void Docking::dockingSearchTest(double R, double beta1, double gamma1, double beta2, double gamma2,vector <pair<double, ScoreConfiguration> >& scores)
{
RotationMatrix rotationMatrixGamma1, rotationMatrixBeta1;
RotationMatrix rotationMatrixGamma2, rotationMatrixBeta2;
rotationMatrixGamma1.calculateMatrix(receptor_.getOrder(), RotationAngle( 0, gamma1) );
rotationMatrixBeta1.calculateMatrix(receptor_.getOrder(), RotationAngle( beta1, 0.0) );
rotationMatrixGamma2.calculateMatrix(receptor_.getOrder(), RotationAngle( 0, gamma2) );
rotationMatrixBeta2.calculateMatrix(receptor_.getOrder(), RotationAngle( beta2, 0.0));
rotReceptor_ = new Protein[1];
rotLigand_ = new Protein[alphaSize_];
receptor_.rotateTo(rotReceptor_[0], rotationMatrixGamma1);
rotReceptor_[0].rotate(rotationMatrixBeta1);
ligand_.rotateTo (rotLigand_[0], rotationMatrixGamma2);
rotLigand_[0].rotate(rotationMatrixBeta2);
Protein *transTmp;
if (R > 0)
{
transTmp = new Protein;
char buffer[100];
sprintf(buffer, "%s/%d/%.6lf.dat", translationPath_.c_str(), receptor_.getOrder(), R);
TranslationMatrix translationmatrix(buffer);
rotReceptor_[0].translateTo(*transTmp, translationmatrix);
}else
{
transTmp = &rotReceptor_[0];
}
set <pair<double, ScoreConfiguration> > bestScores;
scores.clear();
double minScore = 10000000.0, maxScore = -10000000.0;
for (int j = 1; j < alphaSize_; ++j)
{
rotLigand_[0].rotateTo(rotLigand_[j], ((2.0*PI)/alphaSize_) * j);
double tmpScore = scoreIt(*transTmp, rotLigand_[j], penalty_);
printf("%lf \n", tmpScore);
bestScores.insert(make_pair(tmpScore,ScoreConfiguration(R, ((2.0*PI)/alphaSize_) * j, beta1, gamma1, beta2, gamma2)));
minScore = min(minScore, tmpScore);
maxScore = max(maxScore, tmpScore);
while ((int)bestScores.size() > scoresSize_)
{
bestScores.erase(bestScores.begin());
}
}
printf("For R:%lf min score is %lf; max score is %lf\n",R, minScore, maxScore);
for (set <pair<double, ScoreConfiguration> >::iterator itr = bestScores.begin(); itr != bestScores.end(); ++itr)
{
scores.push_back(*itr);
}
if (R>0) delete transTmp;
}
void Docking::preDockingCalculateQRotations(void)
{
if (rotatationsCalculated_ == false)
{
//printf("Kalkulisem Q rotacije\n");
int raSize = 20*(1<<(tessellationOrder_*2));
raSize ++; //dodao zbog nultog kuta
//rotationAngles_ = new RotationAngle[raSize];
rotationAngles_ = new RotationAngle[raSize]; //dodao zbog (0,0) kuta
//printf("Generating Rotational Angles...\n");
Rotational_Angles(tessellationOrder_, rotationAngles_);
//printf("Generated Rotational Angles (%d of them)...\n", raSize);
rotReceptor_ = new Protein[raSize];
qRotLigand_ = new Protein[raSize];
RotationMatrix rotationMatrixGamma, rotationMatrixBeta;
//printf("Rotating receptor & ligand...\n");
for (int i = 0; i < raSize; ++i)
{
/*if ( (abs(rotationAngles_[i].beta) < 0.00001) && (abs(rotationAngles_[i].gamma) < 0.00001) ){
printf("NULA: %lf %lf \n", rotationAngles_[i].beta, rotationAngles_[i].gamma );
}*/
rotationMatrixGamma.calculateMatrix(receptor_.getOrder(), RotationAngle(0, rotationAngles_[i].gamma));
rotationMatrixBeta.calculateMatrix(receptor_.getOrder(), RotationAngle(rotationAngles_[i].beta, 0.0));
receptor_.rotateTo(rotReceptor_[i], rotationMatrixGamma);
rotReceptor_[i].rotate(rotationMatrixBeta);
ligand_.rotateTo (qRotLigand_[i], rotationMatrixGamma);
qRotLigand_[i].rotate(rotationMatrixBeta);
qRotLigand_[i].qTransition(penalty_);
}
//printf("Rotated successfully (total %d receptor, %d ligand)...\n", raSize, raSize*alphaSize_);
rotatationsCalculated_ = true;
}
}
void Docking::preDockingCalculateRotations(void)
{
if (rotatationsCalculated_ == false)
{
//printf("Kalkulisem rotacije\n");
int raSize = 20*(1<<(tessellationOrder_*2))+1;
rotationAngles_ = new RotationAngle[raSize];
//printf("Generating Rotational Angles...\n");
Rotational_Angles(tessellationOrder_, rotationAngles_);
//printf("Generated Rotational Angles (%d of them)...\n", raSize);
rotReceptor_ = new Protein[raSize];
rotLigand_ = new Protein[raSize*alphaSize_];
RotationMatrix rotationMatrixGamma, rotationMatrixBeta;
//printf("Rotating receptor & ligand...\n");
for (int i = 0; i < raSize; ++i)
{
rotationMatrixGamma.calculateMatrix(receptor_.getOrder(), RotationAngle(0, rotationAngles_[i].gamma));
rotationMatrixBeta.calculateMatrix(receptor_.getOrder(), RotationAngle(rotationAngles_[i].beta, 0.0));
receptor_.rotateTo(rotReceptor_[i], rotationMatrixGamma);
rotReceptor_[i].rotate(rotationMatrixBeta);
ligand_.rotateTo (rotLigand_ [i*alphaSize_], rotationMatrixGamma);
rotLigand_[i*alphaSize_].rotate(rotationMatrixBeta);
// if (i%10 == 0) printf("...receptor %d...ligand %d...\n", i, i*alphaSize_);
for (int j = 1; j < alphaSize_; ++j)
{
rotLigand_[i*alphaSize_].rotateTo(rotLigand_[i*alphaSize_+j], ((2.0*PI)/alphaSize_) * j);
}
}
//printf("Rotated successfully (total %d receptor, %d ligand)...\n", raSize, raSize*alphaSize_);
rotatationsCalculated_ = true;
}
}
void Docking::setConfiguration(const ScoreConfiguration& scoreConfiguration, Protein &newReceptor, Protein &newLigand) const
{
// rotate receptor
RotationMatrix rotationMatrix;
rotationMatrix.calculateMatrix(receptor_.getOrder(), RotationAngle(0.0, scoreConfiguration.gamma2));
receptor_.rotateTo(newReceptor, rotationMatrix);
rotationMatrix.calculateMatrix(receptor_.getOrder(), RotationAngle(scoreConfiguration.beta2, 0.0));
newReceptor.rotate(rotationMatrix);
// translate
char buffer[100];
// sprintf(buffer, "%s/%d/%.6lf.dat", "data/trans", receptor_.getOrder(), scoreConfiguration.R);
sprintf(buffer, "%s/%d/%.6lf.dat", translationPath_.c_str(), receptor_.getOrder(), scoreConfiguration.R);
TranslationMatrix translationmatrix(buffer);
newReceptor.translate(translationmatrix);
rotationMatrix.calculateMatrix(receptor_.getOrder(), RotationAngle(0.0, scoreConfiguration.gamma1));
ligand_.rotateTo(newLigand, rotationMatrix);
rotationMatrix.calculateMatrix(receptor_.getOrder(), RotationAngle(scoreConfiguration.beta1, 0.0));
newLigand.rotate(rotationMatrix);
rotationMatrix.calculateMatrix(receptor_.getOrder(), RotationAngle(0.0, scoreConfiguration.alpha));
newLigand.rotate(rotationMatrix);
}
NS_IMETHODIMP
Touch::GetRotationAngle(float* aRotationAngle)
{
*aRotationAngle = RotationAngle();
return NS_OK;
}
void Docking::dockingQsearchTest(double R, double beta1, double gamma1, double beta2, double gamma2,vector <pair<double, ScoreConfiguration> >& scores)
{
RotationMatrix rotationMatrixGamma1, rotationMatrixBeta1;
RotationMatrix rotationMatrixGamma2, rotationMatrixBeta2;
rotationMatrixGamma1.calculateMatrix(receptor_.getOrder(), RotationAngle( 0, gamma1) );
rotationMatrixBeta1.calculateMatrix(receptor_.getOrder(), RotationAngle( beta1, 0.0) );
rotationMatrixGamma2.calculateMatrix(receptor_.getOrder(), RotationAngle( 0, gamma2) );
rotationMatrixBeta2.calculateMatrix(receptor_.getOrder(), RotationAngle( beta2, 0.0));
rotReceptor_ = new Protein[1];
qRotLigand_ = new Protein[1];
receptor_.rotateTo(rotReceptor_[0], rotationMatrixGamma1);
rotReceptor_[0].rotate(rotationMatrixBeta1);
ligand_.rotateTo (qRotLigand_[0], rotationMatrixGamma2);
qRotLigand_[0].rotate(rotationMatrixBeta2);
qRotLigand_[0].qTransition(penalty_);
Protein *transReceptor;
if (R > 0)
{
transReceptor = new Protein;
char buffer[100];
sprintf(buffer, "%s/%d/%.6lf.dat", translationPath_.c_str(), receptor_.getOrder(), R);
TranslationMatrix translationmatrix(buffer);
vector<int> translationIndexes;
rotReceptor_[0].calculateTranslationIndexes( translationIndexes );
rotReceptor_[0].translateTo(*transReceptor, translationmatrix, translationIndexes);
}else
{
transReceptor = &rotReceptor_[0];
}
set <pair<double, ScoreConfiguration> > bestScores;
scores.clear();
double minScore = 10000000.0, maxScore = -10000000.0;
vector<double> qCoeffPlusPlus, qCoeffMinusMinus;
int order = receptor_.getOrder();
qCoeffPlusPlus.resize(order, 0.0);
qCoeffMinusMinus.resize(order, 0.0);
trigonometricCash();
calculateCoeffMapping( );
vector<double> qCoeffPlus;
qCoeffPlus.resize((2* order - 1), 0.0);
vector<double> qCoeffMinus;
qCoeffMinus.resize((2* order - 1), 0.0);
//calculateQcoeffPlusPlus(qCoeffPlusPlus, qCoeffPlus ,*transReceptor, qRotLigand_[0] );
//calculateQcoeffMinusMinus(qCoeffMinusMinus,qCoeffMinus, *transReceptor, qRotLigand_[0] );
calculateQcoeffs(qCoeffPlusPlus, qCoeffPlus, qCoeffMinusMinus, qCoeffMinus,*transReceptor, qRotLigand_[0]);
printf("Q Coeff plus plus : \n");
for(int i = 0 ; i < qCoeffPlusPlus.size(); ++i) printf("%lf \n",qCoeffPlusPlus[i]);
printf("Q Coeff minus minus : \n");
for(int i = 0 ; i < qCoeffMinusMinus.size(); ++i) printf("%lf \n",qCoeffMinusMinus[i]);
printf("Alfa function: \n");
for (int j = 1; j < alphaSize_; ++j)
{
double tmpScore = qCoeffPlusPlus[0];
int index_alfa = j*order;
for (int m = 1; m <= (order-1); ++m)
{
double alfa2angle = j*((2.0*PI)/alphaSize_);
//tmpScore += (qCoeffPlusPlus[m] * cos(m*alfa2angle) ) + (qCoeffMinusMinus[m] * sin(m*alfa2angle) );
tmpScore += (qCoeffPlusPlus[m] * cosValue_->at(index_alfa+m) ) + (qCoeffMinusMinus[m] * sinValue_->at(index_alfa+m) );
}
printf("%lf \n", tmpScore);
bestScores.insert(make_pair(tmpScore,ScoreConfiguration(R, ((2.0*PI)/alphaSize_) * j, beta1, gamma1, beta2, gamma2)));
minScore = min(minScore, tmpScore);
maxScore = max(maxScore, tmpScore);
while ((int)bestScores.size() > scoresSize_)
{
bestScores.erase(bestScores.begin());
}
}
printf("For R:%lf min score is %lf; max score is %lf\n",R, minScore, maxScore);
for (set <pair<double, ScoreConfiguration> >::iterator itr = bestScores.begin(); itr != bestScores.end(); ++itr)
{
scores.push_back(*itr);
}
if (R>0) delete transReceptor;
}
