bool PainterFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
ostream& ofs = *pConv->GetOutStream();
OBMol workingmol(*pmol); // Copy the molecule
//*** Coordinate generation ***
//Generate coordinates only if no existing 2D coordinates
if(!workingmol.Has2D(true))
{
OBOp* pOp = OBOp::FindType("gen2D");
if(!pOp)
{
obErrorLog.ThrowError("PainterFormat", "gen2D not found", obError, onceOnly);
return false;
}
if(!pOp->Do(&workingmol))
{
obErrorLog.ThrowError("PainterFormat", string(workingmol.GetTitle()) + "- Coordinate generation unsuccessful", obError);
return false;
}
}
if(!workingmol.Has2D() && workingmol.NumAtoms()>1)
{
string mes("Molecule ");
mes += workingmol.GetTitle();
mes += " needs 2D coordinates to display in PNG2format";
obErrorLog.ThrowError("PainterFormat", mes, obError);
return false;
}
CommandPainter painter(*pConv->GetOutStream());
OBDepict depictor(&painter);
if(pConv->IsOption("M"))
depictor.SetOption(OBDepict::noMargin);
depictor.DrawMolecule(&workingmol);
return true; //or false to stop converting
}
bool FastSearchFormat::ReadChemObject(OBConversion* pConv)
{
//Searches index file for structural matches
//This function is called only once per search
std::string auditMsg = "OpenBabel::Read fastsearch index ";
std::string description(Description());
auditMsg += description.substr(0,description.find('\n'));
obErrorLog.ThrowError(__FUNCTION__,
auditMsg,
obAuditMsg);
//Derive index name
string indexname = pConv->GetInFilename();
string::size_type pos=indexname.find_last_of('.');
if(pos!=string::npos)
{
indexname.erase(pos);
indexname += ".fs";
}
//Have to open input stream again because needs to be in binary mode
ifstream ifs;
stringstream errorMsg;
if(!indexname.empty())
ifs.open(indexname.c_str(),ios::binary);
if(!ifs)
{
errorMsg << "Couldn't open " << indexname << endl;
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);
return false;
}
string datafilename = fs.ReadIndex(&ifs);
if(datafilename.empty())
{
errorMsg << "Difficulty reading from index " << indexname << endl;
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);
return false;
}
vector<OBMol> patternMols;
if(!ObtainTarget(pConv, patternMols, indexname))
return false;
bool exactmatch = pConv->IsOption("e",OBConversion::INOPTIONS)!=NULL;// -ae option
//Open the datafile and put it in pConv
//datafile name derived from index file probably won't have a file path
//but indexname may. Derive a full datafile name
string path;
pos = indexname.find_last_of("/\\");
if(pos==string::npos)
path = datafilename;
else
path = indexname.substr(0,pos+1) + datafilename;
ifstream datastream(path.c_str());
if(!datastream)
{
errorMsg << "Difficulty opening " << path << endl;
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);
return false;
}
pConv->SetInStream(&datastream);
//Input format is currently fs; set it appropriately
if(!pConv->SetInAndOutFormats(pConv->FormatFromExt(datafilename.c_str()),pConv->GetOutFormat()))
return false;
// If target has dative bonds like -[N+](=O)[O-] convert it to the uncharged form
// (-N(=O)=O and add uncharged form to vector of mols which are sent to
// the -s (SMARTS)filter.
// Also check whether the target has dative bonds in the uncharged form and supply
// the charged form to the -s filter.
// Together with the automatic conversion to the uncharged form when the fs index is made,
// this ensures that both forms are found however they occur in the datafile or the taget.
vector<OBBase*> extraSMARTSMols;
vector<OBMol>extraUnchargedMols;
for(unsigned i=0;i<patternMols.size();++i)
{
if(patternMols[i].ConvertDativeBonds())
extraSMARTSMols.push_back(&patternMols[i]);
else
{
// If target has uncharged dative bonds, still use it for fastsearching,
// but add the charged form for -s filter.
extraUnchargedMols.push_back(patternMols[i]);
if(extraUnchargedMols.back().MakeDativeBonds())
extraSMARTSMols.push_back(&extraUnchargedMols.back());
}
}
OBOp* sFilter = OBOp::FindType("s");
if(sFilter)
sFilter->ProcessVec(extraSMARTSMols);
//Now do searching
const char* p = pConv->IsOption("t",OBConversion::INOPTIONS);
if(p)
{
//Do a similarity search
multimap<double, unsigned int> SeekposMap;
string txt=p;
if(txt.find('.')==string::npos)
{
//Finds n molecules with largest Tanimoto
int n = atoi(p);
fs.FindSimilar(&patternMols[0], SeekposMap, n);
}
else
{
//Finds molecules with Tanimoto > MinTani
double MaxTani = 1.1;
size_t pos = txt.find(',');
if( pos != string::npos ) {
MaxTani = atof( txt.substr( pos + 1 ).c_str() );
}
double MinTani = atof( txt.substr( 0, pos ).c_str() );
fs.FindSimilar(&patternMols[0], SeekposMap, MinTani, MaxTani);
}
//Don't want to filter through SMARTS filter
pConv->RemoveOption("s", OBConversion::GENOPTIONS);
//also because op names are case independent
pConv->RemoveOption("S", OBConversion::GENOPTIONS);
multimap<double, unsigned int>::reverse_iterator itr;
for(itr=SeekposMap.rbegin();itr!=SeekposMap.rend();++itr)
{
datastream.seekg(itr->second);
if(pConv->IsOption("a", OBConversion::INOPTIONS))
{
//Adds Tanimoto coeff to title
//First remove any previous value
pConv->RemoveOption("addtotitle", OBConversion::GENOPTIONS);
stringstream ss;
ss << " " << itr->first;
pConv->AddOption("addtotitle",OBConversion::GENOPTIONS, ss.str().c_str());
}
pConv->SetOneObjectOnly();
if(itr != --SeekposMap.rend())
pConv->SetMoreFilesToCome();//so that not seen as last on output
pConv->Convert(NULL,NULL);
}
}
else
{
//Structure search
int MaxCandidates = 4000;
p = pConv->IsOption("l",OBConversion::INOPTIONS);
if(p && atoi(p))
MaxCandidates = atoi(p);
vector<unsigned int> SeekPositions;
if(exactmatch)
{
//Find mols where all fingerprint bits are the same as the target
fs.FindMatch(&patternMols[0], SeekPositions, MaxCandidates);
// ensure that SMARTS filter in transform.cpp looks only for an exact match
// by setting an option with the number of heavy atoms in the pattern mol included.
stringstream ss;
ss << patternMols[0].NumHvyAtoms();
pConv->AddOption("exactmatch", OBConversion::GENOPTIONS, ss.str().c_str());
}
else
{
//Do a substructure search for each target
vector<OBMol>::iterator iter;
for(iter=patternMols.begin();iter!=patternMols.end();++iter)
fs.Find(&*iter, SeekPositions, MaxCandidates);
clog << SeekPositions.size() << " candidates from fingerprint search phase" << endl;
}
vector<unsigned int>::iterator seekitr,
begin = SeekPositions.begin(), end = SeekPositions.end();
if(patternMols.size()>1)//only sort and eliminate duplicates if necessary
{
sort(begin, end);
end = unique(begin, end); //removed duplicates are after new end
}
//Output the candidate molecules, filtering through s filter, unless it was not requested
if(pConv->IsOption("n", OBConversion::INOPTIONS) )
pConv->RemoveOption("s",OBConversion::GENOPTIONS);
pConv->SetLast(false);
for(seekitr=begin; seekitr!=end; ++seekitr)
{
datastream.seekg(*seekitr);
if(!pConv->GetInFormat()->ReadChemObject(pConv))
return false;
pConv->SetFirstInput(false); //needed for OpSort
}
}
return false; //To finish
}
bool OpAlign::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
map<string,string>::const_iterator itr;
// Is there an -s option?
if(pConv->IsFirstInput())
{
_pOpIsoM = NULL; //assume no -s option
itr = pmap->find("s");
if(itr!=pmap->end())
{
//There is an -s option; check it is ok
_pOpIsoM = static_cast<OpNewS*>(OBOp::FindType("s"));
_stext = itr->second; //get its parameter(s)
if(!_pOpIsoM || _stext.empty())
{
obErrorLog.ThrowError(__FUNCTION__,
"No parameter on -s option, or its OBOp version is not loaded", obError);
pConv->SetOneObjectOnly(); //to finish
return false;
}
}
}
// If the output format is a 2D depiction format, then we should align
// on the 2D coordinates and not the 3D coordinates (if present). This
//means we need to generate the 2D coordinates at this point.
if(pmol->GetDimension()==3 && (pConv->GetOutFormat()->Flags() & DEPICTION2D))
{
OBOp* pgen = OBOp::FindType("gen2D");
if(pgen)
pgen->Do(pmol);
}
// All molecules must have coordinates, so add them if 0D
// They may be added again later when gen2D or gen3D is called, but they will be the same.
// It would be better if this op was called after them, which would happen
// if its name was alphabetically after "gen" (and before "s").
if(pmol->GetDimension()==0)
{
//Will the coordinates be 2D or 3D?
itr = pmap->find("gen3D");
OBOp* pgen = (itr==pmap->end()) ? OBOp::FindType("gen2D") : OBOp::FindType("gen3D");
if(pgen)
pgen->Do(pmol);
}
//Do the alignment in 2D if the output format is svg, png etc. and there is no -xn option
if(pmol->GetDimension()==3 && pConv && !pConv->IsOption("n"))
{
OBFormat* pOutFormat = pConv->GetOutFormat();
if(pOutFormat->Flags() & DEPICTION2D)
{
OBOp* pgen = OBOp::FindType("gen2D");
if(pgen)
pgen->Do(pmol);
}
}
if(pConv->IsFirstInput() || _refMol.NumAtoms()==0)
{
_refvec.clear();
// Reference molecule is basically the first molecule
_refMol = *pmol;
if(!_pOpIsoM)
//no -s option. Use a molecule reference.
_align.SetRefMol(_refMol);
else
{
//If there is a -s option, reference molecule has only those atoms that are matched
//Call the -s option from here
bool ret = _pOpIsoM->Do(pmol, _stext.c_str(), pmap, pConv);
// Get the atoms that were matched
vector<int> ats = _pOpIsoM->GetMatchAtoms();
if(!ats.empty())
{
// Make a vector of the matching atom coordinates...
for(vector<int>::iterator iter=ats.begin(); iter!=ats.end(); ++iter)
_refvec.push_back((pmol->GetAtom(*iter))->GetVector());
// ...and use a vector reference
_align.SetRef(_refvec);
}
// Stop -s option being called normally, although it will still be called once
// in the DoOps loop already started for the current (first) molecule.
pConv->RemoveOption("s",OBConversion::GENOPTIONS);
if(!ret)
{
// the first molecule did not match the -s option so a reference molecule
// could not be made. Keep trying.
_refMol.Clear();
//obErrorLog.ThrowError(__FUNCTION__, "The first molecule did not match the -s option\n"
// "so the reference structure was not derived from it", obWarning, onceOnly);
return false; //not matched
}
}
}
//All molecules
if(pmol->GetDimension()!= _refMol.GetDimension())
{
stringstream ss;
ss << "The molecule" << pmol->GetTitle()
<< " does not have the same dimensions as the reference molecule "
<< _refMol.GetTitle() << " and is ignored.";
obErrorLog.ThrowError(__FUNCTION__, ss.str().c_str(), obError);
return false;
}
if(_pOpIsoM) //Using -s option
{
//Ignore mol if it does not pass -s option
if(!_pOpIsoM->Do(pmol, "", pmap, pConv)) // "" means will use existing parameters
return false;
// Get the atoms equivalent to those in ref molecule
vector<int> ats = _pOpIsoM->GetMatchAtoms();
// Make a vector of their coordinates and get the centroid
vector<vector3> vec;
vector3 centroid;
for(vector<int>::iterator iter=ats.begin(); iter!=ats.end(); ++iter) {
vector3 v = pmol->GetAtom(*iter)->GetVector();
centroid += v;
vec.push_back(v);
}
centroid /= vec.size();
// Do the alignment
_align.SetTarget(vec);
if(!_align.Align())
return false;
// Get the centroid of the reference atoms
vector3 ref_centroid;
for(vector<vector3>::iterator iter=_refvec.begin(); iter!=_refvec.end(); ++iter)
ref_centroid += *iter;
ref_centroid /= _refvec.size();
//subtract the centroid, rotate the target molecule, then add the centroid
matrix3x3 rotmatrix = _align.GetRotMatrix();
for (unsigned int i = 1; i <= pmol->NumAtoms(); ++i)
{
vector3 tmpvec = pmol->GetAtom(i)->GetVector();
tmpvec -= centroid;
tmpvec *= rotmatrix; //apply the rotation
tmpvec += ref_centroid;
pmol->GetAtom(i)->SetVector(tmpvec);
}
}
else //Not using -s option)
{
_align.SetTargetMol(*pmol);
if(!_align.Align())
return false;
_align.UpdateCoords(pmol);
}
//Save rmsd as a property
OBPairData* dp = new OBPairData;
dp->SetAttribute("rmsd");
double val = _align.GetRMSD();
if(val<1e-12)
val = 0.0;
dp->SetValue(toString(val));
dp->SetOrigin(local);
pmol->SetData(dp);
return true;
}
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;
}
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;
}
