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/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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.
***********************************************************************/
#include "bitgrid.h"
#ifndef ATOMTYPE_PATH
#define ATOMTYPE_PATH "hbtypes.txt"
#endif
using namespace OpenBabel;
using namespace std;
BitGrid::BitGrid(void)
{
p.read_rules(ATOMTYPE_PATH);
fuzzy = false;
}
BitGrid::BitGrid(bool f)
{
p.read_rules(ATOMTYPE_PATH);
fuzzy = f;
}
BitGrid::~BitGrid(void)
{
Clear();
}
void BitGrid::Init(OBMol &box, float spacing)
{
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
for ( atom = box.BeginAtom(i) ; atom ; atom = box.NextAtom(i) )
{
if (atom->GetIdx() == 1)
{
xmin = atom->GetX(); xmax = atom->GetX();
ymin = atom->GetY(); ymax = atom->GetY();
zmin = atom->GetZ(); zmax = atom->GetZ();
}
else
{
if (atom->GetX() < xmin) xmin = atom->GetX();
if (atom->GetX() > xmax) xmax = atom->GetX();
if (atom->GetY() < ymin) ymin = atom->GetY();
if (atom->GetY() > ymax) ymax = atom->GetY();
if (atom->GetZ() < zmin) zmin = atom->GetZ();
if (atom->GetZ() > zmax) zmax = atom->GetZ();
}
}
midx = 0.5 * (xmax+xmin);
midy = 0.5 * (ymax+ymin);
midz = 0.5 * (zmax+zmin);
xdim = 3 + (int) ((xmax-xmin)/spacing);
ydim = 3 + (int) ((ymax-ymin)/spacing);
zdim = 3 + (int) ((zmax-zmin)/spacing);
xydim = xdim * ydim;
size = xdim * ydim * zdim;
inv_spa = 1.0 / spacing;
this->spacing = spacing;
grid.Clear();
lipo.Clear();
don.Clear();
acc.Clear();
grid.Resize(size);
lipo.Resize(size);
don.Resize(size);
acc.Resize(size);
}
void BitGrid::Init(float xmi, float ymi, float zmi, float xma, float yma, float zma, float spacing)
{
xmin = xmi; xmax = xma;
ymin = ymi; ymax = yma;
zmin = zmi; zmax = zma;
midx = 0.5 * (xmax+xmin);
midy = 0.5 * (ymax+ymin);
midz = 0.5 * (zmax+zmin);
xdim = 3 + (int) ((xmax-xmin)/spacing);
ydim = 3 + (int) ((ymax-ymin)/spacing);
zdim = 3 + (int) ((zmax-zmin)/spacing);
size = xdim * ydim * zdim;
inv_spa = 1.0 / spacing;
this->spacing = spacing;
grid.Clear();
lipo.Clear();
don.Clear();
acc.Clear();
grid.Resize(size);
lipo.Resize(size);
don.Resize(size);
acc.Resize(size);
}
void BitGrid::Build(OBMol &mol)
{
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
p.assign_types(mol,types);
for ( atom = mol.BeginAtom(i) ; atom ; atom = mol.NextAtom(i) )
SetBits(atom);
}
void BitGrid::Build(OBMol &mol, OBBitVec &bits)
{
OBAtom *atom;
vector<OBNodeBase*>::iterator i;
p.assign_types(mol,types);
for ( atom = mol.BeginAtom(i) ; atom ; atom = mol.NextAtom(i) )
if (bits.BitIsOn(atom->GetIdx()))
SetBits(atom);
}
void BitGrid::Build(OBMol &mol, vector<int> &atoms)
{
vector<int>::iterator i;
p.assign_types(mol,types);
for ( i = atoms.begin() ; i != atoms.end() ; i++ )
SetBits(mol.GetAtom(*i));
}
void BitGrid::SetBits(OBAtom *atom)
{
int i,j,k;
int xpos = (int)rint((atom->GetX() - xmin) * inv_spa);
int ypos = (int)rint((atom->GetY() - ymin) * inv_spa);
int zpos = (int)rint((atom->GetZ() - zmin) * inv_spa);
int startX = (0 > xpos - 1) ? 0 : xpos - 1;
int startY = (0 > ypos - 1) ? 0 : ypos - 1;
int startZ = (0 > zpos - 1) ? 0 : zpos - 1;
int endX = (xdim < xpos + 1) ? xdim : xpos + 1;
int endY = (ydim < ypos + 1) ? ydim : ypos + 1;
int endZ = (zdim < zpos + 1) ? zdim : zpos + 1;
float rad = etab.CorrectedVdwRad(atom->GetAtomicNum(),atom->GetHyb());
if (fuzzy)
{
Vector grid_pt, mol_pt = atom->GetVector();
for ( i = startX ; i <= endX ; i++ )
{
grid_pt.SetX(((float)i * (float)spacing) + xmin);
for ( j = startY ; j <= endY ; j++ )
{
grid_pt.SetY(((float)j * (float)spacing) + ymin);
for ( k = startZ ; k <= endZ ; k++ )
{
grid_pt.SetZ(((float)k * (float)spacing) + zmin);
if ((grid_pt - mol_pt).length() > rad)
continue;
int n = i + (ydim*j) + (xydim*k);
grid.SetBitOn(n);
if (types[atom->GetIdx()] == "DON")
don.SetBitOn(n);
else if ( types[atom->GetIdx()] == "ACC")
acc.SetBitOn(n);
else
lipo.SetBitOn(n);
}
}
}
}
else
{
int n = xpos + (ydim*ypos) + (xydim*zpos);
grid.SetBitOn(n);
if (types[atom->GetIdx()] == "DON")
don.SetBitOn(n);
else if ( types[atom->GetIdx()] == "ACC")
acc.SetBitOn(n);
else
lipo.SetBitOn(n);
}
}
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