Add option to draw all CIP codes in DrawMol.cpp (#8609)

* enable showAllCIPCodes in DrawMol code

* Made consistent with old behavior + add test

* Added python test

* Fixed FREETYPE=OFF tests

* Fixed FREETYPE=OFF tests

* Adjusted pytest

* Enabled JSON drawer option setting + new JSON test

* update JS docs

Code/GraphMol/MolDraw2D/DrawMol.cpp

@@ -33,6 +33,7 @@
 #include <GraphMol/MolEnumerator/LinkNode.h>
 #include <GraphMol/MolTransforms/MolTransforms.h>
 #include <GraphMol/Depictor/RDDepictor.h>
+#include <GraphMol/StereoGroup.h>
 #include <GraphMol/Atropisomers.h>
 
 namespace RDKit {
@@ -194,9 +195,6 @@ void DrawMol::initDrawMolecule(const ROMol &mol) {
     bool removeAffectedStereoGroups = true;
     Chirality::simplifyEnhancedStereo(*drawMol_, removeAffectedStereoGroups);
   }
-  if (drawOptions_.addStereoAnnotation) {
-    Chirality::addStereoAnnotations(*drawMol_);
-  }
   if (drawOptions_.addAtomIndices) {
     addAtomIndices(*drawMol_);
   }
@@ -220,9 +218,10 @@ void DrawMol::extractAll(double scale) {
   extractHighlights(scale);
   extractAttachments();
   extractAtomNotes();
-  if (!drawOptions_.addStereoAnnotation) {
-    extractStereoGroups();
+  if (drawOptions_.addStereoAnnotation) {
+    extractCIPCodes(drawOptions_.showAllCIPCodes);
   }
+  extractStereoGroups(); // always show StereoGroups
   extractBondNotes();
   extractRadicals();
   extractSGroupData();
@@ -465,6 +464,69 @@ void DrawMol::extractAtomNotes() {
   }
 }
 
+// ****************************************************************************
+void DrawMol::extractCIPCodes(bool showAllCIPCodes) {
+  boost::dynamic_bitset<> maskedAtoms(drawMol_->getNumAtoms());
+  boost::dynamic_bitset<> maskedBonds(drawMol_->getNumBonds());
+
+  if(!showAllCIPCodes) { // record atoms and bonds whose codes should be hidden
+    for (const StereoGroup &group : drawMol_->getStereoGroups()) {
+      StereoGroupType stereoGroupType;
+
+      stereoGroupType = group.getGroupType();
+      if(stereoGroupType == RDKit::StereoGroupType::STEREO_OR || \
+         stereoGroupType == RDKit::StereoGroupType::STEREO_AND ) {
+        for (const auto atom : group.getAtoms()) {
+          maskedAtoms.set(atom->getIdx());
+        }
+        for (const auto bond : group.getBonds()) {
+          maskedBonds.set(bond->getIdx());
+        }
+      }
+    }
+  }
+
+  for (auto atom : drawMol_->atoms()) {
+    std::string cip;
+    if (!maskedAtoms[atom->getIdx()] &&
+        atom->getPropIfPresent(common_properties::_CIPCode, cip)) {
+        cip = "(" + cip + ")";
+        DrawAnnotation *annot = new DrawAnnotation(
+          cip, TextAlignType::MIDDLE, "CIP_Code",
+          drawOptions_.annotationFontScale, Point2D(0.0, 0.0),
+          drawOptions_.atomNoteColour, textDrawer_);
+      calcAnnotationPosition(atom, *annot);
+      annotations_.emplace_back(annot);
+    }
+  }
+
+  for (auto bond : drawMol_->bonds()) {
+    std::string cip;
+    // Add E or Z CIP codes if missing to be compatible with previous
+    // implemtnation. In future, user should be responsible for calling
+    // AssignCIPLabels() before drawing to harmonize behavior with
+    // how R,S,M,P CIP codes are handled
+    if (!maskedBonds[bond->getIdx()]) {
+      if (!bond->getPropIfPresent(common_properties::_CIPCode, cip)) {
+        if (bond->getStereo() == Bond::STEREOE) {
+          cip = "E";
+        } else if (bond->getStereo() == Bond::STEREOZ) {
+          cip = "Z";
+        }
+      }
+      if (!cip.empty()) {
+        cip = "(" + cip + ")";
+        DrawAnnotation *annot = new DrawAnnotation(
+          cip, TextAlignType::MIDDLE, "CIP_Code",
+          drawOptions_.annotationFontScale, Point2D(0.0, 0.0),
+          drawOptions_.bondNoteColour, textDrawer_);
+      calcAnnotationPosition(bond, *annot);
+      annotations_.emplace_back(annot);
+      }
+    }
+  }
+}
+
 // ****************************************************************************
 void DrawMol::extractStereoGroups() {
   int orCount(0), andCount(0);

Code/GraphMol/MolDraw2D/DrawMol.h

@@ -112,6 +112,7 @@ class DrawMol {
   void extractRegions();
   void extractAttachments();
   void extractMolNotes();
+  void extractCIPCodes(bool showAllCIPCodes);
   void extractStereoGroups();
   void extractAtomNotes();
   void extractBondNotes();

Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h

@@ -259,6 +259,8 @@ struct RDKIT_MOLDRAW2D_EXPORT MolDrawOptions {
   bool dummyIsotopeLabels = true;  // adds isotope labels to dummy atoms.
 
   bool addStereoAnnotation = false;       // adds E/Z and R/S to drawings.
+  bool showAllCIPCodes = false;           // show CIP codes for 'or' & 'and'
+                                          // StereoGroups that are normally hidden
   bool atomHighlightsAreCircles = false;  // forces atom highlights always to be
                                           // circles. Default (false) is to put
                                           // ellipses round longer labels.

Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp

@@ -241,6 +241,7 @@ void updateMolDrawOptionsFromJSON(MolDrawOptions &opts,
   PT_OPT_GET(isotopeLabels);
   PT_OPT_GET(dummyIsotopeLabels);
   PT_OPT_GET(addStereoAnnotation);
+  PT_OPT_GET(showAllCIPCodes);
   PT_OPT_GET(atomHighlightsAreCircles);
   PT_OPT_GET(centreMoleculesBeforeDrawing);
   PT_OPT_GET(explicitMethyl);

Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp

@@ -922,6 +922,9 @@ BOOST_PYTHON_MODULE(rdMolDraw2D) {
       .def_readwrite("addStereoAnnotation",
                      &RDKit::MolDrawOptions::addStereoAnnotation,
                      "adds R/S and E/Z to drawings. Default False.")
+      .def_readwrite("showAllCIPCodes",
+                     &RDKit::MolDrawOptions::showAllCIPCodes,
+                     "show all defined CIP codes (no hiding!). Default False.")
       .def_readwrite("addAtomIndices", &RDKit::MolDrawOptions::addAtomIndices,
                      "adds atom indices to drawings. Default False.")
       .def_readwrite("addBondIndices", &RDKit::MolDrawOptions::addBondIndices,

Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py

@@ -843,7 +843,19 @@ M  END''')
         do = rdMolDraw2D.MolDrawOptions()
         with self.assertRaises(AttributeError):
             do.rhubarb = True
-            
+
+    def testShowAllCIPCodes(self):
+        m = Chem.MolFromSmiles("Cc1cccc(F)c1-c1c(C)cc([C@H](C)O)cc1Cl |wU:7.7,o1:7,&1:13|")
+        self.assertIsNotNone(m)
+        d2d = rdMolDraw2D.MolDraw2DSVG(-1, -1)
+        opts = d2d.drawOptions()
+        opts.addStereoAnnotation = True
+        opts.showAllCIPCodes = True
+        d2d.DrawMolecule(m)
+        d2d.FinishDrawing()
+        text = d2d.GetDrawingText()
+        #confirm that at least one CIP code is present
+        self.assertTrue("class='CIP_Code'" in text)
 
 if __name__ == "__main__":
     unittest.main()

Code/GraphMol/MolDraw2D/catch_tests.cpp

@@ -10751,4 +10751,99 @@ TEST_CASE("Solid arrowhead in wrong place (Github 8500)") {
                Catch::Matchers::WithinAbs(expVals[i].second, 1.0e-4));
   }
   check_file_hash("testArrowheads.svg");
-}
+}
+
+TEST_CASE("Show all CIP codes (Github 8561)") {
+    auto m = R"CTAB(
+     RDKit          2D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 19 20 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 3.000000 0.000000 0.000000 0
+M  V30 2 C 1.500000 0.000000 0.000000 0
+M  V30 3 C 0.750000 -1.299038 0.000000 0
+M  V30 4 C -0.750000 -1.299038 0.000000 0
+M  V30 5 C -1.500000 0.000000 0.000000 0
+M  V30 6 C -0.750000 1.299038 0.000000 0
+M  V30 7 F -1.500000 2.598076 0.000000 0
+M  V30 8 C 0.750000 1.299038 0.000000 0
+M  V30 9 C 1.500000 2.598076 0.000000 0
+M  V30 10 C 3.000000 2.598076 0.000000 0
+M  V30 11 C 3.750000 1.299038 0.000000 0
+M  V30 12 C 3.750000 3.897114 0.000000 0
+M  V30 13 C 3.000000 5.196152 0.000000 0
+M  V30 14 C 3.750000 6.495191 0.000000 0
+M  V30 15 C 5.250000 6.495191 0.000000 0
+M  V30 16 O 3.000000 7.794229 0.000000 0
+M  V30 17 C 1.500000 5.196152 0.000000 0
+M  V30 18 C 0.750000 3.897114 0.000000 0
+M  V30 19 Cl -0.750000 3.897114 0.000000 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 2 2 3
+M  V30 3 1 3 4
+M  V30 4 2 4 5
+M  V30 5 1 5 6
+M  V30 6 1 6 7
+M  V30 7 2 6 8
+M  V30 8 1 8 9
+M  V30 9 2 9 10
+M  V30 10 1 10 11
+M  V30 11 1 10 12
+M  V30 12 2 12 13
+M  V30 13 1 13 14
+M  V30 14 1 14 15 CFG=1
+M  V30 15 1 14 16
+M  V30 16 1 13 17
+M  V30 17 2 17 18
+M  V30 18 1 18 19
+M  V30 19 1 8 2 CFG=3
+M  V30 20 1 18 9
+M  V30 END BOND
+M  V30 BEGIN COLLECTION
+M  V30 MDLV30/STEREL1 ATOMS=(1 8)
+M  V30 MDLV30/STERAC1 ATOMS=(1 14)
+M  V30 END COLLECTION
+M  V30 END CTAB
+M  END
+)CTAB"_ctab;
+    REQUIRE(m);
+    CIPLabeler::assignCIPLabels(*m);
+    MolDraw2DSVG drawer(350, 300);
+    drawer.drawOptions().addStereoAnnotation = true;
+    drawer.drawOptions().showAllCIPCodes = true;
+    drawer.drawMolecule(*m);
+    drawer.finishDrawing();
+    auto text = drawer.getDrawingText();
+    std::ofstream outs("testShowAllCIPLabels.svg");
+    outs << text;
+    outs.close();
+
+    // Check for Blue (M) CIP label on Bond
+    TEST_ASSERT(
+        text.find("class='CIP_Code'") !=
+        std::string::npos);
+
+    //try again, this tiem using JSON to set options
+    const char *json =
+      "{\"addStereoAnnotation\":true, \"showAllCIPCodes\":true}";
+    MolDraw2DSVG drawer2(350, 300);
+    MolDrawOptions opts;
+    MolDraw2DUtils::updateMolDrawOptionsFromJSON(opts, json);
+    drawer2.drawOptions() = opts;
+    drawer2.drawMolecule(*m);
+    drawer2.finishDrawing();
+    auto text2 = drawer2.getDrawingText();
+    std::ofstream outs2("testShowAllCIPLabels2.svg");
+    outs2 << text2;
+    outs2.close();
+
+    // Check for Blue (M) CIP label on Bond
+    TEST_ASSERT(
+        text2.find("class='CIP_Code'") !=
+        std::string::npos);
+  }
+

Code/GraphMol/MolDraw2D/test1.cpp

@@ -4036,12 +4036,12 @@ void test20Annotate() {
 #ifdef RDK_BUILD_FREETYPE_SUPPORT
 #if DO_TEST_ASSERT
     // last note
-    TEST_ASSERT(text.find("<path class='note' d='M 273.9 236.3") !=
+    TEST_ASSERT(text.find("<path class='CIP_Code' d='M 273.9 236.3") !=
                 std::string::npos);
 #endif
 #else
     // this is the (E)
-    TEST_ASSERT(text.find("<text x='260.3' y='232.0' class='note' "
+    TEST_ASSERT(text.find("<text x='260.3' y='232.0' class='CIP_Code' "
                           "style='font-size:20px;font-style:normal;font-weight:"
                           "normal;fill-opacity:1;stroke:none;font-family:sans-"
                           "serif;text-anchor:start;fill:#7F7FFF' >E</text>") !=

Code/MinimalLib/docs/GettingStartedInJS.html

@@ -185,6 +185,7 @@ addBondIndices,
 isotopeLabels,
 dummyIsotopeLabels,
 addStereoAnnotation,
+showAllCIPLabels,
 atomHighlightsAreCircles,
 centreMoleculesBeforeDrawing,
 explicitMethyl,
@@ -321,4 +322,4 @@ mol1.draw_to_canvas_with_highlights(canvas_mol1, JSON.stringify({ legend: `mol1
     </div>
 </body>
 
-</html>
+</html>