// ------------------------------------------------------------------------
//
// the two-bit matrix returned by this contains:
// 0: if atoms i and j are directly connected
// 1: if atoms i and j are connected via an atom
// 2: if atoms i and j are in a 1,4 relationship
// 3: otherwise
//
// NOTE: the caller is responsible for calling delete []
// on the result
//
// ------------------------------------------------------------------------
boost::shared_array<boost::uint8_t> buildNeighborMatrix(const ROMol &mol) {
const boost::uint8_t RELATION_1_X_INIT = RELATION_1_X
| (RELATION_1_X << 2) | (RELATION_1_X << 4) | (RELATION_1_X << 6);
unsigned int nAtoms = mol.getNumAtoms();
unsigned nTwoBitCells = (nAtoms * (nAtoms + 1) - 1) / 8 + 1;
boost::shared_array<boost::uint8_t> res(new boost::uint8_t[nTwoBitCells]);
std::memset(res.get(), RELATION_1_X_INIT, nTwoBitCells);
for (ROMol::ConstBondIterator bondi = mol.beginBonds(); bondi != mol.endBonds(); ++bondi) {
setTwoBitCell(res, twoBitCellPos(nAtoms, (*bondi)->getBeginAtomIdx(),
(*bondi)->getEndAtomIdx()), RELATION_1_2);
unsigned int bondiBeginAtomIdx = (*bondi)->getBeginAtomIdx();
unsigned int bondiEndAtomIdx = (*bondi)->getEndAtomIdx();
for (ROMol::ConstBondIterator bondj = bondi; ++bondj != mol.endBonds();) {
int idx1 = -1;
int idx3 = -1;
unsigned int bondjBeginAtomIdx = (*bondj)->getBeginAtomIdx();
unsigned int bondjEndAtomIdx = (*bondj)->getEndAtomIdx();
if (bondiBeginAtomIdx == bondjBeginAtomIdx) {
idx1 = bondiEndAtomIdx;
idx3 = bondjEndAtomIdx;
} else if (bondiBeginAtomIdx == bondjEndAtomIdx) {
idx1 = bondiEndAtomIdx;
idx3 = bondjBeginAtomIdx;
} else if (bondiEndAtomIdx == bondjBeginAtomIdx) {
idx1 = bondiBeginAtomIdx;
idx3 = bondjEndAtomIdx;
} else if (bondiEndAtomIdx == bondjEndAtomIdx) {
idx1 = bondiBeginAtomIdx;
idx3 = bondjBeginAtomIdx;
}
if (idx1 > -1) {
setTwoBitCell(res, twoBitCellPos(nAtoms, idx1, idx3), RELATION_1_3);
}
}
}
return res;
}
// ------------------------------------------------------------------------
//
// the two-bit matrix returned by this contains:
// 0: if atoms i and j are directly connected
// 1: if atoms i and j are connected via an atom
// 3: otherwise
//
// NOTE: the caller is responsible for calling delete []
// on the result
//
// ------------------------------------------------------------------------
boost::shared_array<boost::uint8_t> buildNeighborMatrix(const ROMol &mol)
{
unsigned int nAtoms = mol.getNumAtoms();
unsigned nTwoBitCells = (nAtoms * nAtoms - 1) / 4 + 1;
boost::shared_array<boost::uint8_t> res(new boost::uint8_t[nTwoBitCells]);
for (unsigned int i = 0; i < nTwoBitCells; ++i) {
res[i] = 0;
}
for (unsigned int i = 0; i < nAtoms; ++i) {
unsigned int iTab = i * nAtoms;
for (unsigned int j = i; j < nAtoms; ++j) {
setTwoBitCell(res, iTab + j, RELATION_1_X);
setTwoBitCell(res, i + j * nAtoms, RELATION_1_X);
}
}
for (unsigned int i = 0; i < mol.getNumBonds(); ++i) {
const Bond *bondi = mol.getBondWithIdx(i);
setTwoBitCell(res, bondi->getBeginAtomIdx() * nAtoms + bondi->getEndAtomIdx(), RELATION_1_2);
setTwoBitCell(res, bondi->getEndAtomIdx() * nAtoms + bondi->getBeginAtomIdx(), RELATION_1_2);
for (unsigned int j = i + 1; j < mol.getNumBonds(); ++j) {
const Bond *bondj = mol.getBondWithIdx(j);
int idx1 = -1;
int idx3 = -1;
if (bondi->getBeginAtomIdx() == bondj->getBeginAtomIdx()) {
idx1 = bondi->getEndAtomIdx();
idx3 = bondj->getEndAtomIdx();
}
else if (bondi->getBeginAtomIdx() == bondj->getEndAtomIdx()) {
idx1 = bondi->getEndAtomIdx();
idx3 = bondj->getBeginAtomIdx();
}
else if (bondi->getEndAtomIdx() == bondj->getBeginAtomIdx()) {
idx1 = bondi->getBeginAtomIdx();
idx3 = bondj->getEndAtomIdx();
}
else if (bondi->getEndAtomIdx() == bondj->getEndAtomIdx()) {
idx1 = bondi->getBeginAtomIdx();
idx3 = bondj->getBeginAtomIdx();
}
if (idx1 > -1) {
setTwoBitCell(res, idx1 * nAtoms + idx3, RELATION_1_3);
setTwoBitCell(res, idx3 * nAtoms + idx1, RELATION_1_3);
}
}
}
return res;
}