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::dockingSearch(vector <pair<double, ScoreConfiguration> >& scores, vector<double> RadiusSet, vector<double>& MaxScoresRadius)
{
int raSize = 20*(1<<(tessellationOrder_*2))+1;
set <pair<double, ScoreConfiguration> > bestScores;
preDockingCalculateRotations();
//precalculation of all rotations
Protein *transTmp = new Protein;
//printf("Starting docking search...\n");
//scores.clear();
for (unsigned int radiusIndex = 0; radiusIndex < RadiusSet.size(); ++radiusIndex)
{
double R = RadiusSet[radiusIndex];
double minScore = 10000000.0, maxScore = -10000000.0;
char buffer[100];
sprintf(buffer, "%s/%d/%.6lf.dat", translationPath_.c_str(), receptor_.getOrder(), R);
TranslationMatrix translationmatrix(buffer);
for (int i = 0; i < raSize; ++i)
{
rotReceptor_[i].translateTo(*transTmp, translationmatrix);
for (int j = 0; j < raSize*alphaSize_; ++j)
{
double tmpScore = scoreIt(*transTmp, rotLigand_[j], penalty_);
bestScores.insert(make_pair(tmpScore,
ScoreConfiguration(R, (j%alphaSize_) * (2.0*PI/alphaSize_), rotationAngles_[i].beta,
rotationAngles_[i].gamma, rotationAngles_[j/alphaSize_].beta, rotationAngles_[j/alphaSize_].gamma)));
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);
MaxScoresRadius.push_back(R);
MaxScoresRadius.push_back(maxScore);
}
for (set <pair<double, ScoreConfiguration> >::iterator itr = bestScores.begin(); itr != bestScores.end(); ++itr)
{
scores.push_back(*itr);
}
delete transTmp;
}
//
// translate
//
void camera::translate(math3d::vector const& v)
{
/* matrix tmp;
tmp[math3d::matrix::da] = v[math3d::vector::x];
tmp[math3d::matrix::db] = v[math3d::vector::y];
tmp[math3d::matrix::dc] = v[math3d::vector::z];
*/
worldMatrix_ *= translationmatrix(v);
worldMatrixInvers_ = inverse(worldMatrix_);
}
void Docking::dockingSearch(vector <pair<double, ScoreConfiguration> >& scores)
{
int raSize = 20*(1<<(tessellationOrder_*2));
set <pair<double, ScoreConfiguration> > bestScores;
preDockingCalculateRotations();
Protein *transTmp = new Protein;
scores.clear();
for (double R = radiusStart_; R < radiusEnd_; R += 0.5)
{
double minScore = 10000000.0, maxScore = -10000000.0;
printf("R: %lf\n", R);
char buffer[100];
sprintf(buffer, "%s/%d/%.6lf.dat", translationPath_.c_str(), receptor_.getOrder(), R);
TranslationMatrix translationmatrix(buffer);
for (int i = 0; i < raSize; ++i)
{
rotReceptor_[i].translateTo(*transTmp, translationmatrix);
for (int j = 0; j < raSize*alphaSize_; ++j)
{
double tmpScore = scoreIt(*transTmp, rotLigand_[j], penalty_);
bestScores.insert(make_pair(tmpScore,ScoreConfiguration(R,(j%alphaSize_)*(2.0*PI/alphaSize_),rotationAngles_[i].beta,rotationAngles_[i].gamma,rotationAngles_[j/alphaSize_].beta, rotationAngles_[j/alphaSize_].gamma)));
minScore = min(minScore, tmpScore);
maxScore = max(maxScore, tmpScore);
}
while ((int)bestScores.size() > scoresSize_)
{
bestScores.erase(bestScores.begin());
}
}
printf("For this R: min score is %lf; max score is %lf\n", minScore, maxScore);
printf("OK\n");
}
for (set <pair<double, ScoreConfiguration> >::iterator itr = bestScores.begin(); itr != bestScores.end(); ++itr)
{
scores.push_back(*itr);
}
freeMemory();
delete transTmp;
}
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);
}
void Docking::dockingQsearch(vector <pair<double, ScoreConfiguration> >& scores, vector<double> RadiusSet, vector<double>& MaxScoresRadius)
{
int raSize = 20*(1<<(tessellationOrder_*2))+1;
set <pair<double, ScoreConfiguration> > bestScores;
preDockingCalculateQRotations();
//precalculation of all rotations
trigonometricCash();
calculateCoeffMapping( );
Protein *transReceptor = new Protein;
//printf("Starting docking search...\n");
//scores.clear();
vector<double> qCoeffPlusPlus, qCoeffMinusMinus;
int order = receptor_.getOrder();
qCoeffPlusPlus.resize(order, 0.0);
qCoeffMinusMinus.resize(order, 0.0);
vector<double> qCoeffPlus;
qCoeffPlus.resize((2* order - 1), 0.0);
vector<double> qCoeffMinus;
qCoeffMinus.resize((2* order - 1), 0.0);
int timeFlag = 0;
//vector<int> translationIndexes;
//receptor_.calculateTranslationIndexes( translationIndexes );
for (unsigned int radiusIndex = 0; radiusIndex < RadiusSet.size(); ++radiusIndex)
{
double R = RadiusSet[radiusIndex];
double minScore = 10000000.0, maxScore = -10000000.0;
char buffer[100];
sprintf(buffer, "%s/%d/%.6lf.dat", translationPath_.c_str(), receptor_.getOrder(), R);
TranslationMatrix translationmatrix(buffer);
for (int i = 0; i < raSize; ++i)
{
/*clock_t start,end;
start = clock ();*/
//rotReceptor_[i].translateTo(*transReceptor, translationmatrix, translationIndexes);
rotReceptor_[i].translateTo(*transReceptor, translationmatrix);
/*end = clock ();
if (timeFlag == 0) printf("Finished translation in about %d ms. \n",(end-start));
start = clock ();*/
for (int j = 0; j < raSize; ++j)
{
/*calculateQcoeffPlusPlus(qCoeffPlusPlus,qCoeffPlus, *transReceptor, qRotLigand_[j] );
calculateQcoeffMinusMinus(qCoeffMinusMinus,qCoeffMinus, *transReceptor, qRotLigand_[j] );*/
calculateQcoeffs(qCoeffPlusPlus, qCoeffPlus, qCoeffMinusMinus, qCoeffMinus,*transReceptor, qRotLigand_[j]);
double maxScoreAlfa = - 100000.0;
double maxAlfa = 0.0;
for (int k = 0; k < alphaSize_; ++k)
{
int index_alfa = k*order;
double tmpScore = qCoeffPlusPlus[0];
for (int m = 1; m <= (order-1); ++m)
{
tmpScore += (qCoeffPlusPlus[m] * cosValue_->at(index_alfa+m) ) + (qCoeffMinusMinus[m] * sinValue_->at(index_alfa+m) );
}
if (tmpScore > maxScoreAlfa){
maxScoreAlfa = tmpScore;
maxAlfa = k*(2.0*PI/alphaSize_);
}
if ( (i+1 == raSize)&&(j+1==raSize)&& (k==0) ){
printf("R:%lf ,b1:%lf, g1:%lf, a2:%lf, b2:%lf, g2:%lf score:%lf \n",R, k*(2.0*PI/alphaSize_),rotationAngles_[i].beta,rotationAngles_[i].gamma,rotationAngles_[j].beta, rotationAngles_[j].gamma,tmpScore);
}
minScore = min(minScore, tmpScore);
maxScore = max(maxScore, tmpScore);
}
bestScores.insert(make_pair( maxScoreAlfa,ScoreConfiguration(R, maxAlfa ,rotationAngles_[i].beta, rotationAngles_[i].gamma, rotationAngles_[j].beta, rotationAngles_[j].gamma )));
}
while ((int)bestScores.size() > scoresSize_)
{
bestScores.erase(bestScores.begin());
}
/*end = clock ();
if (timeFlag == 0){
printf("Finished rotation in about %d ms. \n", (end-start)/100);
timeFlag = 1;
}*/
}
printf("For R:%lf min score is %E; max score is %E\n",R, minScore, maxScore);
MaxScoresRadius.push_back(R);
MaxScoresRadius.push_back(maxScore);
}
for (set <pair<double, ScoreConfiguration> >::iterator itr = bestScores.begin(); itr != bestScores.end(); ++itr)
{
scores.push_back(*itr);
}
delete transReceptor;
}
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;
}
