//! Convert a SparseBitVector to an ExplicitBitVector
ExplicitBitVect *convertToExplicit(const SparseBitVect *sbv) {
unsigned int sl = sbv->getNumBits();
ExplicitBitVect *ebv = new ExplicitBitVect(sl);
const IntSet *bset = sbv->getBitSet();
for (IntSetConstIter it = bset->begin(); it != bset->end(); it++) {
ebv->setBit(*it);
}
return ebv;
}
void InfoBitRanker::accumulateVotes(const ExplicitBitVect &bv, unsigned int label) {
RANGE_CHECK(0, label, d_classes-1);
CHECK_INVARIANT(bv.getNumBits() == d_dims, "Incorrect bit vector size");
d_nInst += 1;
d_clsCount[label] += 1;
for (unsigned int i=0;i<bv.getNumBits();i++){
if( (*bv.dp_bits)[i] && (!dp_maskBits || dp_maskBits->getBit(i)) ){
d_counts[label][i] += 1;
}
}
}
static python::tuple
getinitargs(const ExplicitBitVect& self)
{
std::string res=self.toString();
python::object retval = python::object(python::handle<>(PyBytes_FromStringAndSize(res.c_str(),res.length())));
return python::make_tuple(retval);
};
//' map a molecule to a maccs fingerprints
//'
//' @param xp a molecule
//' @return a vector
// [[Rcpp::export]]
IntegerVector mol2maccs( SEXP xp){
int i;
RWMol *mol = p_getMol(xp);
if( mol ){
ExplicitBitVect *bv = MACCSFingerprints::getFingerprintAsBitVect ( *mol );
if(bv){
IntegerVector v = IntegerVector( bv->getNumBits ());
for( i = 0; i< bv->getNumBits ();i++ ){
v(i) = bv->getBit(i)?1:0;
}
return v;
}
}
return IntegerVector(0);
}
void testMols(std::vector<std::unique_ptr<ROMol>> &mols, FragFPGenerator &fpGen,
FragCatalog &fcat) {
int nDone = 0;
for (auto &&mi : mols) {
ExplicitBitVect *fp = fpGen.getFPForMol(*mi, fcat);
switch (nDone) {
case 0:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[2]);
break;
case 1:
TEST_ASSERT(fp->getNumOnBits() == 2);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[3]);
break;
case 2:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[4]);
TEST_ASSERT((*fp)[5]);
break;
case 3:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[6]);
TEST_ASSERT((*fp)[7]);
break;
case 4:
TEST_ASSERT(fp->getNumOnBits() == 2);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[8]);
break;
case 5:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[6]);
TEST_ASSERT((*fp)[9]);
break;
case 6:
TEST_ASSERT(fp->getNumOnBits() == 5);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[2]);
TEST_ASSERT((*fp)[3]);
TEST_ASSERT((*fp)[10]);
break;
}
delete fp;
nDone += 1;
}
}
void testMols(std::vector<ROMol *> &mols, FragFPGenerator &fpGen,
FragCatalog &fcat) {
std::vector<ROMol *>::iterator mi;
int nDone = 0;
for (mi = mols.begin(); mi != mols.end(); mi++) {
ExplicitBitVect *fp = fpGen.getFPForMol(*(*mi), fcat);
switch (nDone) {
case 0:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[2]);
break;
case 1:
TEST_ASSERT(fp->getNumOnBits() == 2);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[3]);
break;
case 2:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[4]);
TEST_ASSERT((*fp)[5]);
break;
case 3:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[6]);
TEST_ASSERT((*fp)[7]);
break;
case 4:
TEST_ASSERT(fp->getNumOnBits() == 2);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[8]);
break;
case 5:
TEST_ASSERT(fp->getNumOnBits() == 3);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[6]);
TEST_ASSERT((*fp)[9]);
break;
case 6:
TEST_ASSERT(fp->getNumOnBits() == 5);
TEST_ASSERT((*fp)[0]);
TEST_ASSERT((*fp)[1]);
TEST_ASSERT((*fp)[2]);
TEST_ASSERT((*fp)[3]);
TEST_ASSERT((*fp)[10]);
break;
}
nDone += 1;
}
}
//' map a molecule to a morgan fingerprints (atom environement)
//'
//' @param xp a molecule
//' @param radius radius of scaffold
//' @param nBits final length
//' @param useFeatures useFeatures
//' @return a vector
// [[Rcpp::export]]
IntegerVector mol2morgan( SEXP xp , unsigned int radius=2,unsigned int nBits=2048,
bool useFeatures=false){
// radius = 2 => ecfp4 2^2
// radius = 2 & useFeatures=True => fcfp4
int i;
RWMol *mol = p_getMol(xp);
if( mol ){
ExplicitBitVect *bv = MorganFingerprints::getFingerprintAsBitVect ( *mol , radius,nBits,
0,0,false,useFeatures,false,0);
if(bv){
IntegerVector v = IntegerVector( bv->getNumBits ());
for( i = 0; i< bv->getNumBits ();i++ ){
v(i) = bv->getBit(i)?1:0;
}
delete bv;
return v;
}
}
return IntegerVector(0);
}
void reaccsToFingerprint(struct reaccs_molecule_t *molPtr, ExplicitBitVect &res,
unsigned int bitFlags = 32767U, bool isQuery = false,
bool resetVect = true, unsigned int nBytes = 64) {
PRECONDITION(molPtr, "bad molecule");
PRECONDITION(res.getNumBits() >= nBytes * 8U, "res too small");
if (resetVect) res.clearBits();
char *fingerprint = getFp(molPtr, bitFlags, isQuery, nBytes);
for (unsigned int i = 0; i < nBytes; ++i) {
char byte = fingerprint[i];
if (byte) {
char mask = 1;
for (int j = 0; j < 8; ++j) {
if (byte & mask) {
res.setBit(i * 8 + j);
}
mask = mask << 1;
}
}
}
MyFree(fingerprint);
};
int NumBitsInCommon(const ExplicitBitVect& bv1, const ExplicitBitVect& bv2) {
return bv1.getNumBits() - ((*bv1.dp_bits) ^ (*bv2.dp_bits)).count();
}
static python::tuple
getinitargs(const ExplicitBitVect& self)
{
return python::make_tuple(self.toString());
};
// caller owns the result, it must be deleted
ExplicitBitVect *PatternFingerprintMol(const ROMol &mol, unsigned int fpSize,
std::vector<unsigned int> *atomCounts,
ExplicitBitVect *setOnlyBits) {
PRECONDITION(fpSize != 0, "fpSize==0");
PRECONDITION(!atomCounts || atomCounts->size() >= mol.getNumAtoms(),
"bad atomCounts size");
PRECONDITION(!setOnlyBits || setOnlyBits->getNumBits() == fpSize,
"bad setOnlyBits size");
std::vector<const ROMol *> patts;
patts.reserve(10);
unsigned int idx = 0;
while (1) {
std::string pq = pqs[idx];
if (pq == "") break;
++idx;
const ROMol *matcher = pattern_flyweight(pq).get().getMatcher();
CHECK_INVARIANT(matcher, "bad smarts");
patts.push_back(matcher);
}
if (!mol.getRingInfo()->isInitialized()) {
MolOps::fastFindRings(mol);
}
boost::dynamic_bitset<> isQueryAtom(mol.getNumAtoms()),
isQueryBond(mol.getNumBonds());
ROMol::VERTEX_ITER firstA, lastA;
boost::tie(firstA, lastA) = mol.getVertices();
while (firstA != lastA) {
const Atom *at = mol[*firstA].get();
if (isComplexQuery(at)) {
isQueryAtom.set(at->getIdx());
// std::cerr<<" complex atom: "<<at->getIdx()<<std::endl;
}
++firstA;
}
ROMol::EDGE_ITER firstB, lastB;
boost::tie(firstB, lastB) = mol.getEdges();
while (firstB != lastB) {
const Bond *bond = mol[*firstB].get();
// if( isComplexQuery(bond) ){
if (isPatternComplexQuery(bond)) {
isQueryBond.set(bond->getIdx());
// std::cerr<<" complex bond: "<<bond->getIdx()<<std::endl;
}
++firstB;
}
ExplicitBitVect *res = new ExplicitBitVect(fpSize);
unsigned int pIdx = 0;
BOOST_FOREACH (const ROMol *patt, patts) {
++pIdx;
std::vector<MatchVectType> matches;
// uniquify matches?
// time for 10K molecules w/ uniquify: 5.24s
// time for 10K molecules w/o uniquify: 4.87s
SubstructMatch(mol, *patt, matches, false);
boost::uint32_t mIdx = pIdx + patt->getNumAtoms() + patt->getNumBonds();
BOOST_FOREACH (MatchVectType &mv, matches) {
#ifdef VERBOSE_FINGERPRINTING
std::cerr << "\nPatt: " << pIdx << " | ";
#endif
// collect bits counting the number of occurances of the pattern:
gboost::hash_combine(mIdx, 0xBEEF);
res->setBit(mIdx % fpSize);
#ifdef VERBOSE_FINGERPRINTING
std::cerr << "count: " << mIdx % fpSize << " | ";
#endif
bool isQuery = false;
boost::uint32_t bitId = pIdx;
std::vector<unsigned int> amap(mv.size(), 0);
BOOST_FOREACH (MatchVectType::value_type &p, mv) {
#ifdef VERBOSE_FINGERPRINTING
std::cerr << p.second << " ";
#endif
if (isQueryAtom[p.second]) {
isQuery = true;
#ifdef VERBOSE_FINGERPRINTING
std::cerr << "atom query.";
#endif
break;
}
gboost::hash_combine(bitId,
mol.getAtomWithIdx(p.second)->getAtomicNum());
amap[p.first] = p.second;
}
