From 40e27a65bdc603313918221c6f6cff84dff15ca8 Mon Sep 17 00:00:00 2001
From: David Cosgrove <davidacosgroveaz@gmail.com>
Date: Mon, 12 Sep 2022 03:23:38 +0100
Subject: [PATCH 1/8] Fixed drawing of O in aldehydes. (#5515)

* Fixed drawing of O in aldehydes.

* Added DrawColour::operator!=.

* Remove unused variable.

* Export doLinesIntersect for test.

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---
 Code/GraphMol/MolDraw2D/DrawMol.cpp        | 26 +++++--
 Code/GraphMol/MolDraw2D/DrawMol.h          |  4 +-
 Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h |  1 +
 Code/GraphMol/MolDraw2D/catch_tests.cpp    | 80 +++++++++++++++++++---
 Code/GraphMol/MolDraw2D/rxn_test1.cpp      | 30 ++++----
 Code/GraphMol/MolDraw2D/test1.cpp          |  4 +-
 6 files changed, 110 insertions(+), 35 deletions(-)

diff --git a/Code/GraphMol/MolDraw2D/DrawMol.cpp b/Code/GraphMol/MolDraw2D/DrawMol.cpp
index 9b39419e7a..57fbbb480d 100644
--- a/Code/GraphMol/MolDraw2D/DrawMol.cpp
+++ b/Code/GraphMol/MolDraw2D/DrawMol.cpp
@@ -1659,11 +1659,20 @@ void DrawMol::makeDoubleBondLines(
     // in, for example, an aldehyde, such as in catch_tests.cpp's
     // testGithub_5269_2.svg, might be asymmetrically shorter, so we don't
     // want to change colour at halfway
-    if (bond->getEndAtom()->getDegree() == 1 && !(cols.first == cols.second) &&
-        fabs((l1s - l1f).lengthSq() - (l2s - l2f).lengthSq()) > 0.01) {
-      double midlen = (l1s - l1f).length() / 2.0;
-      Point2D lineDir = l2s.directionVector(l2f);
-      Point2D notMid = l2s + lineDir * midlen;
+    auto l1 = (l1s - l1f).lengthSq();
+    auto l2 = (l2s - l2f).lengthSq();
+    if ((bond->getBeginAtom()->getDegree() == 1 ||
+         bond->getEndAtom()->getDegree() == 1) &&
+        cols.first != cols.second && fabs(l1 - l2) > 0.01) {
+      double midlen = sqrt(l1) / 2.0;
+      Point2D notMid;
+      if (bond->getBeginAtom()->getDegree() == 1) {
+        Point2D lineDir = l2s.directionVector(l2f);
+        notMid = l2s + lineDir * midlen;
+      } else {
+        Point2D lineDir = l2f.directionVector(l2s);
+        notMid = l2f + lineDir * midlen;
+      }
       newBondLine(l2s, notMid, cols.first, cols.first, at1Idx, at2Idx, bondIdx,
                   noDash);
       newBondLine(notMid, l2f, cols.second, cols.second, at1Idx, at2Idx,
@@ -2840,6 +2849,11 @@ void DrawMol::doubleBondTerminal(Atom *at1, Atom *at2, double offset,
     l2s = at1_cds + perp * offset;
     l2f = doubleBondEnd(at1->getIdx(), at2->getIdx(), thirdAtom->getIdx(),
                         offset, true);
+    // if at1 has a label, need to move it so it's centred in between the
+    // two lines (Github 5511).
+    if (atomLabels_[at1->getIdx()]) {
+      atomLabels_[at1->getIdx()]->cds_ += perp * offset * 0.5;
+    }
   }
   if (swapped) {
     std::swap(l1s, l1f);
@@ -2896,8 +2910,6 @@ void DrawMol::findOtherBondVecs(const Atom *atom, const Atom *otherAtom,
   }
   for (unsigned int i = 1; i < atom->getDegree(); ++i) {
     auto thirdAtom = otherNeighbor(atom, otherAtom, i - 1, *drawMol_);
-    auto bond =
-        drawMol_->getBondBetweenAtoms(atom->getIdx(), thirdAtom->getIdx());
     Point2D const &at1_cds = atCds_[atom->getIdx()];
     Point2D const &at2_cds = atCds_[thirdAtom->getIdx()];
     otherBondVecs.push_back(at1_cds.directionVector(at2_cds));
diff --git a/Code/GraphMol/MolDraw2D/DrawMol.h b/Code/GraphMol/MolDraw2D/DrawMol.h
index 5d82559b8e..35765ed611 100644
--- a/Code/GraphMol/MolDraw2D/DrawMol.h
+++ b/Code/GraphMol/MolDraw2D/DrawMol.h
@@ -319,8 +319,8 @@ double getHighlightBondWidth(
 Point2D calcPerpendicular(const Point2D &cds1, const Point2D &cds2);
 Point2D calcInnerPerpendicular(const Point2D &cds1, const Point2D &cds2,
                                const Point2D &cds3);
-// return a point that is end1 moved so as not to clash with any of the
-// rects of a label.  end1 to end2 and the coords of 2 ends of a bond.
+// return a point that is moveEnd moved so as not to clash with any of the
+// rects of a label.  moveEnd to end2 are the coords of 2 ends of a bond.
 void adjustBondEndForString(
     const Point2D &end2, double padding,
     const std::vector<std::shared_ptr<StringRect>> &rects, Point2D &moveEnd);
diff --git a/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h b/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h
index b5c5f05545..c8b89f176d 100644
--- a/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h
+++ b/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h
@@ -34,6 +34,7 @@ struct DrawColour {
   bool operator==(const DrawColour &other) const {
     return r == other.r && g == other.g && b == other.b && a == other.a;
   }
+  bool operator!=(const DrawColour &other) const { return !(*this == other); }
   bool feq(const DrawColour &other, double tol = 0.001,
            bool ignoreAlpha = true) const {
     return fabs(r - other.r) <= tol && fabs(g - other.g) <= tol &&
diff --git a/Code/GraphMol/MolDraw2D/catch_tests.cpp b/Code/GraphMol/MolDraw2D/catch_tests.cpp
index 2f6261ecd4..fa9b81c291 100644
--- a/Code/GraphMol/MolDraw2D/catch_tests.cpp
+++ b/Code/GraphMol/MolDraw2D/catch_tests.cpp
@@ -86,8 +86,8 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testHandDrawn-2.svg", 2605087576U},
     {"testHandDrawn-3.svg", 1015633173U},
     {"testHandDrawn-4.svg", 830784921U},
-    {"testHandDrawn-5a.svg", 3582113444U},
-    {"testHandDrawn-5b.svg", 2974975931U},
+    {"testHandDrawn-5a.svg", 2845825621U},
+    {"testHandDrawn-5b.svg", 476521352U},
     {"testBrackets-1a.svg", 3257646535U},
     {"testBrackets-1b.svg", 776088825U},
     {"testBrackets-1c.svg", 3257646535U},
@@ -97,10 +97,10 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testBrackets-2b.svg", 1408188695U},
     {"testBrackets-2c.svg", 728321376U},
     {"testBrackets-2d.svg", 1408188695U},
-    {"testBrackets-3a.svg", 630742918U},
+    {"testBrackets-3a.svg", 791450653U},
     {"testBrackets-4a.svg", 769125635U},
     {"testBrackets-4b.svg", 4066682338U},
-    {"testBrackets-5a.svg", 2845825621U},
+    {"testBrackets-5a.svg", 1388227932U},
     {"testSGroupData-1a.svg", 1463366807U},
     {"testSGroupData-1b.svg", 223883202U},
     {"testSGroupData-2a.svg", 3547547260U},
@@ -174,8 +174,8 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testGithub4519_2.svg", 2515716875U},
     {"testGithub4519_3.svg", 1017109741U},
     {"testGithub4519_4.svg", 645908829U},
-    {"testBaseFontSize.1a.svg", 3213010239U},
-    {"testBaseFontSize.1b.svg", 1147057058U},
+    {"testBaseFontSize.1a.svg", 3939288880U},
+    {"testBaseFontSize.1b.svg", 2617787443U},
     {"testBaseFontSize.2a.svg", 1031690455U},
     {"testBaseFontSize.2b.svg", 3440038194U},
     {"testFlexiCanvas.1a.svg", 3145560884U},
@@ -214,7 +214,7 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testGithub_5061.svg", 1947248304U},
     {"testGithub_5185.svg", 2944445711U},
     {"testGithub_5269_1.svg", 3660737449U},
-    {"testGithub_5269_2.svg", 2580783009U},
+    {"testGithub_5269_2.svg", 3987247770U},
     {"test_classes_wavy_bonds.svg", 1271445012U},
     {"testGithub_5383_1.svg", 1391972140U},
     {"github5156_1.svg", 695855770U},
@@ -228,7 +228,7 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"acs1996_4.svg", 55815911U},
     {"acs1996_5.svg", 362495488U},
     {"acs1996_6.svg", 4274355858U},
-    {"acs1996_7.svg", 729001900U},
+    {"acs1996_7.svg", 3993278473U},
     {"acs1996_8.svg", 2032371436U},
     {"acs1996_9.svg", 2589221154U},
     {"acs1996_10.svg", 4037187899U},
@@ -244,6 +244,8 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"bond_highlights_7.svg", 2936856212U},
     {"bond_highlights_8.svg", 64473502U},
     {"testGithub5486_1.svg", 1149144091U},
+    {"testGithub5511_1.svg", 940106456U},
+    {"testGithub5511_2.svg", 1448975272U}
 };
 
 // These PNG hashes aren't completely reliable due to floating point cruft,
@@ -263,7 +265,7 @@ static const std::map<std::string, std::hash_result_t> PNG_HASHES = {
     {"testHandDrawn-2.png", 2979412913U},
     {"testHandDrawn-3.png", 1765396301U},
     {"testHandDrawn-4.png", 2989933219U},
-    {"testHandDrawn-5.png", 3794840403U},
+    {"testHandDrawn-5.png", 1526220279U},
     {"testGithub4323_1.png", 3711520691U},
     {"testGithub4323_3.png", 2300228708U},
     {"testFlexiCanvas.2a.png", 3618977786U},
@@ -5713,3 +5715,63 @@ M  END)CTAB"_ctab;
     }
   }
 }
+
+TEST_CASE("Bad O position in aldehydes", "") {
+  std::string nameBase("testGithub5511_");
+  {
+    auto m1 = "O=Cc1cccc(C=O)c1"_smiles;
+    REQUIRE(m1);
+    MolDraw2DUtils::prepareMolForDrawing(*m1);
+    MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
+    drawer.drawOptions().addAtomIndices = true;
+    drawer.drawMolecule(*m1);
+    drawer.finishDrawing();
+    auto text = drawer.getDrawingText();
+    std::string filename = nameBase + "1.svg";
+    std::ofstream outs(filename);
+    outs << text;
+    outs.flush();
+    check_file_hash(filename);
+  }
+  {
+    auto m = R"CTAB(
+     RDKit          2D
+
+ 11 11  0  0  0  0  0  0  0  0999 V2000
+   -4.2885    0.5445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.9895    1.2945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.6818    0.5394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3738    1.2945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9342    0.5394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.2422    1.2945    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.2422    2.7945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9342   -0.9708    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3738   -1.7262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.6818   -0.9708    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.9895   -1.7262    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
+  5  6  1  0
+  6  7  2  0
+  5  8  2  0
+  8  9  1  0
+  9 10  2  0
+ 10 11  1  0
+ 10  3  1  0
+M  END
+)CTAB"_ctab;
+    REQUIRE(m);
+    MolDraw2DSVG drawer(250, 250, -1, -1);
+    drawer.drawOptions().addAtomIndices = true;
+    drawer.drawMolecule(*m);
+    drawer.finishDrawing();
+    std::string text = drawer.getDrawingText();
+    std::string filename = nameBase + "2.svg";
+    std::ofstream outs(filename);
+    outs << text;
+    outs.flush();
+    check_file_hash(filename);
+  }
+}
diff --git a/Code/GraphMol/MolDraw2D/rxn_test1.cpp b/Code/GraphMol/MolDraw2D/rxn_test1.cpp
index 023103c71d..e9236b7757 100644
--- a/Code/GraphMol/MolDraw2D/rxn_test1.cpp
+++ b/Code/GraphMol/MolDraw2D/rxn_test1.cpp
@@ -48,25 +48,25 @@ namespace {
 static const bool DELETE_WITH_GOOD_HASH = true;
 #ifdef RDK_BUILD_FREETYPE_SUPPORT
 static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
-    {"rxn_test1_1.svg", 46725873U},   {"rxn_test1_2.svg", 2822273042U},
+    {"rxn_test1_1.svg", 46725873U},     {"rxn_test1_2.svg", 2822273042U},
     {"rxn_test1_3.svg", 3749362740U},   {"rxn_test1_4.svg", 2720989271U},
-    {"rxn_test1_5.svg", 3245376196U},   {"rxn_test1_6.svg", 1371904127U},
-    {"rxn_test1_7.svg", 3410910592U},   {"rxn_test2_1.svg", 409647324U},
-    {"rxn_test2_2_1.svg", 1275078201U},  {"rxn_test2_2_2.svg", 2689198952U},
+    {"rxn_test1_5.svg", 3245376196U},   {"rxn_test1_6.svg", 1201850884U},
+    {"rxn_test1_7.svg", 3483485271U},   {"rxn_test2_1.svg", 409647324U},
+    {"rxn_test2_2_1.svg", 1275078201U}, {"rxn_test2_2_2.svg", 2689198952U},
     {"rxn_test2_2_3.svg", 3750657998U}, {"rxn_test2_2_4.svg", 844519751U},
-    {"rxn_test3_1.svg", 3370327616U},    {"rxn_test4_1.svg", 1951283390U},
-    {"rxn_test4_2.svg", 1355336361U},
+    {"rxn_test3_1.svg", 2642962178U},   {"rxn_test4_1.svg", 2201210664U},
+    {"rxn_test4_2.svg", 3875105540U},
 };
 #else
 static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"rxn_test1_1.svg", 3077363070U},   {"rxn_test1_2.svg", 343913088U},
     {"rxn_test1_3.svg", 1743857837U},   {"rxn_test1_4.svg", 421748462U},
-    {"rxn_test1_5.svg", 2287478842U},   {"rxn_test1_6.svg", 1059343942U},
-    {"rxn_test1_7.svg", 301064722U},   {"rxn_test2_1.svg", 2821179072U},
-    {"rxn_test2_2_1.svg", 1304295583U},  {"rxn_test2_2_2.svg", 1361778996U},
+    {"rxn_test1_5.svg", 2287478842U},   {"rxn_test1_6.svg", 1657115641U},
+    {"rxn_test1_7.svg", 2526900298U},   {"rxn_test2_1.svg", 2821179072U},
+    {"rxn_test2_2_1.svg", 1304295583U}, {"rxn_test2_2_2.svg", 1361778996U},
     {"rxn_test2_2_3.svg", 2608405344U}, {"rxn_test2_2_4.svg", 574045696U},
-    {"rxn_test3_1.svg", 265057038U},   {"rxn_test4_1.svg", 684852697U},
-    {"rxn_test4_2.svg", 2675536892U},
+    {"rxn_test3_1.svg", 2373233565U},   {"rxn_test4_1.svg", 1661501846U},
+    {"rxn_test4_2.svg", 638174091U},
 };
 #endif
 
@@ -83,12 +83,12 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
 static const std::map<std::string, std::hash_result_t> PNG_HASHES = {
     {"rxn_test1_1.png", 3579100589U},  {"rxn_test1_2.png", 3996724834U},
     {"rxn_test1_3.png", 4153817948U},  {"rxn_test1_4.png", 4175225545U},
-    {"rxn_test1_5.png", 3400977230U},  {"rxn_test1_6.png", 2636974466U},
-    {"rxn_test1_7.png", 4164917700U},  {"rxn_test2_1.png", 2654417911U},
+    {"rxn_test1_5.png", 3400977230U},  {"rxn_test1_6.png", 1819663219U},
+    {"rxn_test1_7.png", 3834655428U},  {"rxn_test2_1.png", 2654417911U},
     {"rxn_test2_2_1.png", 997060634U}, {"rxn_test2_2_2.png", 2090979640U},
     {"rxn_test2_2_3.png", 857100114U}, {"rxn_test2_2_4.png", 610638635U},
-    {"rxn_test3_1.png", 501226401U},  {"rxn_test4_1.png", 4259011005U},
-    {"rxn_test4_2.png", 2214400478U},
+    {"rxn_test3_1.png", 2130633490U},  {"rxn_test4_1.png", 2917597113U},
+    {"rxn_test4_2.png", 3031850382U},
 };
 
 std::hash_result_t hash_file(const std::string &filename) {
diff --git a/Code/GraphMol/MolDraw2D/test1.cpp b/Code/GraphMol/MolDraw2D/test1.cpp
index e8ac38217a..644c87f82a 100644
--- a/Code/GraphMol/MolDraw2D/test1.cpp
+++ b/Code/GraphMol/MolDraw2D/test1.cpp
@@ -158,7 +158,7 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"test21_1.svg", 3363530709U},
     {"test21_2.svg", 3470002858U},
     {"test22_1.svg", 3716192373U},
-    {"test22_2.svg", 1926484323U},
+    {"test22_2.svg", 3812042529U},
     {"testGithub3112_1.svg", 3236038294U},
     {"testGithub3112_2.svg", 1810059147U},
     {"testGithub3112_3.svg", 135218742U},
@@ -287,7 +287,7 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"test20_3.svg", 968052569U},
     {"test20_4.svg", 2298201486U},
     {"test22_1.svg", 3716192373U},
-    {"test22_2.svg", 2843125073U},
+    {"test22_2.svg", 3258508270U},
     {"testGithub3112_1.svg", 2613843920U},
     {"testGithub3112_2.svg", 3639942551U},
     {"testGithub3112_3.svg", 1107662781U},

From cbdec52048aceddc548e7b09325cdd78d3c480c1 Mon Sep 17 00:00:00 2001
From: David Cosgrove <davidacosgroveaz@gmail.com>
Date: Tue, 13 Sep 2022 11:18:20 +0100
Subject: [PATCH 2/8] Fixed scale (#5519)

* Make ACS mode work properly in fixed size drawers.

* Extra comment.

* Update hash codes.

* Export doLinesIntersect.

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---
 Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp |  4 +
 Code/GraphMol/MolDraw2D/catch_tests.cpp    | 97 ++++++++++++++++------
 2 files changed, 75 insertions(+), 26 deletions(-)

diff --git a/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp b/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp
index 884b54381d..b594ff6f6f 100644
--- a/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp
+++ b/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp
@@ -440,6 +440,10 @@ void setACS1996Options(MolDrawOptions &opts, double meanBondLen) {
   // the guideline is for a bond length of 14.4px, and we set things up
   // in pixels per Angstrom.
   opts.scalingFactor = 14.4 / meanBondLen;
+  // setting the fixedBondLength means the drawing won't be scaled
+  // up in a drawer of defined size, so the bond length won't exceed
+  // 14.4 pixels.
+  opts.fixedBondLength = 14.4 / meanBondLen;
   // offset for multiple bonds is 18% of the bond length.
   opts.multipleBondOffset = 0.18;
   opts.highlightBondWidthMultiplier = 32;
diff --git a/Code/GraphMol/MolDraw2D/catch_tests.cpp b/Code/GraphMol/MolDraw2D/catch_tests.cpp
index fa9b81c291..dc02c8e054 100644
--- a/Code/GraphMol/MolDraw2D/catch_tests.cpp
+++ b/Code/GraphMol/MolDraw2D/catch_tests.cpp
@@ -113,10 +113,10 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testPositionVariation-4.svg", 886758688U},
     {"testNoAtomLabels-1.svg", 2648234379U},
     {"testNoAtomLabels-2.svg", 3213096674U},
-    {"testQueryBonds-1a.svg", 674261460U},
-    {"testQueryBonds-1b.svg", 1450309284U},
-    {"testQueryBonds-1c.svg", 74333858U},
-    {"testQueryBonds-2.svg", 1873442183U},
+    {"testQueryBonds-1a.svg", 3288272531U},
+    {"testQueryBonds-1b.svg", 1706839957U},
+    {"testQueryBonds-1c.svg", 333519907U},
+    {"testQueryBonds-2.svg", 69341882U},
     {"testLinkNodes-2-0.svg", 2952965907U},
     {"testLinkNodes-2-30.svg", 4117540200U},
     {"testLinkNodes-2-60.svg", 520576199U},
@@ -203,9 +203,9 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testFlexiCanvas.7b.svg", 4094511140U},
     {"testFlexiCanvas.7c.svg", 918094125U},
     {"testFlexiCanvas.7d.svg", 918094125U},
-    {"testGithub4764.sz1.svg", 2369071854U},
-    {"testGithub4764.sz2.svg", 39314673U},
-    {"testGithub4764.sz3.svg", 901101991U},
+    {"testGithub4764.sz1.svg", 493786705U},
+    {"testGithub4764.sz2.svg", 2704253898U},
+    {"testGithub4764.sz3.svg", 1328896014U},
     {"testDrawArc1.svg", 4039810147U},
     {"testMetalWedges.svg", 3278785383U},
     {"testVariableLegend_1.svg", 3914441319U},
@@ -213,8 +213,8 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"testVariableLegend_3.svg", 1996551457U},
     {"testGithub_5061.svg", 1947248304U},
     {"testGithub_5185.svg", 2944445711U},
-    {"testGithub_5269_1.svg", 3660737449U},
-    {"testGithub_5269_2.svg", 3987247770U},
+    {"testGithub_5269_1.svg", 2368496794U},
+    {"testGithub_5269_2.svg", 567813292U},
     {"test_classes_wavy_bonds.svg", 1271445012U},
     {"testGithub_5383_1.svg", 1391972140U},
     {"github5156_1.svg", 695855770U},
@@ -222,17 +222,18 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"github5156_3.svg", 3284451122U},
     {"test_molblock_wedges.svg", 1106580037U},
     {"github5383_1.svg", 2353351393U},
-    {"acs1996_1.svg", 773284691U},
-    {"acs1996_2.svg", 2884688866U},
-    {"acs1996_3.svg", 2540534250U},
-    {"acs1996_4.svg", 55815911U},
-    {"acs1996_5.svg", 362495488U},
-    {"acs1996_6.svg", 4274355858U},
-    {"acs1996_7.svg", 3993278473U},
-    {"acs1996_8.svg", 2032371436U},
-    {"acs1996_9.svg", 2589221154U},
-    {"acs1996_10.svg", 4037187899U},
-    {"acs1996_11.svg", 3667521405U},
+    {"acs1996_1.svg", 51426601U},
+    {"acs1996_2.svg", 833573044U},
+    {"acs1996_3.svg", 4007912653U},
+    {"acs1996_4.svg", 3372558370U},
+    {"acs1996_5.svg", 2883542240U},
+    {"acs1996_6.svg", 1380727178U},
+    {"acs1996_7.svg", 763391533U},
+    {"acs1996_8.svg", 939325262U},
+    {"acs1996_9.svg", 2607143500U},
+    {"acs1996_10.svg", 199499735U},
+    {"acs1996_11.svg", 2121789178U},
+    {"acs1996_12.svg", 2233727631U},
     {"test_unspec_stereo.svg", 599119798U},
     {"light_blue_h_no_label_1.svg", 3735371135U},
     {"bond_highlights_1.svg", 1150579427U},
@@ -241,7 +242,7 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"bond_highlights_4.svg", 3500788273U},
     {"bond_highlights_5.svg", 3500788273U},
     {"bond_highlights_6.svg", 3008628729U},
-    {"bond_highlights_7.svg", 2936856212U},
+    {"bond_highlights_7.svg", 3900018634U},
     {"bond_highlights_8.svg", 64473502U},
     {"testGithub5486_1.svg", 1149144091U},
     {"testGithub5511_1.svg", 940106456U},
@@ -270,13 +271,13 @@ static const std::map<std::string, std::hash_result_t> PNG_HASHES = {
     {"testGithub4323_3.png", 2300228708U},
     {"testFlexiCanvas.2a.png", 3618977786U},
     {"testFlexiCanvas.2b.png", 2780757414U},
-    {"testGithub4764.sz1.png", 3594553035U},
-    {"testGithub4764.sz2.png", 1203143863U},
-    {"testGithub4764.sz3.png", 310017790U},
+    {"testGithub4764.sz1.png", 2320783268U},
+    {"testGithub4764.sz2.png", 3297570843U},
+    {"testGithub4764.sz3.png", 2178018272U},
     {"testGithub4238_1.png", 458925131U},
     {"github5383_1.png", 2963331215U},
-    {"acs1996_1.png", 2814011866U},
-    {"acs1996_2.png", 3118288179U}};
+    {"acs1996_1.png", 2674458798U},
+    {"acs1996_2.png", 83755168U}};
 
 std::hash_result_t hash_file(const std::string &filename) {
   std::ifstream ifs(filename, std::ios_base::binary);
@@ -4812,6 +4813,7 @@ TEST_CASE("ACS 1996 mode") {
   SECTION("basics") {
     std::string nameBase = "acs1996_";
 #if 1
+
     {
       auto m = R"CTAB(mol1
   ChemDraw05162216032D
@@ -5382,6 +5384,49 @@ M  END
       outs.close();
       check_file_hash(nameBase + "11.svg");
     }
+#endif
+#if 1
+    auto drawnBondLength = [&](const std::string &r1,
+                               const std::string &t) -> double {
+      std::regex regex1(r1);
+      auto match_begin =
+          std::sregex_iterator(t.begin(), t.end(), regex1);
+      auto match_end = std::sregex_iterator();
+      std::vector<Point2D> ends;
+      for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
+        std::smatch match = *i;
+        ends.push_back(Point2D(std::stod(match[1]), std::stod(match[2])));
+        ends.push_back(Point2D(std::stod(match[3]), std::stod(match[4])));
+      }
+      return (ends[0]-ends[1]).length();
+    };
+
+    {
+      // make sure it also works with an arbitrarily sized drawer.
+      auto m = "c1ccccc1"_smiles;
+      REQUIRE(m);
+      MolDraw2DUtils::prepareMolForDrawing(*m);
+      MolDraw2DSVG drawer(500, 500);
+      MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 12", nullptr, nullptr);
+      drawer.finishDrawing();
+      std::string text = drawer.getDrawingText();
+      std::ofstream outs(nameBase + "12.svg");
+      outs << text;
+      outs.flush();
+      outs.close();
+
+      std::string regex =
+          R"(class='bond-0 atom-0 atom-1' d='M ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*)')";
+      double dbl = drawnBondLength(regex, text);
+      // the bonds should all be 14.4 long, but the SVG is only written
+      // to 1 decimal place, so rounding errors are largish.
+      REQUIRE(dbl == Approx(14.4253));
+      regex =
+          R"(class='bond-1 atom-1 atom-2' d='M ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*)')";
+      dbl = drawnBondLength(regex, text);
+      REQUIRE(dbl == Approx(14.4));
+      check_file_hash(nameBase + "12.svg");
+    }
 #endif
   }
 }

From c1f68ea574b16a63158bab6fb0b00299f785a69a Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Tue, 13 Sep 2022 14:49:45 +0200
Subject: [PATCH 3/8] Fixes #5505: problems when kekulizing molecules with
 query bonds (#5550)

* Fixes #5505

* Switch to using hasBondTypeQuery()

* update the docs

* ensure we still fail with non-ring aromatic atoms

* changes in response to review
---
 Code/GraphMol/Kekulize.cpp       | 174 +++++++++++++++++--------------
 Code/GraphMol/MolOps.h           |   8 +-
 Code/GraphMol/Wrap/MolOps.cpp    |  36 ++++---
 Code/GraphMol/catch_graphmol.cpp |  54 +++++++++-
 4 files changed, 177 insertions(+), 95 deletions(-)

diff --git a/Code/GraphMol/Kekulize.cpp b/Code/GraphMol/Kekulize.cpp
index 780f31b890..a087b7cff9 100644
--- a/Code/GraphMol/Kekulize.cpp
+++ b/Code/GraphMol/Kekulize.cpp
@@ -8,6 +8,7 @@
 //  of the RDKit source tree.
 //
 #include <GraphMol/RDKitBase.h>
+#include <GraphMol/QueryOps.h>
 #include <GraphMol/Canon.h>
 #include <GraphMol/Rings.h>
 #include <GraphMol/SanitException.h>
@@ -503,19 +504,28 @@ void kekulizeFused(RWMol &mol, const VECT_INT_VECT &arings,
 namespace MolOps {
 namespace details {
 void KekulizeFragment(RWMol &mol, const boost::dynamic_bitset<> &atomsToUse,
-                      const boost::dynamic_bitset<> &bondsToUse,
-                      bool markAtomsBonds, unsigned int maxBackTracks) {
+                      boost::dynamic_bitset<> bondsToUse, bool markAtomsBonds,
+                      unsigned int maxBackTracks) {
   PRECONDITION(atomsToUse.size() == mol.getNumAtoms(),
                "atomsToUse is wrong size");
   PRECONDITION(bondsToUse.size() == mol.getNumBonds(),
                "bondsToUse is wrong size");
+  // if there are no atoms to use we can directly return
+  if (atomsToUse.none()) {
+    return;
+  }
 
-  // there's no point doing kekulization if there are no aromatic bonds:
+  // there's no point doing kekulization if there are no aromatic bonds
+  // without queries:
   bool foundAromatic = false;
   for (const auto bond : mol.bonds()) {
-    if (bondsToUse[bond->getIdx()] && bond->getIsAromatic()) {
-      foundAromatic = true;
-      break;
+    if (bondsToUse[bond->getIdx()]) {
+      if (QueryOps::hasBondTypeQuery(*bond)) {
+        // we don't kekulize bonds with bond type queries
+        bondsToUse[bond->getIdx()] = 0;
+      } else if (bond->getIsAromatic()) {
+        foundAromatic = true;
+      }
     }
   }
 
@@ -524,7 +534,8 @@ void KekulizeFragment(RWMol &mol, const boost::dynamic_bitset<> &atomsToUse,
   // checking
   auto numAtoms = mol.getNumAtoms();
   INT_VECT valences(numAtoms);
-  boost::dynamic_bitset<> dummyAts(mol.getNumAtoms());
+  boost::dynamic_bitset<> dummyAts(numAtoms);
+
   for (auto atom : mol.atoms()) {
     if (!atomsToUse[atom->getIdx()]) {
       continue;
@@ -541,82 +552,91 @@ void KekulizeFragment(RWMol &mol, const boost::dynamic_bitset<> &atomsToUse,
   if (!foundAromatic) {
     return;
   }
-
-  // A bit on the state of the molecule at this point
-  // - aromatic and non aromatic atoms and bonds may be mixed up
-
-  // - for all aromatic bonds it is assumed that that both the following
-  //   are true:
-  //       - getIsAromatic returns true
-  //       - getBondType return aromatic
-  // - all aromatic atoms return true for "getIsAromatic"
-
-  // first find all the simple rings in the molecule that are not
-  // completely composed of dummy atoms
-  VECT_INT_VECT allringsSSSR;
-  if (!mol.getRingInfo()->isInitialized()) {
-    MolOps::findSSSR(mol, allringsSSSR);
-  }
-  const VECT_INT_VECT &allrings =
-      allringsSSSR.empty() ? mol.getRingInfo()->atomRings() : allringsSSSR;
-  VECT_INT_VECT arings;
-  arings.reserve(allrings.size());
-  auto copyAtomRingsWithinFragmentUnlessAllDummy =
-      [&atomsToUse, &dummyAts](const INT_VECT &ring) {
-        bool ringOk = false;
-        for (auto ai : ring) {
-          if (!atomsToUse[ai]) {
-            return false;
-          }
-          if (!dummyAts[ai]) {
-            ringOk = true;
+  // if any bonds to kekulize then give it a try:
+  if (bondsToUse.any()) {
+    // A bit on the state of the molecule at this point
+    // - aromatic and non aromatic atoms and bonds may be mixed up
+
+    // - for all aromatic bonds it is assumed that that both the following
+    //   are true:
+    //       - getIsAromatic returns true
+    //       - getBondType return aromatic
+    // - all aromatic atoms return true for "getIsAromatic"
+
+    // first find all the simple rings in the molecule that are not
+    // completely composed of dummy atoms
+    VECT_INT_VECT allringsSSSR;
+    if (!mol.getRingInfo()->isInitialized()) {
+      MolOps::findSSSR(mol, allringsSSSR);
+    }
+    const VECT_INT_VECT &allrings =
+        allringsSSSR.empty() ? mol.getRingInfo()->atomRings() : allringsSSSR;
+    VECT_INT_VECT arings;
+    arings.reserve(allrings.size());
+    auto copyAtomRingsWithinFragmentUnlessAllDummy =
+        [&atomsToUse, &dummyAts](const INT_VECT &ring) {
+          bool ringOk = false;
+          for (auto ai : ring) {
+            if (!atomsToUse[ai]) {
+              return false;
+            }
+            if (!dummyAts[ai]) {
+              ringOk = true;
+            }
           }
+          return ringOk;
+        };
+    std::copy_if(allrings.begin(), allrings.end(), std::back_inserter(arings),
+                 copyAtomRingsWithinFragmentUnlessAllDummy);
+
+    VECT_INT_VECT allbrings;
+    RingUtils::convertToBonds(arings, allbrings, mol);
+    VECT_INT_VECT brings;
+    brings.reserve(allbrings.size());
+    auto copyBondRingsWithinFragment = [&bondsToUse](const INT_VECT &ring) {
+      return std::all_of(ring.begin(), ring.end(), [&bondsToUse](const int bi) {
+        return bondsToUse[bi];
+      });
+    };
+    VECT_INT_VECT aringsRemaining;
+    aringsRemaining.reserve(arings.size());
+    for (unsigned i = 0; i < allbrings.size(); ++i) {
+      if (copyBondRingsWithinFragment(allbrings[i])) {
+        brings.push_back(allbrings[i]);
+        aringsRemaining.push_back(arings[i]);
+      }
+    }
+    arings = std::move(aringsRemaining);
+
+    // make a neighbor map for the rings i.e. a ring is a
+    // neighbor to another candidate ring if it shares at least
+    // one bond
+    // useful to figure out fused systems
+    INT_INT_VECT_MAP neighMap;
+    RingUtils::makeRingNeighborMap(brings, neighMap);
+
+    int curr = 0;
+    int cnrs = rdcast<int>(arings.size());
+    boost::dynamic_bitset<> fusDone(cnrs);
+    while (curr < cnrs) {
+      INT_VECT fused;
+      RingUtils::pickFusedRings(curr, neighMap, fused, fusDone);
+      VECT_INT_VECT frings(fused.size());
+      std::transform(fused.begin(), fused.end(), frings.begin(),
+                     [&arings](const int ri) { return arings[ri]; });
+      kekulizeFused(mol, frings, maxBackTracks);
+      int rix;
+      for (rix = 0; rix < cnrs; ++rix) {
+        if (!fusDone[rix]) {
+          curr = rix;
+          break;
         }
-        return ringOk;
-      };
-  std::copy_if(allrings.begin(), allrings.end(), std::back_inserter(arings),
-               copyAtomRingsWithinFragmentUnlessAllDummy);
-
-  VECT_INT_VECT allbrings;
-  RingUtils::convertToBonds(arings, allbrings, mol);
-  VECT_INT_VECT brings;
-  brings.reserve(allbrings.size());
-  auto copyBondRingsWithinFragment = [&bondsToUse](const INT_VECT &ring) {
-    return std::all_of(ring.begin(), ring.end(),
-                       [&bondsToUse](const int bi) { return bondsToUse[bi]; });
-  };
-  std::copy_if(allbrings.begin(), allbrings.end(), std::back_inserter(brings),
-               copyBondRingsWithinFragment);
-
-  // make a neighbor map for the rings i.e. a ring is a
-  // neighbor to another candidate ring if it shares at least
-  // one bond
-  // useful to figure out fused systems
-  INT_INT_VECT_MAP neighMap;
-  RingUtils::makeRingNeighborMap(brings, neighMap);
-
-  int curr = 0;
-  int cnrs = rdcast<int>(arings.size());
-  boost::dynamic_bitset<> fusDone(cnrs);
-  while (curr < cnrs) {
-    INT_VECT fused;
-    RingUtils::pickFusedRings(curr, neighMap, fused, fusDone);
-    VECT_INT_VECT frings(fused.size());
-    std::transform(fused.begin(), fused.end(), frings.begin(),
-                   [&arings](const int ri) { return arings[ri]; });
-    kekulizeFused(mol, frings, maxBackTracks);
-    int rix;
-    for (rix = 0; rix < cnrs; ++rix) {
-      if (!fusDone[rix]) {
-        curr = rix;
+      }
+      if (rix == cnrs) {
         break;
       }
     }
-    if (rix == cnrs) {
-      break;
-    }
   }
-
   if (markAtomsBonds) {
     // if we want the atoms and bonds to be marked non-aromatic do
     // that here.
diff --git a/Code/GraphMol/MolOps.h b/Code/GraphMol/MolOps.h
index 88abdc1f33..464650b58f 100644
--- a/Code/GraphMol/MolOps.h
+++ b/Code/GraphMol/MolOps.h
@@ -615,8 +615,10 @@ RDKIT_GRAPHMOL_EXPORT void adjustHs(RWMol &mol);
    double bond if we hit a wall in the kekulization process
 
    <b>Notes:</b>
-     - even if \c markAtomsBonds is \c false the \c BondType for all aromatic
-       bonds will be changed from \c RDKit::Bond::AROMATIC to \c
+     - this does not modify query bonds which have bond type queries (like those
+       which come from SMARTS) or rings containing them.
+     - even if \c markAtomsBonds is \c false the \c BondType for all modified
+       aromatic bonds will be changed from \c RDKit::Bond::AROMATIC to \c
        RDKit::Bond::SINGLE or RDKit::Bond::DOUBLE during Kekulization.
 
 */
@@ -1018,7 +1020,7 @@ namespace details {
 //! not recommended for use in other code
 RDKIT_GRAPHMOL_EXPORT void KekulizeFragment(
     RWMol &mol, const boost::dynamic_bitset<> &atomsToUse,
-    const boost::dynamic_bitset<> &bondsToUse, bool markAtomsBonds = true,
+    boost::dynamic_bitset<> bondsToUse, bool markAtomsBonds = true,
     unsigned int maxBackTracks = 100);
 }  // namespace details
 
diff --git a/Code/GraphMol/Wrap/MolOps.cpp b/Code/GraphMol/Wrap/MolOps.cpp
index 8d5e106698..63d635be38 100644
--- a/Code/GraphMol/Wrap/MolOps.cpp
+++ b/Code/GraphMol/Wrap/MolOps.cpp
@@ -1495,20 +1495,28 @@ to the terminal dummy atoms.\n\
 
     // ------------------------------------------------------------------------
     docString =
-        "Kekulizes the molecule\n\
-\n\
-  ARGUMENTS:\n\
-\n\
-    - mol: the molecule to use\n\
-\n\
-    - clearAromaticFlags: (optional) if this toggle is set, all atoms and bonds in the \n\
-      molecule will be marked non-aromatic following the kekulization.\n\
-      Default value is False.\n\
-\n\
-  NOTES:\n\
-\n\
-    - The molecule is modified in place.\n\
-\n";
+        R"DOC(Kekulizes the molecule
+
+  ARGUMENTS:
+
+    - mol: the molecule to use
+
+    - clearAromaticFlags: (optional) if this toggle is set, all atoms and bonds in the
+      molecule will be marked non-aromatic following the kekulization.
+      Default value is False.
+
+  NOTES:
+
+    - The molecule is modified in place.
+
+    - this does not modify query bonds which have bond type queries (like those
+      which come from SMARTS) or rings containing them.
+
+    - even if clearAromaticFlags is False the BondType for all modified
+      aromatic bonds will be changed from AROMATIC to SINGLE or DOUBLE
+      Kekulization.
+
+)DOC";
     python::def("Kekulize", kekulizeMol,
                 (python::arg("mol"), python::arg("clearAromaticFlags") = false),
                 docString.c_str());
diff --git a/Code/GraphMol/catch_graphmol.cpp b/Code/GraphMol/catch_graphmol.cpp
index e22bd39f57..b32048b647 100644
--- a/Code/GraphMol/catch_graphmol.cpp
+++ b/Code/GraphMol/catch_graphmol.cpp
@@ -18,6 +18,7 @@
 #include <GraphMol/RDKitBase.h>
 #include <GraphMol/new_canon.h>
 #include <GraphMol/RDKitQueries.h>
+#include <GraphMol/QueryOps.h>
 #include <GraphMol/Chirality.h>
 #include <GraphMol/MonomerInfo.h>
 #include <GraphMol/FileParsers/FileParsers.h>
@@ -2751,4 +2752,55 @@ TEST_CASE(
     REQUIRE(m);
     CHECK(m->getAtomWithIdx(0)->getNumRadicalElectrons() == 0);
   }
-}
\ No newline at end of file
+}
+
+TEST_CASE(
+    "github #5505: Running kekulization on mols with query bonds will either fail or return incorrect results") {
+  SECTION("as reported") {
+    auto m = "[#6]-c1cccc(-[#6])c1"_smarts;
+    REQUIRE(m);
+    REQUIRE(m->getBondWithIdx(2)->hasQuery());
+    REQUIRE(m->getBondWithIdx(2)->getBondType() == Bond::BondType::AROMATIC);
+    MolOps::Kekulize(*m);
+    REQUIRE(m->getBondWithIdx(2)->hasQuery());
+    REQUIRE(m->getBondWithIdx(2)->getBondType() == Bond::BondType::AROMATIC);
+  }
+  SECTION("partial kekulization works") {
+    auto m1 = "c1ccccc1"_smiles;
+    REQUIRE(m1);
+    auto m2 = "c1ccccc1"_smarts;
+    REQUIRE(m2);
+    m1->insertMol(*m2);
+    MolOps::findSSSR(*m1);
+    REQUIRE(!m1->getBondWithIdx(1)->hasQuery());
+    REQUIRE(m1->getBondWithIdx(1)->getBondType() == Bond::BondType::AROMATIC);
+    REQUIRE(m1->getBondWithIdx(6)->hasQuery());
+    REQUIRE(m1->getBondWithIdx(6)->getBondType() == Bond::BondType::AROMATIC);
+    MolOps::Kekulize(*m1);
+    REQUIRE(!m1->getBondWithIdx(1)->hasQuery());
+    REQUIRE(m1->getBondWithIdx(1)->getBondType() != Bond::BondType::AROMATIC);
+    REQUIRE(m1->getBondWithIdx(6)->hasQuery());
+    REQUIRE(m1->getBondWithIdx(6)->getBondType() == Bond::BondType::AROMATIC);
+  }
+  SECTION("kekulization with non-bond-type queries works") {
+    auto m1 = "c1ccccc1"_smiles;
+    REQUIRE(m1);
+    QueryBond qbond;
+    qbond.setBondType(Bond::BondType::AROMATIC);
+    qbond.setIsAromatic(true);
+    qbond.setQuery(makeBondIsInRingQuery());
+    m1->replaceBond(0, &qbond);
+    REQUIRE(m1->getBondWithIdx(0)->hasQuery());
+    REQUIRE(m1->getBondWithIdx(0)->getBondType() == Bond::BondType::AROMATIC);
+    MolOps::Kekulize(*m1);
+    REQUIRE(m1->getBondWithIdx(0)->hasQuery());
+    REQUIRE(m1->getBondWithIdx(0)->getBondType() != Bond::BondType::AROMATIC);
+  }
+  SECTION("make sure single-atom molecules and mols without rings still fail") {
+    std::vector<std::string> expectedFailures = {"p", "c:c"};
+    for (const auto &smi : expectedFailures) {
+      INFO(smi);
+      CHECK_THROWS_AS(SmilesToMol(smi), MolSanitizeException);
+    }
+  }
+}

From 58cdf0309764327e64aaa722e56a575a5dd8addd Mon Sep 17 00:00:00 2001
From: David Cosgrove <davidacosgroveaz@gmail.com>
Date: Tue, 13 Sep 2022 14:41:52 +0100
Subject: [PATCH 4/8] Fix 5534 (#5535)

* Fix crash in brackets extraction.

* Add hashcode, tidy.

* Remove unused variable.

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---
 Code/GraphMol/MolDraw2D/DrawMol.cpp     |   4 +-
 Code/GraphMol/MolDraw2D/catch_tests.cpp | 125 ++++++++++++++++++++++++
 2 files changed, 127 insertions(+), 2 deletions(-)

diff --git a/Code/GraphMol/MolDraw2D/DrawMol.cpp b/Code/GraphMol/MolDraw2D/DrawMol.cpp
index 57fbbb480d..7108e9f473 100644
--- a/Code/GraphMol/MolDraw2D/DrawMol.cpp
+++ b/Code/GraphMol/MolDraw2D/DrawMol.cpp
@@ -595,9 +595,7 @@ void DrawMol::extractBrackets() {
     }
 
     std::vector<std::pair<Point2D, Point2D>> sgBondSegments;
-    int numBrackets = 0;
     for (auto bndIdx : sg.getBonds()) {
-      ++numBrackets;
       const auto bnd = drawMol_->getBondWithIdx(bndIdx);
       if (std::find(sg.getAtoms().begin(), sg.getAtoms().end(),
                     bnd->getBeginAtomIdx()) != sg.getAtoms().end()) {
@@ -610,9 +608,11 @@ void DrawMol::extractBrackets() {
             atCds_[bnd->getEndAtomIdx()], atCds_[bnd->getBeginAtomIdx()]));
       }
     }
+    int numBrackets = 0;
     for (const auto &brk : sg.getBrackets()) {
       // the atom coords have been inverted in y, so the bracket coords
       // must be, too.
+      ++numBrackets;
       Point2D p1{brk[0].x, -brk[0].y};
       Point2D p2{brk[1].x, -brk[1].y};
       trans.TransformPoint(p1);
diff --git a/Code/GraphMol/MolDraw2D/catch_tests.cpp b/Code/GraphMol/MolDraw2D/catch_tests.cpp
index dc02c8e054..946047a9c5 100644
--- a/Code/GraphMol/MolDraw2D/catch_tests.cpp
+++ b/Code/GraphMol/MolDraw2D/catch_tests.cpp
@@ -236,6 +236,7 @@ static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
     {"acs1996_12.svg", 2233727631U},
     {"test_unspec_stereo.svg", 599119798U},
     {"light_blue_h_no_label_1.svg", 3735371135U},
+    {"test_github_5534.svg", 574501211U},
     {"bond_highlights_1.svg", 1150579427U},
     {"bond_highlights_2.svg", 2958558856U},
     {"bond_highlights_3.svg", 3466419491U},
@@ -5820,3 +5821,127 @@ M  END
     check_file_hash(filename);
   }
 }
+
+TEST_CASE("Github5534") {
+  std::string nameBase = "test_github_5534";
+  {
+    auto m = R"CTAB(
+  INFOCHEM          2D 1   1.00000     0.00000     0
+
+ 45 45  0  0  0  0  0  0  0  0999 V2000
+   -1.3388    1.6804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0303    1.6804    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0303    1.9890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.0303    1.3609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0496   -0.6997    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0496   -0.3581    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0496   -0.0386    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0496    0.2810    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0496    0.6116    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0826    0.9532    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0496   -1.0193    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0496   -1.3499    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0496   -1.6694    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116   -0.6997    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116   -0.3581    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116   -0.0386    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116    0.2810    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116    0.6116    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116    0.9532    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116   -1.0193    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116   -1.3499    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    0.6116   -1.6694    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0303    1.6804    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
+    1.0303    2.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0303    1.3609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.3388    1.6804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810   -0.6997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810   -0.3581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810   -0.0386    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810    0.2810    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810    0.6116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810    0.9532    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3361    1.2948    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1708    1.4601    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3581    1.6804    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
+    0.0275    1.6804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3581    1.9890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810   -1.0193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810   -1.3499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810   -1.6694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2810   -2.0000    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.6997    1.6804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3691    1.6804    0.0000 Si  0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3691    1.9890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3691    1.3609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1 23  1  0  0  0  0
+  1 35  1  0  0  0  0
+  2  3  1  0  0  0  0
+  2  4  1  0  0  0  0
+  2 42  1  0  0  0  0
+  5 27  1  0  0  0  0
+  6 28  1  0  0  0  0
+  7 29  1  0  0  0  0
+  8 30  1  0  0  0  0
+  9 31  1  0  0  0  0
+ 10 32  1  0  0  0  0
+ 11 38  1  0  0  0  0
+ 12 39  1  0  0  0  0
+ 13 40  1  0  0  0  0
+ 14 27  1  0  0  0  0
+ 15 28  1  0  0  0  0
+ 16 29  1  0  0  0  0
+ 17 30  1  0  0  0  0
+ 18 31  1  0  0  0  0
+ 19 32  1  0  0  0  0
+ 20 38  1  0  0  0  0
+ 21 39  1  0  0  0  0
+ 22 40  1  0  0  0  0
+ 23 24  1  0  0  0  0
+ 23 25  1  0  0  0  0
+ 23 26  1  0  0  0  0
+ 27 28  1  0  0  0  0
+ 27 38  1  0  0  0  0
+ 28 29  1  0  0  0  0
+ 29 30  1  0  0  0  0
+ 30 31  1  0  0  0  0
+ 31 32  1  0  0  0  0
+ 32 33  1  0  0  0  0
+ 33 34  1  0  0  0  0
+ 34 35  1  0  0  0  0
+ 35 36  1  0  0  0  0
+ 35 37  1  0  0  0  0
+ 36 43  1  0  0  0  0
+ 38 39  1  0  0  0  0
+ 39 40  1  0  0  0  0
+ 40 41  1  0  0  0  0
+ 42 43  1  0  0  0  0
+ 43 44  1  0  0  0  0
+ 43 45  1  0  0  0  0
+M  STY  2   1 GEN   2 GEN
+M  SAL   1 15  27  28  29  30  31  32  33  34  35  36  37  38  39  40  41
+M  SBL   1 15   7  16   8  17   9  18  10  19  11  20  12  21   3  39  13
+M  SBL   1  5  22  14  23  15  24
+M  SDI   1  4   -0.0386    2.0661   -0.0386    1.1846
+M  SDI   1  4    0.4683    2.0661    0.4683    1.1846
+M  SAL   2  4  42  43  44  45
+M  SBL   2  2   6  39
+M  SDI   2  4   -0.7658    2.0661   -0.7658    1.1846
+M  SDI   2  4   -0.2149    2.0661   -0.2149    1.1846
+M  END
+)CTAB"_ctab;
+    REQUIRE(m);
+    {
+      MolDraw2DSVG drawer(300, 300, 300, 300, NO_FREETYPE);
+      drawer.drawMolecule(*m);
+      drawer.finishDrawing();
+      std::string text = drawer.getDrawingText();
+      std::ofstream outs(nameBase + ".svg");
+      outs << text;
+      outs.flush();
+      outs.close();
+      check_file_hash(nameBase + ".svg");
+    }
+  }
+}
\ No newline at end of file

From b47b4891514fc116855469c44531ffc9ae51d10d Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Wed, 14 Sep 2022 04:44:55 +0200
Subject: [PATCH 5/8] Switch yaehmop wrapper to basic cmake (#5558)

* switch to basic cmake from external project
the external project stuff in cmake is overly opaque

* enable yaehmop builds in CI

* disable building of the yaehmop binary

* Update External/YAeHMOP/CMakeLists.txt

Co-authored-by: Ric <ricrogz@users.noreply.github.com>

Co-authored-by: Ric <ricrogz@users.noreply.github.com>
---
 .azure-pipelines/linux_build.yml      |  1 +
 .azure-pipelines/linux_build_java.yml |  1 +
 .azure-pipelines/mac_build.yml        |  1 +
 .azure-pipelines/mac_build_java.yml   |  1 +
 .azure-pipelines/vs_build.yml         |  1 +
 .azure-pipelines/vs_build_dll.yml     |  1 +
 External/YAeHMOP/CMakeLists.txt       | 51 +++++++++++++++------------
 7 files changed, 35 insertions(+), 22 deletions(-)

diff --git a/.azure-pipelines/linux_build.yml b/.azure-pipelines/linux_build.yml
index 27058ea255..59937c050b 100644
--- a/.azure-pipelines/linux_build.yml
+++ b/.azure-pipelines/linux_build.yml
@@ -32,6 +32,7 @@ steps:
     -DRDK_BUILD_FREESASA_SUPPORT=ON \
     -DRDK_BUILD_AVALON_SUPPORT=ON \
     -DRDK_BUILD_INCHI_SUPPORT=ON \
+    -DRDK_BUILD_YAEHMOP_SUPPORT=ON \
     -DRDK_BUILD_CAIRO_SUPPORT=ON \
     -DRDK_BUILD_QT_SUPPORT=ON \
     -DQt5_DIR=/usr/lib/x86_64-linux-gnu/cmake/Qt5 \
diff --git a/.azure-pipelines/linux_build_java.yml b/.azure-pipelines/linux_build_java.yml
index 5613762949..e03beb83b2 100644
--- a/.azure-pipelines/linux_build_java.yml
+++ b/.azure-pipelines/linux_build_java.yml
@@ -24,6 +24,7 @@ steps:
     -DRDK_BUILD_FREESASA_SUPPORT=ON \
     -DRDK_BUILD_AVALON_SUPPORT=ON \
     -DRDK_BUILD_INCHI_SUPPORT=ON \
+    -DRDK_BUILD_YAEHMOP_SUPPORT=ON \
     -DRDK_BUILD_SWIG_WRAPPERS=ON \
     -DRDK_SWIG_STATIC=ON \
     -DRDK_BUILD_THREADSAFE_SSS=ON \
diff --git a/.azure-pipelines/mac_build.yml b/.azure-pipelines/mac_build.yml
index 0110912582..4f511ee386 100644
--- a/.azure-pipelines/mac_build.yml
+++ b/.azure-pipelines/mac_build.yml
@@ -46,6 +46,7 @@ steps:
     -DRDK_BUILD_FREESASA_SUPPORT=ON \
     -DRDK_BUILD_AVALON_SUPPORT=ON \
     -DRDK_BUILD_INCHI_SUPPORT=ON \
+    -DRDK_BUILD_YAEHMOP_SUPPORT=ON \
     -DRDK_BUILD_CAIRO_SUPPORT=ON \
     -DRDK_BUILD_QT_SUPPORT=ON \
     -DRDK_BUILD_SWIG_WRAPPERS=OFF \
diff --git a/.azure-pipelines/mac_build_java.yml b/.azure-pipelines/mac_build_java.yml
index b27a03351c..3c7d0c6894 100644
--- a/.azure-pipelines/mac_build_java.yml
+++ b/.azure-pipelines/mac_build_java.yml
@@ -42,6 +42,7 @@ steps:
     -DRDK_BUILD_FREESASA_SUPPORT=ON \
     -DRDK_BUILD_AVALON_SUPPORT=ON \
     -DRDK_BUILD_INCHI_SUPPORT=ON \
+    -DRDK_BUILD_YAEHMOP_SUPPORT=ON \
     -DRDK_BUILD_SWIG_WRAPPERS=ON \
     -DRDK_SWIG_STATIC=ON \
     -DRDK_BUILD_THREADSAFE_SSS=ON \
diff --git a/.azure-pipelines/vs_build.yml b/.azure-pipelines/vs_build.yml
index d2f1611725..283791f10c 100644
--- a/.azure-pipelines/vs_build.yml
+++ b/.azure-pipelines/vs_build.yml
@@ -31,6 +31,7 @@ steps:
     -DRDK_BUILD_FREESASA_SUPPORT=ON ^
     -DRDK_BUILD_AVALON_SUPPORT=ON ^
     -DRDK_BUILD_INCHI_SUPPORT=ON ^
+    -DRDK_BUILD_YAEHMOP_SUPPORT=ON ^
     -DRDK_BUILD_CAIRO_SUPPORT=ON ^
     -DRDK_BUILD_THREADSAFE_SSS=ON ^
     -DRDK_BUILD_SWIG_WRAPPERS=OFF ^
diff --git a/.azure-pipelines/vs_build_dll.yml b/.azure-pipelines/vs_build_dll.yml
index 350af10597..c938854d49 100644
--- a/.azure-pipelines/vs_build_dll.yml
+++ b/.azure-pipelines/vs_build_dll.yml
@@ -30,6 +30,7 @@ steps:
     -DRDK_BUILD_FREESASA_SUPPORT=ON ^
     -DRDK_BUILD_AVALON_SUPPORT=ON ^
     -DRDK_BUILD_INCHI_SUPPORT=ON ^
+    -DRDK_BUILD_YAEHMOP_SUPPORT=ON ^
     -DRDK_BUILD_CAIRO_SUPPORT=ON ^
     -DRDK_BUILD_THREADSAFE_SSS=ON ^
     -DRDK_BUILD_SWIG_WRAPPERS=OFF ^
diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt
index 0fe86a7c38..6217745c28 100644
--- a/External/YAeHMOP/CMakeLists.txt
+++ b/External/YAeHMOP/CMakeLists.txt
@@ -2,12 +2,29 @@ if(NOT RDK_BUILD_YAEHMOP_SUPPORT)
   return()
 endif(NOT RDK_BUILD_YAEHMOP_SUPPORT)
 
-set(CMAKE_CXX_STANDARD 17)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-
 add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT)
 
-include(ExternalProject)
+if(NOT DEFINED YAEHMOP_DIR)
+  set(YAEHMOP_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop")
+endif()
+
+if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h")
+    set(RELEASE_NO "2022.09.1")
+    set(MD5 "2d5ee5b6b130529544565240597c602a")
+    downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz"
+          "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5})
+    execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf
+      ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz
+      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+
+    file(RENAME "yaehmop-${RELEASE_NO}" "${YAEHMOP_DIR}")
+else()
+  message("-- Found YAeHMOP source in ${YAEHMOP_DIR}")
+endif()
+
+set(yaehmop_INCLUDE_DIRS ${YAEHMOP_DIR}/..
+     CACHE STRING "yaehmop Include File" FORCE)
+include_directories(${yaehmop_INCLUDE_DIRS})
 
 if(CMAKE_COMPILER_IS_GNUCXX AND NOT CYGWIN)
     SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
@@ -16,34 +33,24 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
     SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
 endif()
 
-include_directories( ${RDKit_ExternalDir}/YAeHMOP )
+# bring in the eHT code, but skip the targets (we'll get yaehmop_eht anyway because it's a dependency)
+add_subdirectory(yaehmop/tightbind EXCLUDE_FROM_ALL True)
+
+# set install dir for the yaehmop library:
+INSTALL(TARGETS yaehmop_eht EXPORT rdkit-targets
+        DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST}
+        COMPONENT runtime )
+
 
-ExternalProject_Add(yaehmop_project
-  GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git
-  GIT_TAG master
-  UPDATE_COMMAND ""
-  PATCH_COMMAND ""
-  PREFIX ${CMAKE_CURRENT_SOURCE_DIR}
-  SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop"
-  SOURCE_SUBDIR "tightbind"
-  CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-  TEST_COMMAND "")
 
-include_directories(${PROJECT_BINARY_DIR}/include)
-link_directories(${PROJECT_BINARY_DIR}/lib)
-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build)
 
 set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat )
 install(FILES ${EHT_PARAM_FILE}
         DESTINATION ${RDKit_ShareDir}/Data
         COMPONENT data)
 
-message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include")
-message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build")
-
 rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol )
 target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD)
-add_dependencies(EHTLib yaehmop_project)
 rdkit_headers(EHTTools.h DEST GraphMol)
 rdkit_catch_test(testEHTLib1 test1.cpp
            LINK_LIBRARIES EHTLib FileParsers SmilesParse )

From c305f1252bdb679c9d963cd128d63a055c5399c2 Mon Sep 17 00:00:00 2001
From: greg landrum <greg.landrum@gmail.com>
Date: Wed, 14 Sep 2022 04:56:13 +0200
Subject: [PATCH 6/8] make the xyz2mol functionality optional

---
 CMakeLists.txt                              | 12 ++++++++++++
 Code/GraphMol/CMakeLists.txt                |  4 +++-
 Code/GraphMol/DetermineBonds/CMakeLists.txt |  3 ---
 Code/RDGeneral/RDConfig.h.cmake             |  4 ++++
 4 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 51b724d03b..809da1e82a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -53,6 +53,7 @@ option(RDK_BUILD_COORDGEN_SUPPORT "build the rdkit coordgen wrapper" ON )
 option(RDK_BUILD_MAEPARSER_SUPPORT "build the rdkit MAE parser wrapper" ON )
 option(RDK_BUILD_MOLINTERCHANGE_SUPPORT "build in support for CommonChem molecule interchange" ON )
 option(RDK_BUILD_YAEHMOP_SUPPORT "build support for the YAeHMOP wrapper" OFF)
+option(RDK_BUILD_XYZ2MOL_SUPPORT "build in support for the RDKit's implementation of xyx2mol (in the DetermineBonds library)" OFF )
 option(RDK_BUILD_STRUCTCHECKER_SUPPORT "build in support for the StructChecker alpha (not recommended, use the MolVS integration instead)" OFF )
 option(RDK_USE_URF "Build support for Florian Flachsenberg's URF library" ON)
 option(RDK_INSTALL_DEV_COMPONENT "install libraries and headers" ON)
@@ -205,6 +206,17 @@ if(RDK_USE_URF)
   include_directories(${RDKit_ExternalDir}/RingFamilies/RingDecomposerLib/src/RingDecomposerLib)
 endif()
 
+if(RDK_BUILD_XYZ2MOL_SUPPORT)
+    if(NOT RDK_BUILD_YAEHMOP_SUPPORT)
+        message("Enabling YAeHMOP support because xyz2mol is being built")
+        set(RDK_BUILD_YAEHMOP_SUPPORT ON)
+    endif()
+    add_definitions(-DRDK_BUILD_XYZ2MOL_SUPPORT)
+    include_directories(${RDKit_ExternalDir})
+endif()
+
+
+
 
 if(CMAKE_SIZEOF_VOID_P EQUAL 4)
   target_compile_definitions(rdkit_base INTERFACE "-DRDK_32BIT_BUILD")
diff --git a/Code/GraphMol/CMakeLists.txt b/Code/GraphMol/CMakeLists.txt
index fcc8d12239..0cffaa8729 100644
--- a/Code/GraphMol/CMakeLists.txt
+++ b/Code/GraphMol/CMakeLists.txt
@@ -101,7 +101,9 @@ add_subdirectory(Trajectory)
 add_subdirectory(SubstructLibrary)
 add_subdirectory(RGroupDecomposition)
 
-add_subdirectory(DetermineBonds)
+if(RDK_BUILD_XYZ2MOL_SUPPORT)
+  add_subdirectory(DetermineBonds)
+endif()
 
 if(RDK_BUILD_MOLINTERCHANGE_SUPPORT)
 add_subdirectory(MolInterchange)
diff --git a/Code/GraphMol/DetermineBonds/CMakeLists.txt b/Code/GraphMol/DetermineBonds/CMakeLists.txt
index 858f9d9d76..6efd34331b 100644
--- a/Code/GraphMol/DetermineBonds/CMakeLists.txt
+++ b/Code/GraphMol/DetermineBonds/CMakeLists.txt
@@ -1,6 +1,3 @@
-# FIX: there's probably a better way to do this
-link_directories(${CMAKE_CURRENT_SOURCE_DIR}/../../../External/YAeHMOP/src/yaehmop_project-build)
-
 rdkit_library(DetermineBonds DetermineBonds.cpp
               LINK_LIBRARIES GenericGroups GraphMol RDGeneral FileParsers EHTLib)
 
diff --git a/Code/RDGeneral/RDConfig.h.cmake b/Code/RDGeneral/RDConfig.h.cmake
index 07fc79cde9..fb302cd990 100644
--- a/Code/RDGeneral/RDConfig.h.cmake
+++ b/Code/RDGeneral/RDConfig.h.cmake
@@ -41,3 +41,7 @@
 #cmakedefine RDK_BUILD_FREETYPE_SUPPORT
 
 #cmakedefine RDK_USE_URF
+
+#cmakedefine RDK_BUILD_YAEHMOP_SUPPORT
+
+#cmakedefine RDK_BUILD_XYZ2MOL_SUPPORT

From 8cb4e7f6da37c5c5b50c637560507502c3ac4afc Mon Sep 17 00:00:00 2001
From: greg landrum <greg.landrum@gmail.com>
Date: Wed, 14 Sep 2022 05:24:14 +0200
Subject: [PATCH 7/8] enable that for the CI builds

---
 .azure-pipelines/linux_build.yml      | 1 +
 .azure-pipelines/linux_build_java.yml | 1 +
 .azure-pipelines/mac_build.yml        | 1 +
 .azure-pipelines/mac_build_java.yml   | 1 +
 .azure-pipelines/vs_build.yml         | 1 +
 .azure-pipelines/vs_build_dll.yml     | 1 +
 6 files changed, 6 insertions(+)

diff --git a/.azure-pipelines/linux_build.yml b/.azure-pipelines/linux_build.yml
index 59937c050b..8efe04d089 100644
--- a/.azure-pipelines/linux_build.yml
+++ b/.azure-pipelines/linux_build.yml
@@ -33,6 +33,7 @@ steps:
     -DRDK_BUILD_AVALON_SUPPORT=ON \
     -DRDK_BUILD_INCHI_SUPPORT=ON \
     -DRDK_BUILD_YAEHMOP_SUPPORT=ON \
+    -DRDK_BUILD_XYZ2MOL_SUPPORT=ON \
     -DRDK_BUILD_CAIRO_SUPPORT=ON \
     -DRDK_BUILD_QT_SUPPORT=ON \
     -DQt5_DIR=/usr/lib/x86_64-linux-gnu/cmake/Qt5 \
diff --git a/.azure-pipelines/linux_build_java.yml b/.azure-pipelines/linux_build_java.yml
index e03beb83b2..d80d53947c 100644
--- a/.azure-pipelines/linux_build_java.yml
+++ b/.azure-pipelines/linux_build_java.yml
@@ -25,6 +25,7 @@ steps:
     -DRDK_BUILD_AVALON_SUPPORT=ON \
     -DRDK_BUILD_INCHI_SUPPORT=ON \
     -DRDK_BUILD_YAEHMOP_SUPPORT=ON \
+    -DRDK_BUILD_XYZ2MOL_SUPPORT=ON \
     -DRDK_BUILD_SWIG_WRAPPERS=ON \
     -DRDK_SWIG_STATIC=ON \
     -DRDK_BUILD_THREADSAFE_SSS=ON \
diff --git a/.azure-pipelines/mac_build.yml b/.azure-pipelines/mac_build.yml
index 4f511ee386..3698adea11 100644
--- a/.azure-pipelines/mac_build.yml
+++ b/.azure-pipelines/mac_build.yml
@@ -47,6 +47,7 @@ steps:
     -DRDK_BUILD_AVALON_SUPPORT=ON \
     -DRDK_BUILD_INCHI_SUPPORT=ON \
     -DRDK_BUILD_YAEHMOP_SUPPORT=ON \
+    -DRDK_BUILD_XYZ2MOL_SUPPORT=ON \
     -DRDK_BUILD_CAIRO_SUPPORT=ON \
     -DRDK_BUILD_QT_SUPPORT=ON \
     -DRDK_BUILD_SWIG_WRAPPERS=OFF \
diff --git a/.azure-pipelines/mac_build_java.yml b/.azure-pipelines/mac_build_java.yml
index 3c7d0c6894..3d8cc77c88 100644
--- a/.azure-pipelines/mac_build_java.yml
+++ b/.azure-pipelines/mac_build_java.yml
@@ -43,6 +43,7 @@ steps:
     -DRDK_BUILD_AVALON_SUPPORT=ON \
     -DRDK_BUILD_INCHI_SUPPORT=ON \
     -DRDK_BUILD_YAEHMOP_SUPPORT=ON \
+    -DRDK_BUILD_XYZ2MOL_SUPPORT=ON \
     -DRDK_BUILD_SWIG_WRAPPERS=ON \
     -DRDK_SWIG_STATIC=ON \
     -DRDK_BUILD_THREADSAFE_SSS=ON \
diff --git a/.azure-pipelines/vs_build.yml b/.azure-pipelines/vs_build.yml
index 283791f10c..67b1459945 100644
--- a/.azure-pipelines/vs_build.yml
+++ b/.azure-pipelines/vs_build.yml
@@ -32,6 +32,7 @@ steps:
     -DRDK_BUILD_AVALON_SUPPORT=ON ^
     -DRDK_BUILD_INCHI_SUPPORT=ON ^
     -DRDK_BUILD_YAEHMOP_SUPPORT=ON ^
+    -DRDK_BUILD_XYZ2MOL_SUPPORT=ON ^
     -DRDK_BUILD_CAIRO_SUPPORT=ON ^
     -DRDK_BUILD_THREADSAFE_SSS=ON ^
     -DRDK_BUILD_SWIG_WRAPPERS=OFF ^
diff --git a/.azure-pipelines/vs_build_dll.yml b/.azure-pipelines/vs_build_dll.yml
index c938854d49..c23e4f89aa 100644
--- a/.azure-pipelines/vs_build_dll.yml
+++ b/.azure-pipelines/vs_build_dll.yml
@@ -31,6 +31,7 @@ steps:
     -DRDK_BUILD_AVALON_SUPPORT=ON ^
     -DRDK_BUILD_INCHI_SUPPORT=ON ^
     -DRDK_BUILD_YAEHMOP_SUPPORT=ON ^
+    -DRDK_BUILD_XYZ2MOL_SUPPORT=ON ^
     -DRDK_BUILD_CAIRO_SUPPORT=ON ^
     -DRDK_BUILD_THREADSAFE_SSS=ON ^
     -DRDK_BUILD_SWIG_WRAPPERS=OFF ^

From 35769e26bbedd89d2fcde1d98e6bef286c2d06eb Mon Sep 17 00:00:00 2001
From: Greg Landrum <greg.landrum@gmail.com>
Date: Wed, 14 Sep 2022 13:22:50 +0200
Subject: [PATCH 8/8] Update CMakeLists.txt

Co-authored-by: Sreya Gogineni <74024376+gosreya@users.noreply.github.com>
---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 809da1e82a..7ef50bbbff 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -53,7 +53,7 @@ option(RDK_BUILD_COORDGEN_SUPPORT "build the rdkit coordgen wrapper" ON )
 option(RDK_BUILD_MAEPARSER_SUPPORT "build the rdkit MAE parser wrapper" ON )
 option(RDK_BUILD_MOLINTERCHANGE_SUPPORT "build in support for CommonChem molecule interchange" ON )
 option(RDK_BUILD_YAEHMOP_SUPPORT "build support for the YAeHMOP wrapper" OFF)
-option(RDK_BUILD_XYZ2MOL_SUPPORT "build in support for the RDKit's implementation of xyx2mol (in the DetermineBonds library)" OFF )
+option(RDK_BUILD_XYZ2MOL_SUPPORT "build in support for the RDKit's implementation of xyz2mol (in the DetermineBonds library)" OFF )
 option(RDK_BUILD_STRUCTCHECKER_SUPPORT "build in support for the StructChecker alpha (not recommended, use the MolVS integration instead)" OFF )
 option(RDK_USE_URF "Build support for Florian Flachsenberg's URF library" ON)
 option(RDK_INSTALL_DEV_COMPONENT "install libraries and headers" ON)