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ThreePointData.cpp
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ThreePointData.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.
*/
/*
* ThreePointData.cpp
*
* Created on: Aug 6, 2010
* Author: dkoes
*/
#include "ThreePointData.h"
#include "Triplet.h"
#include "basis.h"
#include "SphereGrid.h"
using namespace boost;
using namespace OpenBabel;
//multplier for float values in reduction
#define REDUCED_FLOAT_SIG (1000.0)
//reduce down to accuracy of a short
short ThreePointData::reduceFloat(double val)
{
int i = round(val * REDUCED_FLOAT_SIG);
if (i > SHRT_MAX)
return SHRT_MAX;
else if (i < SHRT_MIN)
return SHRT_MIN;
return i;
}
//val is assumed to be between -pi and pi
unsigned ThreePointData::reduceAngle(double val)
{
double v = (val+M_PI)/(2*M_PI); //between 0 and 1
return round(v*(1<<TPD_ANGLE_BITS));
}
double ThreePointData::unreduceAngle(int val)
{
double a = val / (double)(1<<TPD_ANGLE_BITS); //between 0 and 1
return a*(2*M_PI)-M_PI;
}
unsigned short ThreePointData::reduceFloatUnsigned(double val)
{
unsigned i = round(val * REDUCED_FLOAT_SIG);
if (i > USHRT_MAX)
return USHRT_MAX;
return i;
}
unsigned ThreePointData::reduceFloatBigUnsigned(double val)
{
if(val < 0) val = 0;
unsigned i = round(val * REDUCED_FLOAT_SIG);
return i;
}
double ThreePointData::unreduceFloat(int val)
{
double ret = val;
ret /= REDUCED_FLOAT_SIG;
return ret;
}
unsigned ThreePointData::reduceWeight(double d)
{
if(d < 128) return 0;
d -= 128;
//range up to 1024+128
unsigned ret = round(d);
if(ret >= 1024)
return 1023;
return ret;
}
double ThreePointData::unreduceWeight(unsigned v)
{
return v + 128;
}
unsigned ThreePointData::reduceRotatable(unsigned nr)
{
if(nr >= (1<<ROTATABLE_BITS))
return (1<<ROTATABLE_BITS)-1;
return nr;
}
//compute value representing orientation of average vector relative to coordinate
//system of i,j,k triangle (if possible)
unsigned ThreePointData::vecValue(const PharmaPoint *pt, const PharmaPoint *I, const PharmaPoint *J, const PharmaPoint *K)
{
if(pt->vecs.size() == 0)
return 0;
CoordinateBasis basis(*I, *J, *K, true);
if(!basis.hasValidBasis())
return 0;
//take average of vectors, but not for aromatic (since they're opposite)
vector3 v(0,0,0);
if(pt->pharma->name == "Aromatic" || pt->vecs.size() == 1)
{
v = pt->vecs[0];
}
else
{
for(unsigned i = 0, n = pt->vecs.size(); i < n; i++)
v += pt->vecs[i];
v /= pt->vecs.size();
}
float x = 0;
float y = 0;
float z = 0;
vector3 zero(0,0,0);
basis.setTranslate(zero);
basis.replot(v.x(), v.y(), v.z(), x, y, z);
unsigned ret = sphereGrid.pointToGrid(x, y, z);
ret++; //zero stands for no vector
return ret;
}
//create the canonical three point from the points and indexes i,j,k
//return simple finger class
ThreePointData::ThreePointData(unsigned offset, double w, unsigned nr, const vector<PharmaPoint>& points, unsigned i, unsigned j, unsigned k)
{
//points are always ordered by pharma kind first
Triplet tri(points, i, j, k);
boost::array<PharmaIndex, 3> PIs = tri.getPoints();
boost::array<TripletRange, 3> ranges = tri.getRanges();
fingerprint.set(PIs[0].index, PIs[1].index, PIs[2].index, points);
weight = reduceWeight(w);
nrot = reduceRotatable(nr);
//points and lines are in canonical order, initialize struct
molPos = offset;
l1 = ranges[0].length;
l2 = ranges[1].length;
l3 = ranges[2].length;
i1 = PIs[0].index;
i2 = PIs[1].index;
i3 = PIs[2].index;
//printf("P(%d,%d,%d) I(%d,%d,%d) L(%d,%d,%d)\n",PIs[0].pharmaIndex,
// PIs[1].pharmaIndex,PIs[2].pharmaIndex, (int)i1, (int)i2, (int)i3, (int)l1,(int)l2,(int)l3);
double X = PIs[0].point->x;
double Y = PIs[0].point->y;
double Z = PIs[0].point->z;
x = reduceFloat(X);
y = reduceFloat(Y);
z = reduceFloat(Z);
double d2 = PharmaPoint::pharmaDist(*PIs[1].point, *PIs[0].point);
theta2 = reduceAngle(atan2(PIs[1].point->y-Y, PIs[1].point->x-X));
phi2 = reduceAngle(acos((PIs[1].point->z-Z)/d2));
double d3 = PharmaPoint::pharmaDist(*PIs[2].point, *PIs[0].point);
theta3 = reduceAngle(atan2(PIs[2].point->y-Y, PIs[2].point->x-X));
phi3 = reduceAngle(acos((PIs[2].point->z-Z)/d3));
extra1 = PIs[0].point->size;
extra2 = PIs[1].point->size;
extra3 = PIs[2].point->size;
//alternatively, vector info
if(PIs[0].point->pharma->getVectors != NULL)
extra1 = vecValue(PIs[0].point, PIs[0].point, PIs[1].point, PIs[2].point);
if(PIs[1].point->pharma->getVectors != NULL)
extra2 = vecValue(PIs[1].point, PIs[0].point, PIs[1].point, PIs[2].point);
if(PIs[2].point->pharma->getVectors != NULL)
extra3 = vecValue(PIs[2].point, PIs[0].point, PIs[1].point, PIs[2].point);
}