bool OBDepict::AddAtomLabels(AtomLabelType type)
{
d->painter->SetPenColor(OBColor("red"));
d->painter->SetFillColor(OBColor("red"));
d->painter->SetFontSize((int)(GetFontSize() * 0.8));// smaller text
OBAtomIterator i;
for (OBAtom *atom = d->mol->BeginAtom(i); atom; atom = d->mol->NextAtom(i)) {
vector3 pos(atom->GetVector());
std::stringstream ss;
switch (type) {
case AtomId:
ss << atom->GetId();
d->painter->DrawText(pos.x(), pos.y(), ss.str());
break;
case AtomSymmetryClass:
ss << GetAtomSymClass(atom);
d->painter->DrawText(pos.x(), pos.y(), ss.str());
break;
case AtomIndex:
ss << atom->GetIdx();
d->painter->DrawText(pos.x(), pos.y(), ss.str());
break;
default:
break;
}
}
return true;
}
void CairoPainter::NewCanvas(double width, double height)
{
double titleheight = m_title.empty() ? 0.0 : 16.0;
if (m_index == 1) {
// create new surface to paint on
if(m_cropping) {
double ratio = width / height;
if(ratio > 1.0)
m_height = m_height / ratio;
else
m_width = m_width * ratio;
}
m_surface = cairo_image_surface_create(CAIRO_FORMAT_ARGB32, static_cast<int> (m_width), static_cast<int> (m_height));
m_cairo = cairo_create(m_surface);
if(m_transparent)
cairo_set_source_rgba (m_cairo, 0.0, 0.0, 0.0, 0.0);
else {
OBColor bg = OBColor(m_fillcolor);
cairo_set_source_rgb (m_cairo, bg.red, bg.green, bg.blue);
}
cairo_paint (m_cairo);
cairo_set_line_width(m_cairo, m_pen_width);
}
else {
// reset transformation matrix
cairo_identity_matrix(m_cairo);
}
// Work out some things!
double cellwidth = m_width/m_ncols;
double cellheight = m_height/m_nrows;
int row = (m_index - 1)/m_ncols + 1;
int col = m_index - ((row-1)*m_ncols);
// Work out the scaling factor
double scale_x = cellwidth / (double) width;
double scale_y = (cellheight-titleheight) / (double) height; // Leave some extra space for the title if present
double scale = std::min(scale_x, scale_y);
// Add the title
if (!m_title.empty()) {
this->SetPenColor(OBColor(m_bondcolor));
this->SetFontSize(static_cast<int>(16.0));
OBFontMetrics fm = this->GetFontMetrics(m_title);
this->DrawText(cellwidth/2.0 - fm.width/2.0 + cellwidth*(col-1),
cellheight - fm.height * 0.25 + cellheight*(row-1), m_title);
}
// Translate the over-scaled dimension into the centre
if (scale < scale_y)
cairo_translate(m_cairo, 0 + cellwidth*(col-1), cellheight/2.0 - scale*height/2.0 + cellheight*(row-1));
else
cairo_translate(m_cairo, cellwidth/2.0 - scale*width/2.0 + cellwidth*(col-1), 0 + cellheight*(row-1));
cairo_scale(m_cairo, scale, scale); // Set a scaling transformation
}
bool SVGFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
ostream &ofs = *pConv->GetOutStream();
//Check for option for single mol in fixed size image
const char* fixedpx = pConv->IsOption("P");
if(!fixedpx)
fixedpx= pConv->IsOption("px", OBConversion::GENOPTIONS);
//If WriteMolecule called directly, e.g. from OBConversion::Write()
//the default mode is a fixed image size of 200px square
if(!fixedpx && !pConv->IsOption("svgwritechemobject"))
fixedpx = "200";
if(fixedpx)
{
_nmax = _nrows = _ncols = 1;
pConv->AddOption("j");
pConv->SetLast(true);
pConv->SetOutputIndex(1);
}
//*** Coordinate generation ***
//Generate coordinates only if no existing 2D coordinates
if( (pConv->IsOption("y") || !pmol->Has2D(true)) && !pConv->IsOption("n") )
{
OBOp* pOp = OBOp::FindType("gen2D");
if(!pOp)
{
obErrorLog.ThrowError("SVGFormat", "gen2D not found", obError, onceOnly);
return false;
}
if(!pOp->Do(pmol))
{
obErrorLog.ThrowError("SVGFormat", string(pmol->GetTitle()) + "- Coordinate generation unsuccessful", obError);
return false;
}
}
if(!pmol->Has2D() && pmol->NumAtoms()>1)//allows 3D coordinates (if passed by -xn above)
{
string mes("Molecule ");
mes += pmol->GetTitle();
mes += " needs 2D coordinates to display in SVGformat";
obErrorLog.ThrowError("SVGFormat", mes, obError);
return false;
}
bool hasTable = (_nrows || _ncols);
bool transparent=false;
string background, bondcolor;
const char* bg = pConv->IsOption("b");
background = bg ? "black" : "white";
bondcolor = bg ? "white" : "black";
if(bg && (!strcmp(bg, "none") || bg[0]=='0'))
{
transparent = true;
bondcolor = "gray";
}
const char* bcol = pConv->IsOption("B");
if(bcol && *bcol)
bondcolor = bcol;
if(bg && *bg)
background = bg;
if(pConv->GetOutputIndex()==1 || fixedpx)
{
//For the first molecule...
if(hasTable)
{
//multiple molecules - use a table
//Outer svg has viewbox for 0 0 100 100 or adjusted for table shape,
//and no width or height - it uses the whole of its containing element.
//Inner svg with width, height, x, y of table cell,
//and viewbox to match molecule min and max x and y
if(!pConv->IsOption("x"))
ofs << "<?xml version=\"1.0\"?>\n";
ofs << "<svg version=\"1.1\" id=\"topsvg\"\n"
"xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n"
"xmlns:cml=\"http://www.xml-cml.org/schema\" ";
//*** Outer viewbox ***
double vbwidth=100, vbheight=100;
if (_nrows>_ncols)
vbwidth = (100*_ncols)/_nrows;
else if(_ncols>_nrows)
vbheight = (100*_nrows)/_ncols;
if(fixedpx)//fixed size image
ofs << "x=\"0\" y=\"0\" width=\"" << fixedpx << "px\" height=\"" << fixedpx <<"px\" ";
else
ofs << "x=\"0\" y=\"0\" width=\"100%\" height=\"100%\" ";
ofs << "viewBox=\"0 0 " << vbwidth << ' ' << vbheight << "\">\n";
ofs << "<title>OBDepict</title>\n";
// Draw the background unless transparent
if(!transparent)
ofs << "<rect x=\"0\" y=\"0\" width=\"" << vbwidth << "\" height=\"" << vbheight
<< "\" fill=\"" << background << "\"/>\n";
}
}
//All mols
double cellsize;
if(hasTable)
{
//*** Parameter for inner svg ***
int nc = _ncols ? _ncols : 1;
int nr = (_nrows ? _nrows : 1);
cellsize = 100. / std::max(nc, nr);
int indx = pConv->GetOutputIndex() - 1;
double innerX = (indx % nc) * cellsize;
double innerY = (indx / nc) * cellsize;
// Change the background in this cell if the condition in the first
// parameter of the -xh option is met. Use a default color if
// the highlight color is not specified in the second parameter.
const char* htxt = pConv->IsOption("h");
if(htxt)
{
vector<string> vec;
tokenize(vec, htxt);
string highlight(vec.size()>1 ? vec[1] : "#f4f0ff");
std::istringstream conditionText(vec[0]);
if(OBDescriptor::FilterCompare(pOb, conditionText, false))
//Still in outer <svg>, unfortunately
ofs << "<rect x=\"" << innerX << "\" y=\"" << innerY
<< "\" width=\"" << cellsize << "\" height=\"" << cellsize
<< "\" fill=\"" << highlight << "\"/>\n";
}
//*** Write molecule name ***
if(!pConv->IsOption("d"))
ofs << "<text text-anchor=\"middle\" font-size=\"" << 0.06*cellsize << "\""
<< " fill =\"" << bondcolor << "\" font-family=\"sans-serif\"\n"
<< "x=\"" << innerX + cellsize * 0.5 << "\" y=\"" << innerY + cellsize - 2.0/nr << "\" >"
<< pmol->GetTitle() << "</text>\n";
SVGPainter painter(*pConv->GetOutStream(), true, cellsize,cellsize,innerX,innerY);
OBDepict depictor(&painter);
if(!pConv->IsOption("C"))
depictor.SetOption(OBDepict::drawTermC);// on by default
if(pConv->IsOption("a"))
depictor.SetOption(OBDepict::drawAllC);
if(pConv->IsOption("A"))
{
AliasData::RevertToAliasForm(*pmol);
depictor.SetAliasMode();
}
painter.SetFontFamily("sans-serif");
painter.SetPenColor(OBColor(bondcolor));
depictor.SetBondColor(bondcolor);
if(pConv->IsOption("t"))
painter.SetPenWidth(4);
else
painter.SetPenWidth(2);
//No element-specific atom coloring if requested
if(pConv->IsOption("u"))
depictor.SetOption(OBDepict::bwAtoms);
if(!pConv->IsOption("U"))
depictor.SetOption(OBDepict::internalColor);
if(pConv->IsOption("s"))
depictor.SetOption(OBDepict::asymmetricDoubleBond);
depictor.DrawMolecule(pmol);
//Draw atom indices if requested
if(pConv->IsOption("i"))
depictor.AddAtomLabels(OBDepict::AtomIndex);
//Embed CML of molecule if requested
if(pConv->IsOption("e"))
EmbedCML(pmol,pConv);
}
else //single molecule
{
//Nothing written until DrawMolecule call
//Final </svg> written at the end of this block (painter destructor)
//This leads to some code duplication.
double factor = 1.0;
SVGPainter painter(*pConv->GetOutStream(), false);
OBDepict depictor(&painter);
//Scale image by specifying the average bond length in pixels.
const char* ppx = pConv->IsOption("p");
if(!ppx)
ppx= pConv->IsOption("px", OBConversion::GENOPTIONS);
if(ppx)
{
double oldblen = depictor.GetBondLength();
double newblen = atof(ppx);
depictor.SetBondLength(newblen);
factor = newblen / oldblen;
//Scale bondspacing and font size by same factor
depictor.SetBondSpacing(depictor.GetBondSpacing() * factor);
depictor.SetFontSize((int)(depictor.GetFontSize() * factor));
}
if(pConv->IsOption("W"))
depictor.SetOption(OBDepict::noWedgeHashGen);
if(!pConv->IsOption("C"))
depictor.SetOption(OBDepict::drawTermC);// on by default
if(pConv->IsOption("a"))
depictor.SetOption(OBDepict::drawAllC);
if(pConv->IsOption("A"))
{
AliasData::RevertToAliasForm(*pmol);
depictor.SetAliasMode();
}
painter.SetFontFamily("sans-serif");
painter.SetPenColor(OBColor(bondcolor));
depictor.SetBondColor(bondcolor);
painter.SetFillColor(OBColor(background));
if(pConv->IsOption("t"))
painter.SetPenWidth(4);
else
painter.SetPenWidth(1);
//No element-specific atom coloring if requested
if(pConv->IsOption("u"))
depictor.SetOption(OBDepict::bwAtoms);
if(!pConv->IsOption("U"))
depictor.SetOption(OBDepict::internalColor);
if(pConv->IsOption("s"))
depictor.SetOption(OBDepict::asymmetricDoubleBond);
depictor.DrawMolecule(pmol);
//Draw atom indices if requested
if(pConv->IsOption("i"))
depictor.AddAtomLabels(OBDepict::AtomIndex);
//*** Write molecule name ***
if(!pConv->IsOption("d"))
ofs << "<text font-size=\"" << 18 * factor << "\""
<< " fill =\"" << bondcolor << "\" font-family=\"sans-serif\"\n"
<< "x=\"" << 10 * factor << "\" y=\"" << 20 * factor << "\" >"
<< pmol->GetTitle() << "</text>\n";
//*** Write page title name ***
ofs << "<title>" << pmol->GetTitle() << " - OBDepict</title>\n";
//Embed CML of molecule if requested
if(pConv->IsOption("e"))
EmbedCML(pmol,pConv);
}
if(hasTable && pConv->IsLast())
{
//Draw grid lines
if(_nrows && _ncols && pConv->IsOption("l"))
{
for(int i=1; i<_nrows; ++i)
ofs << " <line stroke=\"gray\" stroke-width=\"0.1\" x1=\"0\" x2=\"100\""
<< " y1=\"" << i*cellsize << "\" y2=\"" << i*cellsize << "\"/>\n";
for(int i=1; i<_ncols; ++i)
ofs << " <line stroke=\"gray\" stroke-width=\"0.1\" y1=\"0\" y2=\"100\""
<< " x1=\"" << i*cellsize << "\" x2=\"" << i*cellsize << "\"/>\n";
}
//Insert javascript for zooming and panning
if(!pConv->IsOption("j"))
EmbedScript(ofs);
ofs << "</svg>\n" << endl;//Outer svg
}
return !fixedpx; // return false with fixed size image because only 1 mol
}
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;
}
bool SVGFormat::WriteSVG(OBConversion* pConv, vector<OBBase*>& molecules)
{
bool ret=true;
//Check for option for single mol in fixed size image
const char* fixedpx = pConv->IsOption("P");
if(!fixedpx)
fixedpx= pConv->IsOption("px", OBConversion::GENOPTIONS);
//If WriteMolecule called directly, e.g. from OBConversion::Write()
//the default mode is a fixed image size of 200px square
if(!fixedpx && molecules.size()==1)
fixedpx = "200";
if(fixedpx)
{
_nmax = _nrows = _ncols = 1;
pConv->AddOption("j");
}
ostream &ofs = *pConv->GetOutStream();
bool hasTable = (_nrows>1) || (_ncols>1);
bool transparent=false;
string background, bondcolor;
const char* bg = pConv->IsOption("b");
background = bg ? "black" : "white";
bondcolor = bg ? "white" : "black";
if(bg && (!strcmp(bg, "none") || bg[0]=='0'))
{
transparent = true;
bondcolor = "gray";
}
const char* bcol = pConv->IsOption("B");
if(bcol && *bcol)
bondcolor = bcol;
if(bg && *bg)
background = bg;
if(!pConv->IsOption("x"))
ofs << "<?xml version=\"1.0\"?>\n";
ofs << "<svg version=\"1.1\" id=\"topsvg\"\n"
"xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n"
"xmlns:cml=\"http://www.xml-cml.org/schema\" ";
double vbwidth=100, vbheight=100;
if (_nrows>_ncols)
vbwidth = (100*_ncols)/_nrows;
else if(_ncols>_nrows)
vbheight = (100*_nrows)/_ncols;
if(fixedpx)//fixed size image
ofs << "x=\"0\" y=\"0\" width=\"" << fixedpx << "px\" height=\"" << fixedpx <<"px\" ";
else
ofs << "x=\"0\" y=\"0\" width=\"100%\" height=\"100%\" ";
ofs << "viewBox=\"0 0 " << vbwidth << ' ' << vbheight << "\">\n";
if (hasTable)
ofs << "<title>Multiple Molecules - Open Babel Depiction</title>\n";
else if(molecules.size() == 1)
ofs << "<title>" << molecules[0]->GetTitle() << " - Open Babel Depiction</title>\n";
// Draw the background unless transparent
if(!transparent)
ofs << "<rect x=\"0\" y=\"0\" width=\"" << vbwidth << "\" height=\"" << vbheight
<< "\" fill=\"" << background << "\"/>\n";
unsigned opts = 0;
if(pConv->IsOption("u"))
opts |= OBDepict::bwAtoms;
if(!pConv->IsOption("U"))
opts |= OBDepict::internalColor;
if(!pConv->IsOption("C"))
opts |= OBDepict::drawTermC;// on by default
if(pConv->IsOption("a"))
opts |= OBDepict::drawAllC;
if(pConv->IsOption("W"))
opts |= OBDepict::noWedgeHashGen;
if(pConv->IsOption("s"))
opts |= OBDepict::asymmetricDoubleBond;
if(pConv->IsOption("X"))
opts |= OBDepict::allExplicit;
bool balldepict = false;
if(pConv->IsOption("S"))
balldepict = true;
double factor = 1.0;
int nc = _ncols ? _ncols : 1;
int nr = (_nrows ? _nrows : 1);
double cellsize = 100. / std::max(nc, nr);
stringstream molfs;
std::set<ColorGradient> gradients;
OBOp* pOp = OBOp::FindType("gen2D");
if(!pOp)
{
obErrorLog.ThrowError("SVGFormat", "gen2D not found", obError, onceOnly);
return false;
}
vector<OBBase*>::iterator iter;
int indx = 0;
for(iter=_objects.begin(); ret && iter!=_objects.end(); ++iter,++indx)
{
OBMol* pmol = dynamic_cast<OBMol*>(*iter);
if (!pmol)
continue;
//*** Coordinate generation ***
//Generate coordinates only if no existing 2D coordinates
if( (pConv->IsOption("y") || !pmol->Has2D(true)) && !pConv->IsOption("n") )
{
if(!pOp->Do(pmol))
{
obErrorLog.ThrowError("SVGFormat", string(pmol->GetTitle()) + "- Coordinate generation unsuccessful", obError);
return false;
}
}
if(!pmol->Has2D() && pmol->NumAtoms()>1)//allows 3D coordinates (if passed by -xn above)
{
string mes("Molecule ");
mes += pmol->GetTitle();
mes += " needs 2D coordinates to display in SVGformat";
obErrorLog.ThrowError("SVGFormat", mes, obError);
return false;
}
double innerX = 0.0;
double innerY = 0.0;
if(hasTable)
{
//*** Parameter for inner svg ***
innerX = (indx % nc) * cellsize;
innerY = (indx / nc) * cellsize;
// Change the background in this cell if the condition in the first
// parameter of the -xh option is met. Use a default color if
// the highlight color is not specified in the second parameter.
const char* htxt = pConv->IsOption("h");
if(htxt)
{
vector<string> vec;
tokenize(vec, htxt);
string highlight(vec.size()>1 ? vec[1] : "#f4f0ff");
std::istringstream conditionText(vec[0]);
if(OBDescriptor::FilterCompare(*iter, conditionText, false))
//Still in outer <svg>, unfortunately
molfs << "<rect x=\"" << innerX << "\" y=\"" << innerY
<< "\" width=\"" << cellsize << "\" height=\"" << cellsize
<< "\" fill=\"" << highlight << "\"/>\n";
}
}
SVGPainter painter(molfs, &gradients, true, cellsize, cellsize);
OBDepict depictor(&painter, balldepict);
depictor.SetOption(opts);
if(pConv->IsOption("A"))
{
AliasData::RevertToAliasForm(*pmol);
depictor.SetAliasMode();
}
painter.SetFontFamily("sans-serif");
painter.SetPenColor(OBColor(bondcolor));
depictor.SetBondColor(bondcolor);
if(pConv->IsOption("t"))
painter.SetPenWidth(4);
else
painter.SetPenWidth(2);
molfs << "<g transform=\"translate(" << innerX << "," << innerY << ")\">\n";
ret = depictor.DrawMolecule(pmol);
//Draw atom indices if requested
if(pConv->IsOption("i"))
depictor.AddAtomLabels(OBDepict::AtomIndex);
painter.EndCanvas();
//Embed CML of molecule if requested
if(pConv->IsOption("e"))
EmbedCML(pmol, pConv, &molfs);
molfs <<"</g>\n";
//*** Write molecule name ***
if(!pConv->IsOption("d"))
if(hasTable)
molfs << "<text text-anchor=\"middle\" font-size=\"" << 0.06*cellsize << "\""
<< " fill =\"" << bondcolor << "\" font-family=\"sans-serif\"\n"
<< "x=\"" << innerX + cellsize * 0.5 << "\" y=\"" << innerY + cellsize - 2.0/nr << "\" >"
<< pmol->GetTitle() << "</text>\n";
else
molfs << "<text font-size=\"" << 18 * factor << "\""
<< " fill =\"" << bondcolor << "\" font-family=\"sans-serif\"\n"
<< "x=\"" << 10 * factor << "\" y=\"" << 20 * factor << "\" >"
<< pmol->GetTitle() << "</text>\n";
}
// finally write svg defs
SVGPainter painter(ofs, &gradients, true, cellsize,cellsize);
painter.WriteDefs();
// and stream back all molecule data
ofs << molfs.str();
//Draw grid lines
if(hasTable && pConv->IsOption("l"))
{
for(int i=1; i<_nrows; ++i)
ofs << " <line stroke=\"gray\" stroke-width=\"0.1\" x1=\"0\" x2=\"100\""
<< " y1=\"" << i*cellsize << "\" y2=\"" << i*cellsize << "\"/>\n";
for(int i=1; i<_ncols; ++i)
ofs << " <line stroke=\"gray\" stroke-width=\"0.1\" y1=\"0\" y2=\"100\""
<< " x1=\"" << i*cellsize << "\" x2=\"" << i*cellsize << "\"/>\n";
}
//Insert javascript for zooming and panning
if(!pConv->IsOption("j"))
EmbedScript(ofs);
ofs << "</svg>\n";
return ret;
}
bool SVGFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
ostream &ofs = *pConv->GetOutStream();
//*** Coordinate generation ***
//Generate coordinates only if no existing 2D coordinates
if( (pConv->IsOption("y") || !pmol->Has2D(true)) && !pConv->IsOption("n") )
{
OBOp* pOp = OBOp::FindType("gen2D");
if(!pOp)
{
obErrorLog.ThrowError("SVGFormat", "gen2D not found", obError, onceOnly);
return false;
}
if(!pOp->Do(pmol))
{
obErrorLog.ThrowError("SVGFormat", string(pmol->GetTitle()) + "- Coordinate generation unsuccessful", obError);
return false;
}
}
if(!pmol->Has2D() && pmol->NumAtoms()>1)//allows 3D coordinates (if passed by -xn above)
{
string mes("Molecule ");
mes += pmol->GetTitle();
mes += " needs 2D coordinates to display in SVGformat";
obErrorLog.ThrowError("SVGFormat", mes, obError);
return false;
}
bool hasTable = (_nrows || _ncols);
string background = pConv->IsOption("b") ? "black" : "white";
string bondcolor = pConv->IsOption("b") ? "white" : "black";
if(pConv->GetOutputIndex()==1)
{
//For the first molecule...
if(hasTable)
{
//multiple molecules - use a table
//Outer svg has viewbox for 0 0 100 100 or adjusted for table shape,
//and no width or height - it uses the whole of its containing element.
//Inner svg with width, height, x, y of table cell,
//and viewbox to match molecule min and max x and y
if(!pConv->IsOption("x"))
ofs << "<?xml version=\"1.0\"?>\n";
ofs << "<svg version=\"1.1\" id=\"topsvg\"\n"
"xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"\n"
"xmlns:cml=\"http://www.xml-cml.org/schema\" ";
//*** Outer viewbox ***
double vbwidth=100, vbheight=100;
if (_nrows>_ncols)
vbwidth = (100*_ncols)/_nrows;
else if(_ncols>_nrows)
vbheight = (100*_nrows)/_ncols;
ofs << "viewBox=\"0 0 " << vbwidth << ' ' << vbheight << "\">\n";
ofs << "<title>OBDepict</title>\n";
// Draw the background
ofs << "<rect x=\"0\" y=\"0\" width=\"" << vbwidth << "\" height=\"" << vbheight
<< "\" fill=\"" << background << "\"/>\n";
}
}
//All mols
double cellsize;
if(hasTable)
{
//*** Parameter for inner svg ***
int nc = _ncols ? _ncols : 1;
int nr = (_nrows ? _nrows : 1);
cellsize = 100. / std::max(nc, nr);
int indx = pConv->GetOutputIndex() - 1;
double innerX = (indx % nc) * cellsize;
double innerY = (indx / nc) * cellsize;
//*** Write molecule name ***
if(!pConv->IsOption("d"))
ofs << "<text text-anchor=\"middle\" font-size=\"" << 0.06*cellsize << "\""
<< " fill =\"" << bondcolor << "\" font-family=\"sans-serif\"\n"
<< "x=\"" << innerX + cellsize * 0.5 << "\" y=\"" << innerY + cellsize - 2.0/nr << "\" >"
<< pmol->GetTitle() << "</text>\n";
SVGPainter painter(*pConv->GetOutStream(), true, cellsize,cellsize,innerX,innerY);
OBDepict depictor(&painter);
if(pConv->IsOption("w"))
depictor.SetOption(OBDepict::genWedgeHash);
if(!pConv->IsOption("C"))
depictor.SetOption(OBDepict::drawTermC);// on by default
if(pConv->IsOption("a"))
depictor.SetOption(OBDepict::drawAllC);
if(pConv->IsOption("A"))
{
AliasData::RevertToAliasForm(*pmol);
depictor.SetAliasMode();
}
painter.SetFontFamily("sans-serif");
painter.SetPenColor(OBColor(bondcolor));
depictor.SetBondColor(bondcolor);
painter.SetPenWidth(2);
//No element-specific atom coloring if requested
if(pConv->IsOption("u"))
depictor.SetOption(OBDepict::bwAtoms);
if(!pConv->IsOption("U"))
depictor.SetOption(OBDepict::internalColor);
depictor.DrawMolecule(pmol);
//Draw atom indices if requested
if(pConv->IsOption("i"))
depictor.AddAtomLabels(OBDepict::AtomIndex);
//Embed CML of molecule if requested
if(pConv->IsOption("e"))
EmbedCML(pmol,pConv);
}
else //single molecule
{
//Nothing written until DrawMolecule call
//Final </svg> written at the end of this block (painter destructor)
//This leads to some code duplication.
double factor = 1.0;
SVGPainter painter(*pConv->GetOutStream());
OBDepict depictor(&painter);
//Scale image by specifying the average bond length in pixels.
if(pConv->IsOption("p"))
{
double oldblen = depictor.GetBondLength();
double newblen = atof(pConv->IsOption("p"));
depictor.SetBondLength(newblen);
factor = newblen / oldblen;
//Scale bondspacing and font size by same factor
depictor.SetBondSpacing(depictor.GetBondSpacing() * factor);
depictor.SetFontSize((int)(depictor.GetFontSize() * factor));
}
if(!pConv->IsOption("w"))
depictor.SetOption(OBDepict::genWedgeHash);
if(!pConv->IsOption("C"))
depictor.SetOption(OBDepict::drawTermC);// on by default
if(pConv->IsOption("a"))
depictor.SetOption(OBDepict::drawAllC);
if(pConv->IsOption("A"))
{
AliasData::RevertToAliasForm(*pmol);
depictor.SetAliasMode();
}
painter.SetFontFamily("sans-serif");
painter.SetPenColor(OBColor(bondcolor));
depictor.SetBondColor(bondcolor);
painter.SetFillColor(OBColor(background));
painter.SetPenWidth(1);
//No element-specific atom coloring if requested
if(pConv->IsOption("u"))
depictor.SetOption(OBDepict::bwAtoms);
if(!pConv->IsOption("U"))
depictor.SetOption(OBDepict::internalColor);
depictor.DrawMolecule(pmol);
//Draw atom indices if requested
if(pConv->IsOption("i"))
depictor.AddAtomLabels(OBDepict::AtomIndex);
//*** Write molecule name ***
if(!pConv->IsOption("d"))
ofs << "<text font-size=\"" << 18 * factor << "\""
<< " fill =\"" << bondcolor << "\"\n"
<< "x=\"" << 140 * factor << "\" y=\"" << 20 * factor << "\" >"
<< pmol->GetTitle() << "</text>\n";
//*** Write page title name ***
ofs << "<title>" << pmol->GetTitle() << " - OBDepict</title>\n";
//Embed CML of molecule if requested
if(pConv->IsOption("e"))
EmbedCML(pmol,pConv);
}
if(hasTable && pConv->IsLast())
{
//Draw grid lines
if(_nrows && _ncols && pConv->IsOption("l"))
{
for(int i=1; i<_nrows; ++i)
ofs << " <line stroke=\"gray\" stroke-width=\"0.1\" x1=\"0\" x2=\"100\""
<< " y1=\"" << i*cellsize << "\" y2=\"" << i*cellsize << "\"/>\n";
for(int i=1; i<_ncols; ++i)
ofs << " <line stroke=\"gray\" stroke-width=\"0.1\" y1=\"0\" y2=\"100\""
<< " x1=\"" << i*cellsize << "\" x2=\"" << i*cellsize << "\"/>\n";
}
//Insert javascript for zooming and panning
if(!pConv->IsOption("j"))
EmbedScript(ofs);
ofs << "</svg>\n" << endl;//Outer svg
}
return true;
}
SVGPainter::SVGPainter(ostream& ofs, std::set<ColorGradient>* gradients, bool withViewBox,
double width, double height)
: m_ofs(ofs), m_withViewBox(withViewBox), m_width(width), m_height(height),
m_Pencolor("black"), m_Fillcolor("white"), m_Gradientcolor(make_pair(OBColor("white"),OBColor("white"))), m_PenWidth(1),
m_fontPointSize(16), m_isFillcolor(true), m_Gradients(gradients) {}
