void fingerprint2::getFragments(vector<int> levels, vector<int> curfrag,
int level, OBAtom* patom, OBBond* pbond)
{
//Recursive routine to analyse schemical structure and populate fragset and ringset
//Hydrogens,charges(except dative bonds), spinMultiplicity ignored
const int Max_Fragment_Size = 7;
int bo=0;
if(pbond)
{
bo = pbond->IsAromatic() ? 5 : pbond->GetBO();
// OBAtom* pprevat = pbond->GetNbrAtom(patom);
// if(patom->GetFormalCharge() && (patom->GetFormalCharge() == -pprevat->GetFormalCharge()))
// ++bo; //coordinate (dative) bond eg C[N+]([O-])=O is seen as CN(=O)=O
}
curfrag.push_back(bo);
curfrag.push_back(patom->GetAtomicNum());
levels[patom->GetIdx()-1] = level;
vector<OBEdgeBase*>::iterator itr;
OBBond *pnewbond;
// PrintFpt(curfrag,(int)patom);
for (pnewbond = patom->BeginBond(itr);pnewbond;pnewbond = patom->NextBond(itr))
{
if(pnewbond==pbond) continue; //don't retrace steps
OBAtom* pnxtat = pnewbond->GetNbrAtom(patom);
if(pnxtat->IsHydrogen()) continue;
int atlevel = levels[pnxtat->GetIdx()-1];
if(atlevel) //ring
{
if(atlevel==1)
{
//If complete ring (last bond is back to starting atom) add bond at front
//and save in ringset
curfrag[0] = bo;
ringset.insert(curfrag);
}
}
else //no ring
{
if(level<Max_Fragment_Size)
{
// TRACE("level=%d size=%d %p frag[0]=%p\n",level, curfrag.size(),&curfrag, &(curfrag[0]));
//Do the next atom; levels, curfrag are passed by value and hence copied
getFragments(levels, curfrag, level+1, pnxtat, pnewbond);
}
}
}
//do not save C,N,O single atom fragments
if(curfrag[0]==0 &&
(level>1 || patom->GetAtomicNum()>8 || patom->GetAtomicNum()<6))
{
fragset.insert(curfrag); //curfrag ignored if an identical fragment already present
// PrintFpt(curfrag,level);
}
}
bool fingerprint2::GetFingerprint(OBBase* pOb, vector<unsigned int>&fp, int nbits)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol) return false;
fp.resize(1024/Getbitsperint());
fragset.clear();//needed because now only one instance of fp class
ringset.clear();
//identify fragments starting at every atom
OBAtom *patom;
vector<OBNodeBase*>::iterator i;
for (patom = pmol->BeginAtom(i);patom;patom = pmol->NextAtom(i))
{
if(patom->IsHydrogen()) continue;
vector<int> curfrag;
vector<int> levels(pmol->NumAtoms());
getFragments(levels, curfrag, 1, patom, NULL);
}
// TRACE("%s %d frags before; ",pmol->GetTitle(),fragset.size());
//Ensure that each chemically identical fragment is present only in a single
DoRings();
DoReverses();
SetItr itr;
_ss.str("");
for(itr=fragset.begin();itr!=fragset.end();++itr)
{
//Use hash of fragment to set a bit in the fingerprint
int hash = CalcHash(*itr);
SetBit(fp,hash);
if(!(Flags() & FPT_NOINFO))
PrintFpt(*itr,hash);
}
if(nbits)
Fold(fp, nbits);
// TRACE("%d after\n",fragset.size());
return true;
}
bool OBDepict::DrawMolecule(OBMol *mol)
{
if (!d->painter)
return false;
d->mol = mol;
double width=0.0, height=0.0;
OBAtom *atom;
OBBondIterator j;
OBAtomIterator i;
if(mol->NumAtoms()>0) {
// scale bond lengths
double bondLengthSum = 0.0;
for (OBBond *bond = mol->BeginBond(j); bond; bond = mol->NextBond(j))
bondLengthSum += bond->GetLength();
const double averageBondLength = bondLengthSum / mol->NumBonds();
const double f = mol->NumBonds() ? d->bondLength / averageBondLength : 1.0;
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
atom->SetVector(atom->GetX() * f, atom->GetY() * f, 0.0);
// find min/max values
double min_x, max_x;
double min_y, max_y;
atom = mol->BeginAtom(i);
min_x = max_x = atom->GetX();
min_y = max_y = atom->GetY();
for (atom = mol->NextAtom(i); atom; atom = mol->NextAtom(i)) {
min_x = std::min(min_x, atom->GetX());
max_x = std::max(max_x, atom->GetX());
min_y = std::min(min_y, atom->GetY());
max_y = std::max(max_y, atom->GetY());
}
const double margin = 40.0;
// translate all atoms so the bottom-left atom is at margin,margin
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
atom->SetVector(atom->GetX() - min_x + margin, atom->GetY() - min_y + margin, 0.0);
width = max_x - min_x + 2*margin;
height = max_y - min_y + 2*margin;
//d->painter->SetPenWidth(d->penWidth);
//d->painter->SetPenColor(d->pen));
//d->painter->SetFillColor(OBColor("black"));
}
d->painter->NewCanvas(width, height);
// draw bonds
if(d->options & genWedgeHash)
d->SetWedgeAndHash(mol);
for (OBBond *bond = mol->BeginBond(j); bond; bond = mol->NextBond(j)) {
OBAtom *begin = bond->GetBeginAtom();
OBAtom *end = bond->GetEndAtom();
if((d->options & internalColor) && bond->HasData("color"))
d->painter->SetPenColor(OBColor(bond->GetData("color")->GetValue()));
else
d->painter->SetPenColor(d->bondColor);
if (bond->IsWedge()) {
d->DrawWedge(begin, end);
} else if (bond->IsHash()) {
d->DrawHash(begin, end);
} else if (!bond->IsInRing()) {
d->DrawSimpleBond(begin, end, bond->GetBO());
}
}
// draw ring bonds
std::vector<OBRing*> rings(mol->GetSSSR());
OBBitVec drawnBonds;
for (std::vector<OBRing*>::iterator k = rings.begin(); k != rings.end(); ++k) {
OBRing *ring = *k;
std::vector<int> indexes = ring->_path;
vector3 center(VZero);
for (std::vector<int>::iterator l = indexes.begin(); l != indexes.end(); ++l) {
center += mol->GetAtom(*l)->GetVector();
}
center /= indexes.size();
for (unsigned int l = 0; l < indexes.size(); ++l) {
OBAtom *begin = mol->GetAtom(indexes[l]);
OBAtom *end;
if (l+1 < indexes.size())
end = mol->GetAtom(indexes[l+1]);
else
end = mol->GetAtom(indexes[0]);
OBBond *ringBond = mol->GetBond(begin, end);
if (drawnBonds.BitIsSet(ringBond->GetId()))
continue;
if((d->options & internalColor) && ringBond->HasData("color"))
d->painter->SetPenColor(OBColor(ringBond->GetData("color")->GetValue()));
else
d->painter->SetPenColor(d->bondColor);
d->DrawRingBond(begin, end, center, ringBond->GetBO());
drawnBonds.SetBitOn(ringBond->GetId());
}
}
// draw atom labels
for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i)) {
double x = atom->GetX();
double y = atom->GetY();
int alignment = GetLabelAlignment(atom);
bool rightAligned = false;
switch (alignment) {
case TopRight:
case CenterRight:
case BottomRight:
rightAligned = true;
default:
break;
}
if((d->options & internalColor) && atom->HasData("color"))
d->painter->SetPenColor(OBColor(atom->GetData("color")->GetValue()));
else if(d->options & bwAtoms)
d->painter->SetPenColor(d->bondColor);
else
d->painter->SetPenColor(OBColor(etab.GetRGB(atom->GetAtomicNum())));
//charge and radical
int charge = atom->GetFormalCharge();
int spin = atom->GetSpinMultiplicity();
if(charge || spin) {
OBFontMetrics metrics = d->painter->GetFontMetrics("N");
double yoffset = d->HasLabel(atom) ? 0.4 * metrics.height : 0.0;
switch (GetLabelAlignment(atom)) {
case TopCenter:
case TopRight:
case TopLeft:
case CenterLeft:
case CenterRight:
yoffset = - 1.2 * metrics.height;
}
stringstream ss;
if(charge) {
if(abs(charge)!=1)
ss << abs(charge);
ss << (charge>0 ? "+" : "-") ;
}
if(spin) {
ss << (spin==2 ? "." : "..");
yoffset += 0.5 * metrics.height;
}
if(spin || charge<0)
d->painter->SetFontSize(2 * metrics.fontSize);
d->painter->DrawText(x-0.4*metrics.width, y-yoffset, ss.str());
d->painter->SetFontSize(metrics.fontSize);//restore
}
if (atom->IsCarbon()) {
if(!(d->options & drawAllC))
{
if (atom->GetValence() > 1)
continue;
if ((atom->GetValence() == 1) && !(d->options & drawTermC))//!d->drawTerminalC)
continue;
}
}
stringstream ss;
AliasData* ad = NULL;
if(d->aliasMode && atom->HasData(AliasDataType))
ad = static_cast<AliasData*>(atom->GetData(AliasDataType));
//For unexpanded aliases use appropriate form of alias instead of element symbol, Hs, etc
if(ad && !ad->IsExpanded())
{
ss <<ad->GetAlias(rightAligned);
OBColor aliasColor = !ad->GetColor().empty() ? ad->GetColor() : d->bondColor;
d->painter->SetPenColor(aliasColor);
}
else {
const char* atomSymbol;
if(atom->IsHydrogen() && atom->GetIsotope()>1)
atomSymbol = atom->GetIsotope()==2 ? "D" : "T";
else
atomSymbol = etab.GetSymbol(atom->GetAtomicNum());
unsigned int hCount = atom->ImplicitHydrogenCount();
// rightAligned:
// false CH3
// true H3C
if (hCount && rightAligned)
ss << "H";
if ((hCount > 1) && rightAligned)
ss << hCount;
ss << atomSymbol;
if (hCount && !rightAligned)
ss << "H";
if ((hCount > 1) && !rightAligned)
ss << hCount;
}
d->DrawAtomLabel(ss.str(), alignment, vector3(x, y, 0.0));
}
return true;
}