rdkit/Code/JavaWrappers/Depict.h

/* 
*
*  Copyright (c) 2011, Novartis Institutes for BioMedical Research Inc.
*  All rights reserved.
* 
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met: 
*
*     * Redistributions of source code must retain the above copyright 
*       notice, this list of conditions and the following disclaimer.
*     * Redistributions in binary form must reproduce the above
*       copyright notice, this list of conditions and the following 
*       disclaimer in the documentation and/or other materials provided 
*       with the distribution.
*     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
*       nor the names of its contributors may be used to endorse or promote 
*       products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

#include <GraphMol/MolDrawing/MolDrawing.h>

namespace {
  std::string getColor(int atNum){
    std::string res="#000000";
    switch(atNum){
    case 7: res="#0000FF";break;
    case 8: res="#FF0000";break;
    case 9: res="#33CCCC";break;
    case 15: res="#FF7F00";break;
    case 16: res="#CCCC00";break;
    case 17: res="#00CC00";break;
    case 35: res="#7F4C19";break;
    case 0: res="#7F7F7F";break;
    default: res="#000000";
    }
    return res;
  }
  void drawLine(std::vector<int>::const_iterator &pos,std::ostringstream &sstr,
                unsigned int lineWidthMult){
    int width=*pos++;
    width*=lineWidthMult;

    int dashed=*pos++;
    std::string dashString="";
    if(dashed){
      dashString=";stroke-dasharray:6, 6";
    }
    int an1=*pos++;
    int an2=*pos++;
    std::string c1=getColor(an1);
    std::string c2=getColor(an2);
    if(c1==c2){
      sstr<<"<svg:path ";
      sstr<<"d='M "<<*pos<<","<<*(pos+1)<<" "<<*(pos+2)<<","<<*(pos+3)<<"' ";
      pos+=4;
      sstr<<"style='fill:none;fill-rule:evenodd;stroke:"<<c1<<";stroke-width:"<<width<<"px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"<<dashString<<"'";
      sstr<<" />\n";
    } else {
      int xp1 = *pos++;
      int yp1 = *pos++;
      int xp2 = *pos++;
      int yp2 = *pos++;
      int mx = xp1+(xp2-xp1)/2;
      int my = yp1+(yp2-yp1)/2;
      sstr<<"<svg:path ";
      sstr<<"d='M "<<xp1<<","<<yp1<<" "<<mx<<","<<my<<"' ";
      sstr<<"style='fill:none;fill-rule:evenodd;stroke:"<<c1<<";stroke-width:"<<width<<"px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"<<dashString<<"'";
      sstr<<" />\n";
      sstr<<"<svg:path ";
      sstr<<"d='M "<<mx<<","<<my<<" "<<xp2<<","<<yp2<<"' ";
      sstr<<"style='fill:none;fill-rule:evenodd;stroke:"<<c2<<";stroke-width:"<<width<<"px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"<<dashString<<"'";
      sstr<<" />\n";
    }
  }

  void drawAtom(std::vector<int>::const_iterator &pos,std::ostringstream &sstr,unsigned int fontSz){
    int atNum=*pos++;
    int xp=*pos++;
    int yp=*pos++;
    int slen=*pos++;
    std::string label="";
    for(unsigned int i=0;i<slen;++i){
      label+=(char)*pos++;
    }
    int orient=*pos++;
    int width=fontSz*label.length();
    int height=fontSz;
    sstr<<"<svg:g transform='translate("<<xp<<","<<yp<<")'><svg:rect ";
    sstr<<"style='opacity:1.0;fill:#FFFFFF;stroke:none'";
    sstr<<" width='"<<width<<"' height='"<<height<<"'";
    sstr<<" x='-"<<width/2<<"' y='-"<<height/2<<"'";
    sstr<<"> </svg:rect>\n";
    sstr<<"<svg:text";
    sstr<<" style='font-size:"<<fontSz<<"px;font-style:normal;font-weight:normal;line-height:125%;letter-spacing:0px;word-spacing:0px;fill-opacity:1;stroke:none;font-family:Sans;text-anchor:middle"<<";fill:"<<getColor(atNum)<<"'";
    sstr<<" y='"<<.75*fontSz/2<<"'>";
    sstr<<"<svg:tspan>";
    sstr<<label<<"</svg:tspan>";
    sstr<<"</svg:text>";
    sstr<<"</svg:g>\n";
  }

  std::string DrawingToSVG(const std::vector<int> &drawing,
                           unsigned int lineWidthMult=2,unsigned int fontSize=50){
    std::vector<int>::const_iterator pos=drawing.begin()+2;
    if(*pos!= RDKit::Drawing::BOUNDS){
      std::cerr<<"no bounds token found"<<std::endl;
      return "";
    }
    pos+=3;
    int width=300,height=300;
    width = *pos++;
    height = *pos++;
    std::ostringstream sstr;
    sstr<<"<?xml version='1.0' encoding='iso-8859-1'?>\n";
    sstr << "<svg:svg version='1.1' baseProfile='full'\n      \
        xmlns:svg='http://www.w3.org/2000/svg'\n                \
        xmlns:xlink='http://www.w3.org/1999/xlink'\n          \
        xml:space='preserve'\n";
    sstr<<"width='"<<width<<"px' height='"<<height<<"px' >\n";
    sstr<<"<svg:g transform='translate("<<width*.05<<","<<height*.05<<") scale(.85,.85)'>";
    while(pos!=drawing.end()){
      int token=*pos++;
      switch(token){
      case  RDKit::Drawing::LINE:
        drawLine(pos,sstr,lineWidthMult);
        break;
      case  RDKit::Drawing::ATOM:
        drawAtom(pos,sstr,fontSize);
        break;
      default:
        std::cerr<<"unrecognized token: "<<token<<std::endl;
      }
    }

    sstr<<"</svg:g></svg:svg>";
    return sstr.str();
  }
}

std::vector<int> MolToDrawing(const RDKit::ROMol &mol,const std::vector<int> *highlightAtoms=0){
  RDKit::RWMol *cp = new RDKit::RWMol(mol);
  try{
    RDKit::MolOps::Kekulize(*cp);
  } catch (...) {
    delete cp;
    cp = new RDKit::RWMol(mol);
  }
  if(!mol.getNumConformers()) {
    RDDepict::compute2DCoords(*cp);
  }
  std::vector<int> drawing=RDKit::Drawing::DrawMol(*cp,-1,highlightAtoms);
  delete cp;
  return drawing;
}