double pickRandomDistMat(const BoundsMatrix &mmat,
RDNumeric::SymmMatrix<double> &distMat,
RDKit::double_source_type &rng) {
// make sure the sizes match up
unsigned int npt = mmat.numRows();
CHECK_INVARIANT(npt == distMat.numRows(), "Size mismatch");
double largestVal = -1.0;
double *ddata = distMat.getData();
for (unsigned int i = 1; i < npt; i++) {
unsigned int id = i * (i + 1) / 2;
for (unsigned int j = 0; j < i; j++) {
double ub = mmat.getUpperBound(i, j);
double lb = mmat.getLowerBound(i, j);
CHECK_INVARIANT(ub >= lb, "");
double rval = rng();
// std::cerr<<i<<"-"<<j<<": "<<rval<<std::endl;
double d = lb + (rval) * (ub - lb);
ddata[id + j] = d;
if (d > largestVal) {
largestVal = d;
}
}
}
return largestVal;
}
double pickRandomDistMat(const BoundsMatrix &mmat,
RDNumeric::SymmMatrix<double> &distMat,
int seed) {
// make sure the sizes match up
unsigned int npt = mmat.numRows();
CHECK_INVARIANT(npt == distMat.numRows(), "Size mismatch");
RDKit::rng_type &generator = RDKit::getRandomGenerator();
if (seed > 0) {
generator.seed(seed);
}
double largestVal=-1.0;
double *ddata = distMat.getData();
for (unsigned int i = 1; i < npt; i++) {
unsigned int id = i*(i+1)/2;
for (unsigned int j = 0; j < i; j++) {
double ub = mmat.getUpperBound(i,j);
double lb = mmat.getLowerBound(i,j);
CHECK_INVARIANT(ub >= lb, "");
double rval = RDKit::getRandomVal();
double d = lb + (rval)*(ub - lb);
ddata[id+j] = d;
if(d>largestVal){
largestVal=d;
}
}
}
return largestVal;
}
void readFromFile(const std::ifstream& input_file) {
std::vector<std::string> lines;
std::string line;
while(!input_file.eof()) {
std::getline(input_file, line);
lines.push_back(line);
}
matrix.setDimensions(line.length(), lines.size());
for (int i = 0; i < lines.size(); i++) {
line = lines.at(i);
for (int j = 0; j < line.length(); j++) {
short value = (line.at(j) == 'o' ? 1 : 0);
matrix.set(j, i, value);
}
}
}
void test1() {
// test triangle smoothing
unsigned int npt = 5;
double x = sqrt(3.0);
BoundsMatrix *mmat = new BoundsMatrix(npt);
mmat->setUpperBound(0, 1, 1.0);
mmat->setLowerBound(0, 1, 1.0);
mmat->setUpperBound(0, 2, x);
mmat->setLowerBound(0, 2, x);
mmat->setUpperBound(0, 3, 10.0);
mmat->setLowerBound(0, 3, 0.0);
mmat->setUpperBound(0, 4, 10.0);
mmat->setLowerBound(0, 4, 0.0);
mmat->setUpperBound(1, 2, 1.0);
mmat->setLowerBound(1, 2, 1.0);
mmat->setUpperBound(1, 3, x);
mmat->setLowerBound(1, 3, x);
mmat->setUpperBound(1, 4, 10.0);
mmat->setLowerBound(1, 4, 0.0);
mmat->setUpperBound(2, 3, 1.0);
mmat->setLowerBound(2, 3, 1.0);
mmat->setUpperBound(2, 4, x);
mmat->setLowerBound(2, 4, x);
mmat->setUpperBound(3, 4, 1.0);
mmat->setLowerBound(3, 4, 1.0);
BoundsMatPtr mptr(mmat);
triangleSmoothBounds(mptr);
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(0, 1), 1.0, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(0, 1), 1.0, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(0, 2), 1.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(0, 2), 1.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(0, 3), 2.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(0, 3), 0.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(0, 4), 3.464, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(0, 4), 0.0, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(1, 2), 1.0, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(1, 2), 1.0, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(1, 3), 1.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(1, 3), 1.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(1, 4), 2.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(1, 4), 0.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(2, 3), 1.0, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(2, 3), 1.0, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(2, 4), 1.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(2, 4), 1.732, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getUpperBound(3, 4), 1.0, 0.001), "");
CHECK_INVARIANT(RDKit::feq(mmat->getLowerBound(3, 4), 1.0, 0.001), "");
DoubleSymmMatrix dmat(npt, 0.0);
RDKit::rng_type generator(42u);
generator.seed(100);
RDKit::uniform_double distrib(0, 1.0);
RDKit::double_source_type rng(generator, distrib);
pickRandomDistMat(*mmat, dmat, rng);
double sumElem = 0.0;
for (unsigned int i = 0; i < dmat.getDataSize(); i++) {
sumElem += dmat.getData()[i];
}
CHECK_INVARIANT(RDKit::feq(sumElem, 14.3079, 0.001), "");
}
unsigned int dimy() {
return matrix.dimy();
}
void markLand(unsigned int x, unsigned int y) {
matrix.set(x, y, 100);
}