Fix bond join smoothing in images of reaction products (#8210)

* Fix bond smoothing - apply atom index offset to products.
Update Hash codes.
Tweak side_by_side_images.py.

* Added hash code for new file.  Doh!

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>

Code/GraphMol/MolDraw2D/DrawMol.cpp

@@ -3485,6 +3485,10 @@ void DrawMol::smoothBondJoins() {
   // classes for the atoms and bond it involves, and people use this to
   // identify the lines for other purposes.
   for (auto atom : drawMol_->atoms()) {
+    // If there's an atom label, there is no join.
+    if (atomLabels_[atom->getIdx()]) {
+      continue;
+    }
     bool doIt = false;
     if (atom->getDegree() == 2) {
       doIt = true;
@@ -3499,15 +3503,16 @@ void DrawMol::smoothBondJoins() {
         }
       }
     }
+    int adjAtomIdx = atom->getIdx() + activeAtmIdxOffset_;
     if (doIt) {
       bool done = false;
       for (unsigned int i = 0; i < singleBondLines_.size(); ++i) {
         auto &sbl1 = bonds_[singleBondLines_[i]];
         int p1 = -1;
         int p2 = -1;
-        if (static_cast<int>(atom->getIdx()) == sbl1->atom1_) {
+        if (adjAtomIdx == sbl1->atom1_) {
           p1 = 0;
-        } else if (static_cast<int>(atom->getIdx()) == sbl1->atom2_) {
+        } else if (adjAtomIdx == sbl1->atom2_) {
           p1 = 1;
         }
         if (p1 != -1) {
@@ -3516,9 +3521,9 @@ void DrawMol::smoothBondJoins() {
               continue;
             }
             auto &sbl2 = bonds_[singleBondLines_[j]];
-            if (static_cast<int>(atom->getIdx()) == sbl2->atom1_) {
+            if (adjAtomIdx == sbl2->atom1_) {
               p2 = 0;
-            } else if (static_cast<int>(atom->getIdx()) == sbl2->atom2_) {
+            } else if (adjAtomIdx == sbl2->atom2_) {
               p2 = 1;
             }
             if (p2 != -1) {

Code/GraphMol/MolDraw2D/MolDraw2D.cpp

@@ -315,7 +315,7 @@ void MolDraw2D::drawReaction(
     frac *= 5 / delta;
   }
   xOffset = drawReactionPart(agents, 0, xOffset, offsets);
-  xOffset = drawReactionPart(products, plusWidth, xOffset, offsets);
+  drawReactionPart(products, plusWidth, xOffset, offsets);
   auto osbw = drawOptions().scaleBondWidth;
   if (reagents.empty() && products.empty() && agents.empty()) {
     // if it's an empty reaction, we won't have a DrawMol with a scale,

Code/GraphMol/MolDraw2D/catch_tests.cpp

@@ -159,8 +159,8 @@ const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testHydrogenBonds2.svg", 645414593U},
     {"testGithub3912.1.svg", 2513727029U},
     {"testGithub3912.2.svg", 3814673891U},
-    {"testGithub2976.svg", 2669316911U},
-    {"testReactionCoords.svg", 402445764U},
+    {"testGithub2976.svg", 3717916234U},
+    {"testReactionCoords.svg", 2572146469U},
     {"testAnnotationColors.svg", 2216313312U},
     {"testGithub4323_1.svg", 2536621192U},
     {"testGithub4323_2.svg", 2120846759U},
@@ -319,9 +319,9 @@ const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"lasso_highlights_6.svg", 2113147733U},
     {"lasso_highlights_7.svg", 514868036U},
     {"lasso_highlights_8.svg", 3231367552U},
-    {"testGithub6685_1.svg", 1835717197U},
-    {"testGithub6685_2.svg", 116380465U},
-    {"testGithub6685_3.svg", 409385402U},
+    {"testGithub6685_1.svg", 1206031802U},
+    {"testGithub6685_2.svg", 1946154328U},
+    {"testGithub6685_3.svg", 617181155U},
     {"testGithub6685_4.svg", 1239628830U},
     {"bad_lasso_1.svg", 726527516U},
     {"AtropCanon1.svg", 526339583U},
@@ -351,6 +351,7 @@ const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testAtomAbbreviationsClash.svg", 1847939197U},
     {"testBlackAtomsUnderHighlight.svg", 3916069581U},
     {"testSmallReactionCanvas.svg", 1288652415U},
+    {"testReactionProductSmoothCorners.svg", 1712682118U},
 };
 
 // These PNG hashes aren't completely reliable due to floating point cruft,
@@ -10264,4 +10265,30 @@ TEST_CASE("Github8195 - Reaction rendering looks odd at small scales") {
     }
   }
 #endif
-}
+}
+
+TEST_CASE("Github8209 - Reaction products not having bond corners smoothed") {
+  std::string smiles =
+      "[#6]1-[#6]=[#6]-[#6]=[#6]-[#6]=1-[#6:1](=[#8])-[#8]."
+      "[#1:7]-[#7:4](-[#1,#6:5])-[#1,#6:6]>>"
+      "[#6]1(-[#6:1](-[#7:4](-[#1,#6:5])-[#1,#6:6])"
+      "=[#8])-[#6]=[#6]-[#6]=[#6]-[#6]=1";
+  bool useSmiles = false;
+  std::unique_ptr<ChemicalReaction> rxn(
+      RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles));
+  REQUIRE(rxn);
+  MolDraw2DSVG drawer(450, 200, -1, -1, NO_FREETYPE);
+  drawer.drawReaction(*rxn);
+  drawer.finishDrawing();
+  auto text = drawer.getDrawingText();
+  std::ofstream outs("testReactionProductSmoothCorners.svg");
+  outs << text;
+  outs.close();
+  std::regex path(
+      "<path d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)' style='fill:none;stroke:#000000");
+  size_t nOccurrences =
+      std::distance(std::sregex_token_iterator(text.begin(), text.end(), path),
+                    std::sregex_token_iterator());
+  CHECK(nOccurrences == 10);
+  check_file_hash("testReactionProductSmoothCorners.svg");
+}

Code/GraphMol/MolDraw2D/rxn_test1.cpp

@@ -51,10 +51,10 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"rxn_test1_1.svg", 2645695747U},   {"rxn_test1_2.svg", 2640646320U},
     {"rxn_test1_3.svg", 2781928588U},   {"rxn_test1_4.svg", 437863065U},
     {"rxn_test1_5.svg", 2762972460U},   {"rxn_test1_6.svg", 2941728011U},
-    {"rxn_test1_7.svg", 1389845691U},   {"rxn_test2_1.svg", 3791815067U},
-    {"rxn_test2_2_1.svg", 2068242269U}, {"rxn_test2_2_2.svg", 269990608U},
-    {"rxn_test2_2_3.svg", 1544919807U}, {"rxn_test2_2_4.svg", 2015871327U},
-    {"rxn_test3_1.svg", 1359061920U},   {"rxn_test4_1.svg", 1727161552U},
+    {"rxn_test1_7.svg", 1831465890U},   {"rxn_test2_1.svg", 250961412U},
+    {"rxn_test2_2_1.svg", 3044844617U}, {"rxn_test2_2_2.svg", 269990608U},
+    {"rxn_test2_2_3.svg", 1940920292U}, {"rxn_test2_2_4.svg", 2015871327U},
+    {"rxn_test3_1.svg", 3415200111U},   {"rxn_test4_1.svg", 2557609172U},
     {"rxn_test4_2.svg", 2032588691U},
 };
 #else

Code/GraphMol/MolDraw2D/side_by_side_images.py

@@ -51,7 +51,7 @@ with open(args.outfile, 'w') as f:
         fns = fn.replace('.svg', '')
         f.write(f'''      <tr>
         <td>{fns}</td>
-        <td><img src="{d1}/{fn}" alt="{fns}"/></td>
+        <td><span style="float:right"><img src="{d1}/{fn}" alt="{fns}"/></span></td>
         <td><img src="{d2}/{fn}" alt="{fns}"/></td>
         </tr>\n''')