Commit c553b9e1 authored by Vedran Miletić's avatar Vedran Miletić

Remove, comment out, or use unused variables

parent 442426b4
......@@ -181,6 +181,10 @@ double OccupancyTest::CompareScoresForDisabledAndNoSolvent() {
}
m_workSpace->SetSolvent(m_solventList);
double scoreEnabledSolvent = pSF->Score();
std::cout << "Score no solvent = " << scoreNoSolvent << std::endl;
std::cout << "Score enabled solvent = " << scoreEnabledSolvent << std::endl;
std::cout << "Score disabled solvent = " << scoreDisabledSolvent
<< std::endl;
retVal = fabs(scoreNoSolvent - scoreDisabledSolvent);
}
return retVal;
......
......@@ -22,7 +22,6 @@ std::string RbtGPChromosome::_CT("RbtGPChromosome");
RbtGPChromosome::RbtGPChromosome(int npi, int nfi, int nn, int no, int nr,
int nc) {
chrom = RbtIntList(nn * (nfi + 1) + no);
int i = 0, n;
nProgramInputs = npi;
nFunctionsInputs = nfi;
int ncells = nn + npi; // number of nodes + inputs
......
......@@ -85,7 +85,6 @@ double RbtGPFFCHK1::CalculateFitness(RbtGPGenomePtr g, RbtReturnTypeArray &it,
double hitlimit = 0.0;
for (unsigned int i = 0; i < it.size(); i++) {
RbtReturnTypeList inputs(it[i]);
RbtReturnType pred;
for (unsigned int j = 0; j < inputs.size(); j++)
contextp->Assign(j, *(inputs[j]));
RbtReturnTypeList SFValues = sft[i];
......@@ -134,7 +133,6 @@ double RbtGPFFCHK1::CalculateFitness(RbtGPGenomePtr g, RbtReturnTypeArray &it,
double actualOutput, predictedOutput;
for (unsigned int i = 0; i < it.size(); i++) {
RbtReturnTypeList inputs(it[i]);
RbtReturnType pred;
for (unsigned int j = 0; j < inputs.size(); j++)
contextp->Assign(j, *(inputs[j]));
RbtReturnTypeList SFValues = sft[i];
......
......@@ -56,7 +56,7 @@ double RbtGPFFGold::CalculateFitness(RbtGPGenomePtr g, RbtReturnTypeArray &it,
RbtGPGenome::GetNN(), RbtGPGenome::GetNO());
RbtReturnTypeList o;
double tot = 0.0;
double range = 10.0;
// double range = 10.0;
double good = 0.0;
double bad = 0.0;
double hitlimit = 2.0;
......
......@@ -83,15 +83,11 @@ double RbtGPFFHSP90::CalculateFitness(
bool function) {
RbtReturnTypeArray o;
// o.push_back(new RbtReturnType(1.1));
RbtReturnType oldo;
double tot = 0.0;
double good = 0.0;
double bad = 0.0;
RbtGPChromosomePtr c(g->GetChrom());
RbtParser p2;
RbtCellTokenIterPtr ti(new RbtCellTokenIter(c, contextp));
RbtFilterExpressionPtr fe(p2.Parse(ti, contextp));
double meanReal = 0.0, meanPred = 0.0;
// double meanReal = 0.0, meanPred = 0.0;
for (unsigned int i = 0; i < it.size(); i++) {
RbtReturnTypeList inputs(it[i]);
RbtReturnTypeList pred;
......@@ -99,7 +95,6 @@ double RbtGPFFHSP90::CalculateFitness(
for (unsigned int j = 0; j < inputs.size(); j++)
contextp->Assign(j, *(inputs[j]));
RbtReturnTypeList SFValues = sft[i];
double hit = *(SFValues[SFValues.size() - 1]);
EvaluateVisitor visitor(contextp);
fe->Accept(visitor);
pred.push_back(new RbtReturnType(fe->GetValue()));
......@@ -139,10 +134,6 @@ double RbtGPFFHSP90::CalculateFitness(RbtGPGenomePtr g, RbtReturnTypeArray &it,
RbtReturnTypeArray &sft, double limit,
bool function) {
RbtReturnTypeArray o;
RbtReturnType oldo;
double tot = 0.0;
double good = 0.0;
double bad = 0.0;
RbtGPChromosomePtr c(g->GetChrom());
RbtParser p2;
RbtCellTokenIterPtr ti(new RbtCellTokenIter(c, contextp));
......@@ -155,7 +146,6 @@ double RbtGPFFHSP90::CalculateFitness(RbtGPGenomePtr g, RbtReturnTypeArray &it,
for (unsigned int j = 0; j < inputs.size(); j++)
contextp->Assign(j, *(inputs[j]));
RbtReturnTypeList SFValues = sft[i];
double hit = *(SFValues[SFValues.size() - 1]);
EvaluateVisitor visitor(contextp);
fe->Accept(visitor);
pred.push_back(new RbtReturnType(fe->GetValue()));
......
......@@ -78,8 +78,6 @@ double RbtGPFFSpike::CalculateFitness(RbtGPGenomePtr g, RbtReturnTypeArray &it,
// RbtGPGenome::GetNN(), RbtGPGenome::GetNO());
RbtReturnTypeList o;
o.push_back(new RbtReturnType(1.1));
RbtReturnType oldo;
double tot = 0.0;
double good = 0.0;
double bad = 0.0;
double hitlimit = 0.0;
......@@ -131,7 +129,7 @@ double RbtGPFFSpike::CalculateFitness(RbtGPGenomePtr g, RbtReturnTypeArray &it,
// RbtGPParser p(g->GetNIP(), g->GetNIF(), g->GetNN(), g->GetNO());
RbtReturnTypeList o;
o.push_back(new RbtReturnType(1.1));
RbtReturnType oldo;
// RbtReturnType oldo;
double truehits = 0.0;
double falsehits = 0.0;
double truemisses = 0.0;
......
......@@ -93,7 +93,6 @@ void RbtGPGenome::SetStructure(int inpi, int infi, int insfi, int ino, int inf,
}
void RbtGPGenome::Initialise() {
int s = chrom->size();
int g = 0, max, min;
for (int i = 0; i < nc; i++) {
for (int j = 0; j < nr; j++) {
......@@ -188,7 +187,6 @@ void RbtGPGenome::UniformCrossover(const RbtGPGenome &mom,
void RbtGPGenome::Crossover(RbtGPGenome &) {}
std::ostream &RbtGPGenome::Print(std::ostream &s) const {
int g = 0;
// Print structure
s << npi << " " << nfi << " " << nsfi << " " << no << " " << nf << " " << nr
<< " " << nc << " " << l << std::endl;
......
......@@ -267,7 +267,6 @@ int main(int argc, char *argv[]) {
int nAtoms = spModel->GetNumAtoms();
int nBonds = spModel->GetNumBonds();
int nSegs = spModel->GetNumSegments();
RbtAtomList atomList = spModel->GetAtomList();
RbtBondList bondList = spModel->GetBondList();
......
......@@ -245,7 +245,6 @@ int main(int argc, char *argv[]) {
// std::cout << "Constructing grid of size " << nX << " x " << nY << " x "
// << nZ << std::endl;
RbtRealGridPtr spGrid(new RbtRealGrid(minCoord, gridStep, nX, nY, nZ));
float *gridData = spGrid->GetGridData();
// Create probes
RbtModelList probes = CreateProbes(strAtomType);
......@@ -253,7 +252,6 @@ int main(int argc, char *argv[]) {
// write the grid into a MOE grid file
std::cout << "==================================" << std::endl;
std::cout << "Generating MOE grid " << std::endl;
int dim = 3; // its a 3D grid
// grid extents are in minCoord and maxCoord
vector<double> grid_origin;
grid_origin.push_back(minCoord.x);
......
......@@ -100,7 +100,6 @@ void EnumerateSymCoords::Setup() {
std::not1(Rbt::isAtomicNo_eq(1)));
m_symBondList.clear();
RbtBondList bondList = m_spModel->GetBondList();
int nBonds = bondList.size();
RbtStringList symBonds = m_spModel->GetDataValue("SYMMETRIC_BONDS");
for (RbtStringListConstIter iter = symBonds.begin(); iter != symBonds.end();
iter++) {
......@@ -314,7 +313,7 @@ int main(int argc, char *argv[]) {
// (*rIter) << std::endl;
}
zMean /= zTot;
double zVar = zMean2 / zTot - (zMean * zMean);
// double zVar = zMean2 / zTot - (zMean * zMean);
// std::cout << "zRMSD," << zTot << "," << zMean << "," << std::sqrt(zVar)
// << std::endl;
} catch (RbtError &e) {
......
......@@ -107,8 +107,6 @@ double RbtStringContext::Get(RbtModelPtr lig, std::string name) {
if (name == "LIG_NATOMS")
return lig->GetNumAtoms();
int nAtoms = lig->GetNumAtoms();
int nBonds = lig->GetNumBonds();
int nSegs = lig->GetNumSegments();
RbtAtomList atomList = lig->GetAtomList();
RbtBondList bondList = lig->GetBondList();
if (name == "LIG_NLIPOC")
......
......@@ -94,7 +94,6 @@ void RbtSAIdxSF::SetupReceptor() {
// Use a larger increment
for (HHS_SolvationRListConstIter iter = theFlexList.begin();
iter != theFlexList.end(); iter++) {
RbtAtom *pAtom = (*iter)->GetAtom();
theIdxGrid->SetHHSLists(*iter, (*iter)->GetR_i() + flexIncr);
}
}
......@@ -152,7 +151,6 @@ void RbtSAIdxSF::SetupReceptor() {
// Index the rigid interaction centers within range of the docking site
for (HHS_SolvationRListConstIter iter = theCavList.begin();
iter != theCavList.end(); iter++) {
RbtAtom *pAtom = (*iter)->GetAtom();
theIdxGrid->SetHHSLists(*iter, (*iter)->GetR_i() + idxIncr);
}
......@@ -549,6 +547,12 @@ void RbtSAIdxSF::ScoreMap(RbtStringVariantMap &scoreMap) const {
// First we need to force the calculation of all the raw score components
EnableAnnotations(true);
double rs = RawScore();
int iTrace = GetTrace();
if (iTrace > 1) {
std::cout << std::endl << _CT << "::ScoreMap()" << std::endl;
std::cout << _CT << ": Maximum radius of any atom type =" << rs
<< std::endl;
}
EnableAnnotations(false);
std::string name = GetFullName();
......
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