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basis.cpp
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basis.cpp
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/*
Pharmer: Efficient and Exact 3D Pharmacophore Search
Copyright (C) 2011 David Ryan Koes and the University of Pittsburgh
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; either version 2
of the License, or (at your option) any later version.
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.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
/*
* basis.cpp
*
* Created on: Dec 14, 2009
* Author: dkoes
*/
#include "basis.h"
using namespace OpenBabel;
const double minDist = .2; //minimum distance between basis points
ostream& operator<<(ostream& out, const CoordinateBasis& x)
{
out << x.origin << "\n" << x.transform;
return out;
}
//given the passed points, generate a new canonical basis that can be
//used to replot the other points
//use the order specified if fixedOrder is true
//return true if a valid basis is found
bool CoordinateBasis::constructBasis(const PharmaPoint&i, const PharmaPoint& j,
const PharmaPoint& k, bool fixedOrder)
{
unsigned iindex = 0;
unsigned jindex = 1;
unsigned kindex = 2;
valid = false;
//first check distances
double d_ij = PharmaPoint::pharmaDist(i, j);
if (d_ij < minDist)
return false;
double d_jk = PharmaPoint::pharmaDist(j, k);
if (d_jk < minDist)
return false;
double d_ki = PharmaPoint::pharmaDist(k, i);
if (d_ki < minDist)
return false;
//find the largest and second largest vectors with a joined tail
vector3 first;
vector3 second;
if (fixedOrder)
{
//center on k
origin.Set(k.x, k.y, k.z);
first.Set(i.x - k.x, i.y - k.y, i.z - k.z);
second.Set(j.x - k.x, j.y - k.y, j.z - k.z);
basisOrder[0] = kindex;
basisOrder[1] = iindex;
basisOrder[2] = jindex;
basisDistances[0] = d_ki;
basisDistances[1] = d_jk;
basisDistances[2] = d_ij;
}
else
{
if (d_ij > d_jk && d_ij > d_ki)
{ //ij largest
if (d_jk > d_ki)
{
//centered at j
origin.Set(j.x, j.y, j.z);
first.Set(i.x - j.x, i.y - j.y, i.z - j.z);
second.Set(k.x - j.x, k.y - j.y, k.z - j.z);
basisOrder[0] = jindex;
basisOrder[1] = iindex;
basisOrder[2] = kindex;
basisDistances[0] = d_ij;
basisDistances[1] = d_jk;
basisDistances[2] = d_ki;
}
else
{ //d_ki second largest, centered at i
origin.Set(i.x, i.y, i.z);
first.Set(j.x - i.x, j.y - i.y, j.z - i.z);
second.Set(k.x - i.x, k.y - i.y, k.z - i.z);
basisOrder[0] = iindex;
basisOrder[1] = jindex;
basisOrder[2] = kindex;
basisDistances[0] = d_ij;
basisDistances[1] = d_ki;
basisDistances[2] = d_jk;
}
}
else if (d_jk > d_ij && d_jk > d_ki)
{ //jk largest
if (d_ij > d_ki)
{ //centered at j
origin.Set(j.x, j.y, j.z);
first.Set(k.x - j.x, k.y - j.y, k.z - j.z);
second.Set(i.x - j.x, i.y - j.y, i.z - j.z);
basisOrder[0] = jindex;
basisOrder[1] = kindex;
basisOrder[2] = iindex;
basisDistances[0] = d_jk;
basisDistances[1] = d_ij;
basisDistances[2] = d_ki;
}
else
{ //d_ki largest, centered at k
origin.Set(k.x, k.y, k.z);
first.Set(j.x - k.x, j.y - k.y, j.z - k.z);
second.Set(i.x - k.x, i.y - k.y, i.z - k.z);
basisOrder[0] = kindex;
basisOrder[1] = jindex;
basisOrder[2] = iindex;
basisDistances[0] = d_jk;
basisDistances[1] = d_ki;
basisDistances[2] = d_ij;
}
}
else
{//ki largest (or equilateral, which we don't handle properly)
if (d_ij > d_jk)
{ //centered on i
origin.Set(i.x, i.y, i.z);
first.Set(k.x - i.x, k.y - i.y, k.z - i.z);
second.Set(j.x - i.x, j.y - i.y, j.z - i.z);
basisOrder[0] = iindex;
basisOrder[1] = kindex;
basisOrder[2] = jindex;
basisDistances[0] = d_ki;
basisDistances[1] = d_ij;
basisDistances[2] = d_jk;
}
else
{ //jk larger, centered on k
origin.Set(k.x, k.y, k.z);
first.Set(i.x - k.x, i.y - k.y, i.z - k.z);
second.Set(j.x - k.x, j.y - k.y, j.z - k.z);
basisOrder[0] = kindex;
basisOrder[1] = iindex;
basisOrder[2] = jindex;
basisDistances[0] = d_ki;
basisDistances[1] = d_jk;
basisDistances[2] = d_ij;
}
}
}
//now take the cross product
vector3 product = cross(first, second);
if (product.length() < minDist)
return false; //too close to colinear, a smaller cutoff coudl probably be used
//first, second, and product define a new basis
//orthonormalize it to eliminate skew (Gram-Schmidt)
first.normalize();
//u2 = v2 - proj_u1(v2)
second = second - dot(second, first) * first;
second.normalize();
//u3 = v3 - proj_u1(v3) - proj_u2(v3)
product = product - dot(product, first) * first - dot(product, second)
* second;
product.normalize();
//now have an orthonormal basis
//compute the transformation matrix
transform = matrix3x3(first, second, product).transpose().inverse();
valid = true;
return true;
}
//generate new coordinates for x,y, and z using current basis
void CoordinateBasis::replot(double x, double y, double z, float &nx,
float& ny, float& nz) const
{
vector3 orig(x, y, z);
orig -= origin;
vector3 res = transform * orig;
nx = res.x();
ny = res.y();
nz = res.z();
cout.precision(8);
}
void CoordinateBasis::replot_vector(double x, double y, double z, float &nx,
float& ny, float& nz) const
{
vector3 orig(x, y, z);
vector3 res = transform * orig;
nx = res.x();
ny = res.y();
nz = res.z();
}