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Triplet.h
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Triplet.h
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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.
*/
/*
* Triplet.h
*
* Created on: Aug 5, 2010
* Author: dkoes
*
* Three points make a triplet. Has a canonical form.
*/
#ifndef TRIPLET_H_
#define TRIPLET_H_
#include "RMSD.h"
#include "pharmarec.h"
#include "ThreePointData.h"
#include <boost/array.hpp>
#include "BoundingBox.h"
#include "QueryTripletFingerprint.h"
#include "SimpleFingers.h"
#include "basis.h"
#include "SphereGrid.h"
//convenience class for dealing with indexed pharma points
struct PharmaIndex
{
const PharmaPoint* point;
unsigned index;
unsigned pharmaIndex;
PharmaIndex()
{
}
PharmaIndex(const PharmaPoint& p, unsigned i) :
point(&p), index(i), pharmaIndex(p.pharma->index)
{
}
bool operator<(const PharmaIndex& rhs) const
{
return pharmaIndex < rhs.pharmaIndex;
}
};
struct TripletRange
{
unsigned short min;
unsigned short max;
unsigned short length;
};
class Triplet
{
protected:
boost::array<PharmaIndex, 3> PIs;
boost::array<TripletRange, 3> range;
unsigned nextUnconnectIndex; //vertex not connect to very next triplet
unsigned prevUnconnectIndex; //vertex not conneted to previous triplet
enum DupKind
{
AllDifferent, FirstTwoSame, LastTwoSame, AllSame
} kind;
void computeLengths()
{
range[0].length = ThreePointData::reduceFloatUnsigned(
PharmaPoint::pharmaDist(*PIs[0].point, *PIs[1].point));
range[1].length = ThreePointData::reduceFloatUnsigned(
PharmaPoint::pharmaDist(*PIs[1].point, *PIs[2].point));
range[2].length = ThreePointData::reduceFloatUnsigned(
PharmaPoint::pharmaDist(*PIs[2].point, *PIs[0].point));
//mins
range[0].min = 0;
range[1].min = 0;
range[2].min = 0;
unsigned short dist = ThreePointData::reduceFloatUnsigned(
PIs[0].point->radius + PIs[1].point->radius);
if (dist < range[0].length)
range[0].min = range[0].length - dist;
dist = ThreePointData::reduceFloatUnsigned(PIs[1].point->radius
+ PIs[2].point->radius);
if (dist < range[1].length)
range[1].min = range[1].length - dist;
dist = ThreePointData::reduceFloatUnsigned(PIs[2].point->radius
+ PIs[0].point->radius);
if (dist < range[2].length)
range[2].min = range[2].length - dist;
//maxs
range[0].max = range[0].length + ThreePointData::reduceFloatUnsigned(
PIs[0].point->radius + PIs[1].point->radius);
range[1].max = range[1].length + ThreePointData::reduceFloatUnsigned(
PIs[1].point->radius + PIs[2].point->radius);
range[2].max = range[2].length + ThreePointData::reduceFloatUnsigned(
PIs[2].point->radius + PIs[0].point->radius);
}
//swap points i and j in p and update ranges appropriately
void swap(unsigned i, unsigned j)
{
::swap(PIs[i], PIs[j]);
if (nextUnconnectIndex == i)
nextUnconnectIndex = j;
else if (nextUnconnectIndex == j)
nextUnconnectIndex = i;
if (prevUnconnectIndex == i)
prevUnconnectIndex = j;
else if (prevUnconnectIndex == j)
prevUnconnectIndex = i;
switch (i)
{
case 0:
if (j == 1)
{
::swap(range[1], range[2]);
}
else if (j == 2)
{
::swap(range[0], range[1]);
}
break;
case 1:
if (j == 0)
{
::swap(range[1], range[2]);
}
else if (j == 2)
{
::swap(range[0], range[2]);
}
break;
case 2:
if (j == 0)
{
::swap(range[0], range[1]);
}
else if (j == 1)
{
::swap(range[0], range[2]);
}
break;
}
}
//put in canonical order
void canonize()
{
//4 cases
//all different kinds
if (PIs[0].pharmaIndex != PIs[1].pharmaIndex && PIs[0].pharmaIndex
!= PIs[2].pharmaIndex && PIs[1].pharmaIndex
!= PIs[2].pharmaIndex)
{
//use the current order, it's fully constrained
kind = AllDifferent;
}
//all the same kind
else if (PIs[0].pharmaIndex == PIs[1].pharmaIndex && PIs[1].pharmaIndex
== PIs[2].pharmaIndex)
{
kind = AllSame;
//sort completely on length
//do manual "sort"
//the first point is between the smallest and largest length
if (range[0].length <= range[1].length && range[0].length
<= range[2].length)
{
if (range[1].length <= range[2].length)
{
//perfect, no change necessary
}
else
{
//need to swap first and second point
swap(0, 1);
}
}
else if (range[1].length <= range[0].length && range[1].length
<= range[2].length)
{
if (range[0].length <= range[2].length)
{
//swap first and third
swap(0, 2);
}
else
{
swap(0, 1);
swap(1, 2);
}
}
else //l2 is shortest
{
if (range[0].length <= range[1].length)
{
swap(0, 2);
swap(1, 2);
}
else
{
swap(1, 2);
}
}
}
//first two are the same kind
else if (PIs[0].pharmaIndex == PIs[1].pharmaIndex)
{
kind = FirstTwoSame;
//may need to swap
if (range[1].length > range[2].length)
{
swap(0, 1);
}
}
//last two the same
else if (PIs[1].pharmaIndex == PIs[2].pharmaIndex)
{
kind = LastTwoSame;
//may need to swap
if (range[0].length > range[2].length)
{
swap(1, 2);
}
}
else
abort(); //huh?
}
Triplet(const boost::array<PharmaIndex, 3>& pis, const boost::array<TripletRange, 3>& r,
unsigned nc, unsigned pc) :
PIs(pis), range(r), nextUnconnectIndex(nc), prevUnconnectIndex(pc)
{
}
public:
Triplet()
{
}
Triplet(const vector<PharmaPoint>& points, unsigned i, unsigned j,
unsigned k) :
nextUnconnectIndex(0), prevUnconnectIndex(0)
{
//points are always ordered by pharma kind first
PIs[0] = PharmaIndex(points[i], i);
PIs[1] = PharmaIndex(points[j], j);
PIs[2] = PharmaIndex(points[k], k);
sort(PIs.begin(), PIs.end());
computeLengths();
canonize();
}
virtual ~Triplet()
{
}
//index k is not is not connected to the next triplet
//and the next's triplet's unconnected point is kpoint
void setNextUnconnected(unsigned k)
{
nextUnconnectIndex = k;
}
//volume
double getV() const
{
double ret = 1.0;
for (unsigned i = 0; i < 3; i++)
{
ret *= ThreePointData::unreduceFloat(range[i].max - range[i].min);
}
return ret;
}
//return which point of this triplet ordering is not connected to the next triplet
unsigned getNextUnconnected() const
{
return nextUnconnectIndex;
}
unsigned getPrevUnconnected() const
{
return prevUnconnectIndex;
}
const boost::array<PharmaIndex, 3>& getPoints() const
{
return PIs;
}
const boost::array<TripletRange, 3>& getRanges() const
{
return range;
}
unsigned getPharma(unsigned p) const
{
return PIs[p].point->pharma->index;
}
void dump() const
{
for (unsigned i = 0; i < 3; i++)
{
cout << PIs[i].index << " " << PIs[i].pharmaIndex << " "
<< range[i].length << " " << range[i].min << " "
<< range[i].max << " | ";
}
cout << "N" << nextUnconnectIndex << " P" << prevUnconnectIndex << "\n";
}
};
static unsigned sharedR[3][3] =
{
{ 0, 1, 0 },
{ 1, 0, 2 },
{ 0, 2, 0 } }; //radii index shared be lengths i/j
static unsigned unsharedR[3][3] =
{
{ 0, 0, 1 },
{ 2, 0, 1 },
{ 2, 0, 0 } }; //radii index of i not shared with j
static unsigned sharedA[3][3] =
{
{ 0, 2, 1 },
{ 2, 0, 0 },
{ 1, 0, 0 } }; //index of shared angle between lengths i/j
class QueryTriplet: public Triplet
{
protected:
//used by search
BoundingBox mybox;
boost::array<double, 9> ref;
double a, b, c; //lengths, shortest to longest
double aang, bang, cang; //opposing angle
double r0, r1, r2;
double smallAthresholdsmallB; // if a <=, b a bounded
double smallAthresholdlargeB;
double smallAthresholdlargeC;
double largeCthresholdsmallA;
double lengths[3];
double angles[3];
double radii[3];
double tangd[3];
double tangdM[3];
double smallLowerThresholds[3][3]; //if first index is smaller than threshold then second has lower bound
double smallUpperThresholds[3][3]; //if first index is smaller than threshold then second has upper bound
double largeLowerThresholds[3][3]; //if first index is larger than threshold then second has lower bound
double largeUpperThresholds[3][3]; //if first index is larger than threshold then second has upper bound
QueryTripletFingerprint fingerprint;
//min/max distances to previous triplet's unconnects to successor triplet points
//indexed by number of hops back (so prev triplet is at index 0, it's prev is at 1)
vector<unsigned> minkdistsq;
vector<unsigned> maxkdistsq;
bool skipfingers;
//optional constraints, if zero ignore
unsigned minSize[3];
unsigned maxSize[3];
unsigned long vectorMask[3];
bool hasExtra;
//set parameters for any extra constraints
void setExtra(const PharmaPoint* p, unsigned& min, unsigned& max, unsigned long& mask)
{
if(p->maxSize < UINT_MAX || p->minSize > 0) //has a range
{
max = p->maxSize;
min = p->minSize;
hasExtra = true;
}
if(p->vecs.size() > 0)
{
//just take first!
CoordinateBasis basis(*PIs[0].point, *PIs[1].point, *PIs[2].point, true);
if(basis.hasValidBasis())
{
hasExtra = true;
OpenBabel::vector3 v = p->vecs[0];
float x = 0;
float y = 0;
float z = 0;
basis.setTranslate(OpenBabel::vector3(0,0,0));
basis.replot(v.x(), v.y(), v.z(), x, y, z);
unsigned g = sphereGrid.pointToGrid(x ,y, z);
//very approximate and poorly calibrated to query tolerances masks
if(p->pharma->name == "Aromatic")
{
//can be in either direction, so use 45 degrees
mask = sphereGrid.searchMask(g, 45);
unsigned g2 = sphereGrid.pointToGrid(-x,-y,-z);
mask |= sphereGrid.searchMask(g2, 45);
}
else
{
mask = sphereGrid.searchMask(g, 60);
}
//0 is reserved
mask <<= 1;
}
}
}
//return true if extra isn't appropriate for this query
bool extraFails(unsigned min, unsigned max, unsigned long mask, unsigned extra) const
{
if(max > 0)
{
if(extra >= min && extra <= max)
return false;
return true;
}
else if(mask != 0 && extra != 0)
{
if((1<<extra)&mask)
return false;
return true;
}
return false;
}
void setExtras()
{
hasExtra = false;
memset(minSize, 0, sizeof(minSize));
memset(maxSize, 0, sizeof(maxSize));
memset(vectorMask, 0, sizeof(vectorMask));
for(unsigned i = 0; i < 3; i++)
{
setExtra(PIs[i].point, minSize[i], maxSize[i], vectorMask[i]);
}
}
//the distance between a center c and the closest tangent plane of the other two spheres
double computeTangDMin(double ra, double rb, double ab, double theta, double ac)
{
//find distance between circle and plane (from maple);
double t1, t3, t4, t8, t10, t11, t12, t15, t16, t19, t22, t25, t28;
double x3 = cos(theta)*ac;
double y3 = sin(theta)*ac;
t1 = ra - rb;
t3 = 1.0 / ab;
t4 = t3 * t1 * ra;
t8 = ab + t3 * t1 * rb - t4;
t10 = (t1 * t1);
t11 = ab * ab;
t12 = 1.0 / t11;
t15 = sqrt((double) (1 - t12 * t10));
t16 = t15 * ra;
t19 = t15 * rb - t16;
t22 = (double) t12 * (t8 * (x3 - t4) + t19 * (y3 - t16));
double x = t4 + t8*t22;
t25 = x3 - x;
double y = t16 + t19 * t22;
t28 = y3 - y;
//figure out distance from centerline to d and c
double a = atan2(t28, t25);
double x2 = y/tan(a);
double ddist = sqrt(x2*x2 + y*y);
double cdist = sqrt((x3-x+x2)*(x3-x+x2)+y3*y3);
if(cdist < ddist)
return 0;
t25 *= t25;
t28 *= t28;
double d = sqrt(t25 + t28);
return d;
}
double computeTangDMax(double ra, double rb, double ab, double theta, double ac)
{
double t1, t3, t4, t8, t10, t11, t12, t15, t16, t19, t22, t25, t28;
double x3 = cos(theta)*ac;
double y3 = sin(theta)*ac;
t1 = ra - rb;
t3 = 1.0 / ab;
t4 = t3 * t1 * ra;
t8 = ab + t3 * t1 * rb - t4;
t10 = (t1 * t1);
t11 = ab * ab;
t12 = 1.0 / t11;
t15 = sqrt((double) (1 - t12 * t10));
t16 = t15 * ra;
t19 = -t15 * rb + t16;
t22 = (t8 * (x3 - t4) + (y3 + t16) * t19) * (double) t12;
double x = t4 + t8 * t22;
t25 = x3 - x;
t25 *= t25;
double y = -t16 + t19 * t22;
t28 = y3 - y;
t28 *= t28;
double d = sqrt(t25 + t28);
return d;
}
//cache data used by search, but not creation
void computeSearchData()
{
setExtras();
mybox.minx = range[0].min;
mybox.maxx = range[0].max;
mybox.miny = range[1].min;
mybox.maxy = range[1].max;
mybox.minz = range[2].min;
mybox.maxz = range[2].max;
for (unsigned i = 0; i < 3; i++)
{
ref[3 * i] = PIs[i].point->x;
ref[3 * i + 1] = PIs[i].point->y;
ref[3 * i + 2] = PIs[i].point->z;
}
//compute the minimum and maximum perimeters of valid triangles
//first get the angles (law of cos)
a = range[0].length;
b = range[1].length;
c = range[2].length;
r0 = ThreePointData::reduceFloatUnsigned(PIs[0].point->radius);
r1 = ThreePointData::reduceFloatUnsigned(PIs[1].point->radius);
r2 = ThreePointData::reduceFloatUnsigned(PIs[2].point->radius);
radii[0] = r0;
radii[1] = r1;
radii[2] = r2;
lengths[0] = a;
lengths[1] = b;
lengths[2] = c;
cang = acos((c * c - a * a - b * b) / (-2 * a * b));
bang = acos((b * b - a * a - c * c) / (-2 * a * c));
aang = acos((a * a - b * b - c * c) / (-2 * b * c));
angles[0] = aang;
angles[1] = bang;
angles[2] = cang;
tangd[2] = computeTangDMin(r0,r1,a,bang,c)-r2;
tangd[0] = computeTangDMin(r1,r2,b,cang,a)-r0;
tangd[1] = computeTangDMin(r2,r0,c,aang,b)-r1;
//don't compute max if within tangent range
tangdM[2] = tangd[2] > -r2 ? computeTangDMax(r0,r1,a,bang,c)+r2 : HUGE_VAL;
tangdM[0] = tangd[0] > -r0 ? computeTangDMax(r1,r2,b,cang,a)+r0 : HUGE_VAL;
tangdM[1] = tangd[1] > -r1 ? computeTangDMax(r2,r0,c,aang,b)+r1 : HUGE_VAL;
//if a is short enough, it provides a lower bound on the other distances
//must be shorter than connecting to other distances shortest point
smallAthresholdsmallB = floor(sqrt(a * a + r1 * r1 - 2 * a * r1 * cos(
cang)) - r0);
smallAthresholdlargeB = floor(sqrt(a * a + r1 * r1 - 2 * a * r1 * cos(
M_PI - cang)) - r0);
smallAthresholdlargeC = sqrt(a * a + r0 * r0 - 2 * a * r0 * cos(M_PI
- bang)) - r1;
//if c is large enough provides bounds on other distances
largeCthresholdsmallA = sqrt(c * c + r0 * r0 - 2 * c * r0 * cos(bang))
+ r2;
memset(smallLowerThresholds, 0, sizeof(smallLowerThresholds));
memset(smallUpperThresholds, 0, sizeof(smallUpperThresholds));
memset(largeLowerThresholds, 0, sizeof(largeLowerThresholds));
memset(largeUpperThresholds, 0, sizeof(largeUpperThresholds));
//compute 2D thresholds
//in theory you can further narrow by considering all three lengths, but that's really complicated
for (unsigned i = 0; i < 3; i++)
{
for (unsigned j = 0; j < 3; j++)
{
if (i == j)
continue;
//if i's length is less than a certain threshold, j has a lower bound
double sR = radii[sharedR[i][j]];
double l = lengths[i];
double sA = angles[sharedA[i][j]];
double iR = radii[unsharedR[i][j]];
smallLowerThresholds[i][j] = floor(sqrt(l * l + sR * sR - 2 * l
* sR * cos(sA)) - iR);
//and an upper bound
smallUpperThresholds[i][j] = floor(sqrt(l * l + sR * sR - 2 * l
* sR * cos(M_PI - sA)) - iR);
//if i is larger than threshold, j has lower bound
largeLowerThresholds[i][j] = ceil(sqrt(l * l + sR * sR - 2 * l
* sR * cos(sA)) + iR);
//and an upper bound
largeUpperThresholds[i][j] = ceil(sqrt(l * l + sR * sR - 2 * l
* sR * cos(M_PI-sA)) + iR);
}
}
}
QueryTriplet(const boost::array<PharmaIndex, 3>& pis,
const boost::array<TripletRange, 3>& r, unsigned nc, unsigned pc) :
Triplet(pis, r, nc, pc), aang(0), bang(0), cang(0),minkdistsq(0), maxkdistsq(0), skipfingers(false)
{
computeSearchData();
}
public:
void setFingerPrints(const PharmerQuery& query)
{
fingerprint.set(PIs[0].index, PIs[1].index, PIs[2].index, query);
}
protected:
//do not use in a ranged context
bool distancekTooLargeForij(unsigned i, double Li, unsigned j, double Lj, unsigned k, double Lk) const
{
//consider the plane tangent to two circles, and the line segment perpindicular to
//this plane that intersects the third; use lengths i and j to find a maximum bound on k
double d = tangd[sharedR[i][j]];
if(d <= 0)
return false; //no gap
double maxk = sqrt(Li*Li-d*d)+sqrt(Lj*Lj-d*d);
if(Lk > maxk)
{
return true;
}
//additionally consider large i/j
double rc = radii[sharedR[i][j]];
if(Li > lengths[i]+rc && Lj > lengths[j]+rc)
{
//the mutually constrain each other - don't attempt a perfect calculation
//though, just consider each individual constraint and add
double ac = lengths[i];
double ra = radii[sharedR[i][k]];
double t1 = ac * ac;
double t2 = ra * ra;
double t4 = Li - rc;
t4 *= t4;
double t11 = acos((t1 + t2 - t4) / ac / ra / 0.2e1);
double aa = M_PI - t11;
double A = angles[sharedA[k][k]];
if(aa < A)
{
double bc = lengths[j];
double rb = radii[sharedR[j][k]];
t1 = bc * bc;
t2 = rb * rb;
t4 = Lj - rc;
t4 *= t4;
t11 = acos((t1 + t2 - t4) / bc / rb / 0.2e1);
double bb = M_PI - t11;
double B = angles[sharedA[j][k]];
if(bb < B)
{
double ab = lengths[k];
double Aang = A-aa;
double Bang = B-bb;
t1 = cos(Bang);
double t3 = cos(Aang);
double t6 = ab + rb * t1 + ra * t3;
t6 *= t6;
double t7 = sin(Bang);
double t9 = sin(Aang);
double t12 = -rb * t7 + ra * t9;
t12*=t12;
double m = sqrt(t6 + t12);
if(Lk >= m)
return true;
}
}
}
return false;
}
//don't use this in a ranged context
bool distancekTooSmallForij(unsigned i, double Li, unsigned j, double Lj, unsigned k, double Lk) const
{
//consider the plane tangent to bottom two circles, and the line segment perpindicular to
//this plane that intersects the third; use lengths i and j to find a minimum bound on k
double d = tangdM[sharedR[i][j]];
if(Li < d || Lj < d)
return false; //not long enough to be constrained
double v1 = sqrt(Li*Li-d*d);
double v2 = sqrt(Lj*Lj-d*d);
double mink = v1+v2;
if(Lk < mink)
{
//actually two possible traingles, one of which is unconstraining
double limit = lengths[k] - radii[sharedR[k][j]] - radii[sharedR[k][i]];
//alternate triangle must be useless
if(fabs(v1-v2) < limit)
{
return true;
}
}
return false;
}
//return true if bounds are not met
bool distancejTooSmallForSmalli(unsigned i, double Li, unsigned j,
double Lj) const
{
if (Li <= smallLowerThresholds[i][j])
{
double A = angles[sharedA[i][j]];
if (isfinite(A))
{
double iR = radii[unsharedR[i][j]];
double jR = radii[unsharedR[j][i]];
double sR = radii[sharedR[i][j]];
double l = Li + iR;
double l2 = Lj + jR;
double iL = lengths[i];
double jL = lengths[j];
double min = -2 * cos(-acos(.5 * (-l * l + iL * iL + sR * sR)
/ (iL * sR)) + A) * jL * sR + jL * jL + sR * sR;
if (l2 * l2 < min)
return true;
}
}
return false;
}
//return true if bounds are not met
bool distancejTooSmallForLargei(unsigned i, double Li, unsigned j,
double Lj) const
{
abort(); //this function is redudant in most cases to distancejTooLargeForSmalli
if (Li >= largeLowerThresholds[i][j])
{
double A = angles[sharedA[i][j]];
if (isfinite(A))
{
double iR = radii[unsharedR[i][j]];
double jR = radii[unsharedR[j][i]];
double sR = radii[sharedR[i][j]];
double l = Li - iR;
double l2 = Lj + jR;
double iL = lengths[i];
double jL = lengths[j];
double min = -2 * cos(acos(.5 * (-l * l + iL * iL + sR * sR)
/ (iL * sR)) - A) * jL * sR + jL * jL + sR * sR;
if (l2 * l2 < min)
return true;
}
}
return false;
}
//return true if j is too large for i
bool distancejTooLargeForSmalli(unsigned i, double Li, unsigned j,
double Lj) const
{
if (Li <= smallUpperThresholds[i][j])
{
double A = angles[sharedA[i][j]];
if (isfinite(A))
{
double iR = radii[unsharedR[i][j]];
double jR = radii[unsharedR[j][i]];
double sR = radii[sharedR[i][j]];
double l = Li + iR;
double l2 = Lj - jR;
double iL = lengths[i];
double jL = lengths[j];
double max = jL * jL + sR * sR - 2.0 * jL * sR * cos(A + acos(
(-l * l + iL * iL + sR * sR) / iL / sR / 2.0));
if (l2 * l2 > max)
{
return true;
}
}
}
return false;
}
bool distancejTooLargeForLargei(unsigned i, double Li, unsigned j,
double Lj) const
{
if (Li >= largeUpperThresholds[i][j])
{
double A = angles[sharedA[i][j]];
double iR = radii[unsharedR[i][j]];
double jR = radii[unsharedR[j][i]];
double l = Li - iR;
double l2 = Lj - jR;
if (l > 0 && l2 > 0 && isfinite(A))
{
double sR = radii[sharedR[i][j]];
double iL = lengths[i];
double jL = lengths[j];
double max = -2 * cos(2*M_PI - acos(.5 * (-l * l + iL * iL + sR * sR)
/ (iL * sR)) - A) * jL * sR + jL * jL + sR * sR;
if (l2 * l2 > max)
return true;
}
}
return false;
}
//return true if any distances don't work
//note the relations are not symetric
//distances must be in order
bool distancesAreBad(double Li, double Lj, double Lk) const
{
double d[3] =
{ Li, Lj, Lk };
for (unsigned i = 0; i < 3; i++)
{
for (unsigned j = 0; j < 3; j++)
{
if (i != j)
{
if (distancejTooLargeForSmalli(i, d[i], j, d[j]))
return true;
if (distancejTooSmallForSmalli(i, d[i], j, d[j]))
return true;
if (distancejTooLargeForLargei(i, d[i], j, d[j]))
return true;
}
}
}
if(distancekTooLargeForij(0, Li, 1, Lj, 2, Lk))
return true;
if(distancekTooLargeForij(0, Li, 2, Lk, 1, Lj))
return true;
if(distancekTooLargeForij(1, Lj, 2, Lk, 0, Li))
return true;
if(distancekTooSmallForij(0, Li, 1, Lj, 2, Lk))
return true;
if(distancekTooSmallForij(0, Li, 2, Lk, 1, Lj))
return true;
if(distancekTooSmallForij(1, Lj, 2, Lk, 0, Li))
return true;
return false;
}
//return true if l1/l2 are valid based on precomputed thresholds for sides AB
bool BtooSmallForSmallA(unsigned short L1, unsigned short L2) const
{
if (L1 < smallAthresholdsmallB)
{
double l = L1 + r0;
double l2 = L2 + r2;
double min = -2 * cos(-acos((.5) * (-l * l + a * a + r1 * r1) / (a
* r1)) + cang) * b * r1 + b * b + r1 * r1;
if (l2 * l2 < min)
{
return true;
}
}
return false;
}
bool BtooBigForSmallA(unsigned short L1, unsigned short L2) const
{
if (L1 < smallAthresholdlargeB)
{
double l = L1 + r0;
double l2 = L2 - r2;
double max = b * b + r1 * r1 - 2.0 * b * r1 * cos(cang + acos((-l
* l + a * a + r1 * r1) / a / r1 / 2.0));
if (l2 * l2 > max)
{
return true;
}
}
return false;
}
bool CtooBigForSmallA(unsigned short L1, unsigned short L3) const
{
if (L1 < smallAthresholdlargeC)
{
float l = L1 + r1;
float l2 = L3 - r2;
float max = c * c + r0 * r0 - 2.0 * c * r0 * cos(bang + acos((-l
* l + a * a + r0 * r0) / a / r0 / 2.0));
if (l2 * l2 > max)
{
return true;
}
}
return false;
}
public:
QueryTriplet()
{
}
QueryTriplet(const vector<PharmaPoint>& points, unsigned i, unsigned j,
unsigned k) :
Triplet(points, i, j, k), skipfingers(false)
{
computeSearchData();
}
virtual ~QueryTriplet()
{
}
const QueryTripletFingerprint& getFingerPrint() const { return fingerprint; }
//return true if order is at least partially canonical (ranges overlap appropriately)
bool validOverlap() const
{
switch (kind)
{
case AllDifferent:
//only one ordering
return true;
case AllSame:
if (range[0].min < range[1].max && range[1].min < range[2].max)
return true;
return false;
case FirstTwoSame:
if (range[0].min < range[1].max)
return true;
return false;
case LastTwoSame:
if (range[1].min < range[2].max)
return true;
return false;
}
return false;
}
//return number of useful orderings
unsigned numOrderings() const
{
switch (kind)
{
case AllDifferent:
//only one ordering
return 1;
case AllSame:
return 6;
case FirstTwoSame:
case LastTwoSame:
return 2;
}
return 1;
}