static void WriteMolFile(OBMol* pmol, OBConversion* pconv, OBFormat* pformat)
{
ostream &ofs = *pconv->GetOutStream();
ofs << "$MOL" << '\n';
// Treat a dummy atom with "rxndummy" as the empty file
if (pmol->NumAtoms() == 1) {
OBAtom *atm = pmol->GetFirstAtom();
if (atm->GetAtomicNum() == 0 && atm->HasData("rxndummy"))
pmol->DeleteAtom(atm);
}
pformat->WriteMolecule(pmol, pconv);
}
void AliasData::DeleteExpandedAtoms(OBMol& mol)
{
//The atom that carries the AliasData object remains as an Xx atom with no charge;
//the others are deleted. All the attached hydrogens are also deleted.
for(unsigned i=0;i<_expandedatoms.size();++i)
{
OBAtom* at = mol.GetAtomById(_expandedatoms[i]);
if(!at)
continue;
mol.DeleteHydrogens(at);
if(at->HasData(AliasDataType))
{
at->SetAtomicNum(0);
at->SetFormalCharge(0);
at->SetSpinMultiplicity(0);
}
else
mol.DeleteAtom(at);
}
_expandedatoms.clear();
}
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;
}