//linear interpolation routine |
| 494 |
|
|
double Interpolate(double x,double y,double z) |
| 495 |
|
|
{ |
| 496 |
|
|
int n; |
| 497 |
|
|
int igx,igy,igz; |
| 498 |
|
|
double scale,gx,gy,gz,fgx,fgy,fgz; |
| 499 |
|
|
double qzpypx,qzpynx,qznynx,qznypx,qznyx,qzpyx; |
| 500 |
|
|
|
| 501 |
|
|
scale=_inv_spa; |
| 502 |
|
|
|
| 503 |
|
|
if((x<=_xmin)||(x>=_xmax)) |
| 504 |
|
|
return(0.0); |
| 505 |
|
|
if((y<=_ymin)||(y>=_ymax)) |
| 506 |
|
|
return(0.0); |
| 507 |
|
|
if((z<=_zmin)||(z>=_zmax)) |
| 508 |
|
|
return(0.0); |
| 509 |
|
|
|
| 510 |
|
|
gx=(x-_xmin-_halfSpace)*scale; |
| 511 |
|
|
igx=(int) gx; |
| 512 |
|
|
fgx= gx - (double) igx; |
| 513 |
|
|
gy=(y-_ymin-_halfSpace)*scale; |
| 514 |
|
|
igy=(int) gy; |
| 515 |
|
|
fgy= gy - (double) igy; |
| 516 |
|
|
gz=(z-_zmin-_halfSpace)*scale; |
| 517 |
|
|
igz=(int) gz; |
| 518 |
|
|
fgz= gz - (double) igz; |
| 519 |
|
|
|
| 520 |
|
|
int xydim=_xdim*_ydim; |
| 521 |
|
|
n=igx+ _xdim*igy + xydim*igz; |
| 522 |
|
|
qzpypx=fgx*(_val[n+1+_xdim+xydim]-_val[n+_xdim+xydim]) + _val[n+_xdim+xydim]; |
| 523 |
|
|
qzpynx=fgx*(_val[n+1+xydim] -_val[n+xydim]) + _val[n+xydim]; |
| 524 |
|
|
qznypx=fgx*(_val[n+1+_xdim] -_val[n+_xdim]) + _val[n+_xdim]; |
| 525 |
|
|
qznynx=fgx*(_val[n+1] -_val[n]) + _val[n]; |
| 526 |
|
|
qzpyx =fgy*(-qzpynx+qzpypx)+qzpynx; |
| 527 |
|
|
qznyx =fgy*(-qznynx+qznypx)+qznynx; |
| 528 |
|
|
|
| 529 |
|
|
return(fgz*(qzpyx-qznyx)+qznyx); |
| 530 |
|
|
} |
| 531 |
|
|
#endif |
| 532 |
|
|
|
| 533 |
|
|
} // end namespace OpenBabel |
| 534 |
|
|
|
| 535 |
|
|
//! \file grid.cpp |
| 536 |
|
|
//! \brief Handle grids of values. |
| 537 |
|
|
|
