String CSSSupportsRule::cssText() const
{
StringBuilder result;
result.appendLiteral("@supports ");
result.append(conditionText());
result.appendLiteral(" {\n");
appendCSSTextForItems(result);
result.append('}');
return result.toString();
}
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 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;
}