From 4e90f88ab76ed0c1f8e19df291e904fb1616d4a5 Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Thu, 20 Sep 2012 04:12:24 +0000
Subject: [PATCH] get dashes working in the cairo drawing; additional
 improvements to the drawing

---
 Code/Demos/RDKit/Draw/MolDrawing.h | 15 ++++++------
 Code/Demos/RDKit/Draw/demo.cpp     | 37 +++++++++++++++++++++++++-----
 2 files changed, 38 insertions(+), 14 deletions(-)

diff --git a/Code/Demos/RDKit/Draw/MolDrawing.h b/Code/Demos/RDKit/Draw/MolDrawing.h
index 56ee4801b..b9f6de554 100644
--- a/Code/Demos/RDKit/Draw/MolDrawing.h
+++ b/Code/Demos/RDKit/Draw/MolDrawing.h
@@ -137,7 +137,7 @@ namespace RDKit {
           int atnum1 = mol[*bAts]->getAtomicNum();
           int atnum2 = mol.getAtomWithIdx(a2Idx)->getAtomicNum();
 
-          if( !mol.getRingInfo()->numBondRings(bond->getIdx()) && !bond->getBondType()==Bond::AROMATIC ) {
+          if( !mol.getRingInfo()->numBondRings(bond->getIdx()) && bond->getBondType()!=Bond::AROMATIC ) {
             // acyclic bonds
             RDGeom::Point2D obv=a2-a1;
             RDGeom::Point2D perp=obv;
@@ -169,7 +169,8 @@ namespace RDKit {
                           dotsPerAngstrom*(a2.y-perp.y) );
 
               }
-            } else if( bond->getBondType()==Bond::SINGLE || bond->getBondType()==Bond::TRIPLE ) {
+            }
+            if( bond->getBondType()==Bond::SINGLE || bond->getBondType()==Bond::TRIPLE ) {
               DrawLine( res , atnum1 , atnum2 , lineWidth , false ,
                         dotsPerAngstrom*(a1.x) ,
                         dotsPerAngstrom*(a1.y) ,
@@ -238,12 +239,10 @@ namespace RDKit {
             }
           }
         }
-        double massDiff=fabs(PeriodicTable::getTable()->getAtomicWeight(mol[*bAts]->getAtomicNum()) -
-                             mol[*bAts]->getMass());
-        static double massTol=0.001;
+        int isotope = mol[*bAts]->getIsotope();
         if(mol[*bAts]->getAtomicNum()!=6 ||
            mol[*bAts]->getFormalCharge()!=0 ||
-           massDiff>massTol ){
+           isotope ){
           res.push_back(ATOM);
           res.push_back(mol[*bAts]->getAtomicNum());
           res.push_back(static_cast<ElementType>(dotsPerAngstrom*a1.x));
@@ -254,8 +253,8 @@ namespace RDKit {
             leftToRight=false;
           }
 
-          if(massDiff>massTol){
-            symbol = boost::lexical_cast<std::string>(int(mol[*bAts]->getMass()+.1))+symbol;
+          if(isotope){
+            symbol = boost::lexical_cast<std::string>(isotope)+symbol;
           }
           if(mol[*bAts]->getAtomicNum()!=6){
             int nHs=mol[*bAts]->getTotalNumHs();
diff --git a/Code/Demos/RDKit/Draw/demo.cpp b/Code/Demos/RDKit/Draw/demo.cpp
index 121a3c193..0dd1dc52b 100644
--- a/Code/Demos/RDKit/Draw/demo.cpp
+++ b/Code/Demos/RDKit/Draw/demo.cpp
@@ -1,6 +1,6 @@
-// $Id: sample.cpp 793 2008-08-17 14:33:30Z glandrum $
+// $Id$
 //
-//  Copyright (C) 2009 Greg Landrum
+//  Copyright (C) 2009-2012 Greg Landrum
 //  This file is part of the RDKit.
 //  The contents are covered by the terms of the BSD license
 //  which is included in the file license.txt, found at the root
@@ -176,6 +176,12 @@ void drawLineCairo(std::vector<int>::const_iterator &pos,
   int width=*pos++;
   cairo_set_line_width(cr,width*10);
   int dashed=*pos++;
+  if(dashed){
+    double dashes[]={20.0,20.0};
+    cairo_set_dash(cr,dashes,sizeof(dashes)/sizeof(dashes[0]),0);    
+  } else {
+    cairo_set_dash(cr,0,0,0);
+  }
   int an1=*pos++;
   int an2=*pos++;
   int xp1 = *pos++;
@@ -256,10 +262,16 @@ void MolToCairo(const ROMol &mol,cairo_t *cr,int width,int height,
                 int fontSize=14,int maxDotsPerAngstrom=30){
   PRECONDITION(cr,"no context");
   PRECONDITION(width>0 && height>0,"bad dimensions");
-  RWMol cp(mol);
-  RDKit::MolOps::Kekulize(cp);
-  RDDepict::compute2DCoords(cp);
-  std::vector<int> drawing=RDKit::Drawing::DrawMol(cp);
+  RWMol *cp = new RWMol(mol);
+  try{
+    RDKit::MolOps::Kekulize(*cp);
+  } catch (...) {
+    delete cp;
+    cp = new RDKit::RWMol(mol);
+  }
+  RDDepict::compute2DCoords(*cp);
+  std::vector<int> drawing=RDKit::Drawing::DrawMol(*cp);
+  delete cp;
 
   cairo_set_source_rgb (cr, 1.0, 1.0, 1.0);
   cairo_rectangle(cr,0,0,width,height);
@@ -381,6 +393,19 @@ void DrawDemo(){
     cairo_surface_destroy (surface);
     delete mol;
   }
+  {
+    RWMol *mol=SmilesToMol("Nccc(CCO)n",0,false);
+    mol->updatePropertyCache();
+    cairo_surface_t *surface =
+      cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 300, 300);
+    cairo_t *cr = cairo_create (surface);
+    MolToCairo(*mol,cr,300,300);
+
+    cairo_destroy (cr);
+    cairo_surface_write_to_png (surface, "mol4.png");
+    cairo_surface_destroy (surface);
+    delete mol;
+  }
 #endif
 }