From 1cefbfb3ee5c9dd9ca98b2490c60e87412a23cf1 Mon Sep 17 00:00:00 2001
From: Yechen Qiao <yqiao@sapiosciences.com>
Date: Tue, 14 May 2024 16:34:11 -0400
Subject: [PATCH 1/5] =?UTF-8?q?[Sapio]=20[CHEMBUGS-184]=20In=20molfile=5Fs?=
 =?UTF-8?q?aver.cpp,=20we=20need=20to=20change=20it=20so=20the=20BEGIN=20S?=
 =?UTF-8?q?GROUP=20is=20before=20BEGIN=20COLLECTION=20This=20is=20consiste?=
 =?UTF-8?q?nt=20with=20RDKIt=20in=20https://github.com/rdkit/rdkit/blob/ma?=
 =?UTF-8?q?ster/Code/GraphMol/FileParsers/MolFileParser.cpp=20=20and=20tha?=
 =?UTF-8?q?t=20of=20the=20manual=20in=20https://www.daylight.com/meetings/?=
 =?UTF-8?q?mug05/Kappler/ctfile.pdf=20(Page=2085=20vs=2090)=20RDKIT=20will?=
 =?UTF-8?q?=20fail=20the=20load=20if=20the=20BEGIN=20SGROUP=20is=20after?=
 =?UTF-8?q?=20BEGIN=20COLLECTION.=20Also,=20while=20loading=20CTAB=20v2000?=
 =?UTF-8?q?/v3000,=20the=20add=20implicit=20h=20=E2=80=9Cadd=5Fimplicit=5F?=
 =?UTF-8?q?h=E2=80=9D=20adds=20s=20groups=20after=20the=20number=20of=20s?=
 =?UTF-8?q?=20group=20counts=20is=20already=20written=20in=20the=20header.?=
 =?UTF-8?q?=20So=20if=20that=20was=20ever=20executed,=20RKit=20will=20have?=
 =?UTF-8?q?=20a=20read=20failure.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .../molecule/src/molfile_saver.cpp            | 178 +++++++-------
 core/indigo-core/tests/common.cpp             |   9 +
 core/indigo-core/tests/tests/molecule.cpp     |  45 +++-
 data/reactions/other/stereo_reaction.rxn      | 217 ++++++++++++++++++
 4 files changed, 360 insertions(+), 89 deletions(-)
 create mode 100644 data/reactions/other/stereo_reaction.rxn

diff --git a/core/indigo-core/molecule/src/molfile_saver.cpp b/core/indigo-core/molecule/src/molfile_saver.cpp
index db45ca31c3..2c753b40bb 100644
--- a/core/indigo-core/molecule/src/molfile_saver.cpp
+++ b/core/indigo-core/molecule/src/molfile_saver.cpp
@@ -444,6 +444,7 @@ void MolfileSaver::_writeMultiString(Output& output, const char* string, int len
 
 void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
 {
+    add_implicit_h = false;
     _handleCIP(mol);
     if (mol.tgroups.getTGroupCount())
         _handleMonomers(mol);
@@ -787,94 +788,6 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
 
     output.writeStringCR("M  V30 END BOND");
 
-    MoleculeStereocenters& stereocenters = mol.stereocenters;
-
-    if (stereocenters.begin() != stereocenters.end() || mol.hasHighlighting())
-    {
-        output.writeStringCR("M  V30 BEGIN COLLECTION");
-
-        QS_DEF(Array<int>, processed);
-
-        processed.clear_resize(mol.vertexEnd());
-        processed.zerofill();
-
-        for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
-        {
-            if (processed[i])
-                continue;
-
-            ArrayOutput out(buf);
-            int j, type = stereocenters.getType(i);
-
-            if (type == MoleculeStereocenters::ATOM_ABS)
-                out.writeString("MDLV30/STEABS ATOMS=(");
-            else if (type == MoleculeStereocenters::ATOM_OR)
-                out.printf("MDLV30/STEREL%d ATOMS=(", stereocenters.getGroup(i));
-            else if (type == MoleculeStereocenters::ATOM_AND)
-                out.printf("MDLV30/STERAC%d ATOMS=(", stereocenters.getGroup(i));
-            else
-                continue;
-
-            QS_DEF(Array<int>, list);
-
-            list.clear();
-            list.push(i);
-
-            for (j = mol.vertexNext(i); j < mol.vertexEnd(); j = mol.vertexNext(j))
-                if (stereocenters.sameGroup(i, j))
-                {
-                    list.push(j);
-                    processed[j] = 1;
-                }
-
-            out.printf("%d", list.size());
-            for (j = 0; j < list.size(); j++)
-                out.printf(" %d", _atom_mapping[list[j]]);
-            out.writeChar(')');
-
-            _writeMultiString(output, buf.ptr(), buf.size());
-        }
-
-        if (mol.hasHighlighting())
-        {
-            if (mol.countHighlightedBonds() > 0)
-            {
-                ArrayOutput out(buf);
-
-                out.printf("MDLV30/HILITE BONDS=(%d", mol.countHighlightedBonds());
-
-                for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
-                    if (mol.isBondHighlighted(i))
-                        out.printf(" %d", _bond_mapping[i]);
-                out.writeChar(')');
-
-                _writeMultiString(output, buf.ptr(), buf.size());
-            }
-            if (mol.countHighlightedAtoms() > 0)
-            {
-                ArrayOutput out(buf);
-                out.printf("MDLV30/HILITE ATOMS=(%d", mol.countHighlightedAtoms());
-                for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
-                    if (mol.isAtomHighlighted(i))
-                        out.printf(" %d", _atom_mapping[i]);
-                out.writeChar(')');
-
-                _writeMultiString(output, buf.ptr(), buf.size());
-            }
-        }
-        if (mol.custom_collections.size() > 0)
-        {
-            for (i = mol.custom_collections.begin(); i != mol.custom_collections.end(); i = mol.custom_collections.next(i))
-            {
-                ArrayOutput out(buf);
-                out.printf("%s", mol.custom_collections.at(i));
-                _writeMultiString(output, buf.ptr(), buf.size());
-            }
-        }
-
-        output.writeStringCR("M  V30 END COLLECTION");
-    }
-
     QS_DEF(Array<int>, sgs_sorted);
     _checkSGroupIndices(mol, sgs_sorted);
 
@@ -1074,6 +987,94 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
         _removeImplicitSGroups(mol, implicit_sgroups_indexes);
     }
 
+    MoleculeStereocenters& stereocenters = mol.stereocenters;
+
+    if (stereocenters.begin() != stereocenters.end() || mol.hasHighlighting())
+    {
+        output.writeStringCR("M  V30 BEGIN COLLECTION");
+
+        QS_DEF(Array<int>, processed);
+
+        processed.clear_resize(mol.vertexEnd());
+        processed.zerofill();
+
+        for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
+        {
+            if (processed[i])
+                continue;
+
+            ArrayOutput out(buf);
+            int j, type = stereocenters.getType(i);
+
+            if (type == MoleculeStereocenters::ATOM_ABS)
+                out.writeString("MDLV30/STEABS ATOMS=(");
+            else if (type == MoleculeStereocenters::ATOM_OR)
+                out.printf("MDLV30/STEREL%d ATOMS=(", stereocenters.getGroup(i));
+            else if (type == MoleculeStereocenters::ATOM_AND)
+                out.printf("MDLV30/STERAC%d ATOMS=(", stereocenters.getGroup(i));
+            else
+                continue;
+
+            QS_DEF(Array<int>, list);
+
+            list.clear();
+            list.push(i);
+
+            for (j = mol.vertexNext(i); j < mol.vertexEnd(); j = mol.vertexNext(j))
+                if (stereocenters.sameGroup(i, j))
+                {
+                    list.push(j);
+                    processed[j] = 1;
+                }
+
+            out.printf("%d", list.size());
+            for (j = 0; j < list.size(); j++)
+                out.printf(" %d", _atom_mapping[list[j]]);
+            out.writeChar(')');
+
+            _writeMultiString(output, buf.ptr(), buf.size());
+        }
+
+        if (mol.hasHighlighting())
+        {
+            if (mol.countHighlightedBonds() > 0)
+            {
+                ArrayOutput out(buf);
+
+                out.printf("MDLV30/HILITE BONDS=(%d", mol.countHighlightedBonds());
+
+                for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
+                    if (mol.isBondHighlighted(i))
+                        out.printf(" %d", _bond_mapping[i]);
+                out.writeChar(')');
+
+                _writeMultiString(output, buf.ptr(), buf.size());
+            }
+            if (mol.countHighlightedAtoms() > 0)
+            {
+                ArrayOutput out(buf);
+                out.printf("MDLV30/HILITE ATOMS=(%d", mol.countHighlightedAtoms());
+                for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
+                    if (mol.isAtomHighlighted(i))
+                        out.printf(" %d", _atom_mapping[i]);
+                out.writeChar(')');
+
+                _writeMultiString(output, buf.ptr(), buf.size());
+            }
+        }
+        if (mol.custom_collections.size() > 0)
+        {
+            for (i = mol.custom_collections.begin(); i != mol.custom_collections.end(); i = mol.custom_collections.next(i))
+            {
+                ArrayOutput out(buf);
+                out.printf("%s", mol.custom_collections.at(i));
+                _writeMultiString(output, buf.ptr(), buf.size());
+            }
+        }
+
+        output.writeStringCR("M  V30 END COLLECTION");
+    }
+
     output.writeStringCR("M  V30 END CTAB");
 
     int n_rgroups = mol.rgroups.getRGroupCount();
@@ -1212,6 +1213,7 @@ void MolfileSaver::_writeTGroup(Output& output, BaseMolecule& mol, int tg_idx)
 
 void MolfileSaver::_writeCtab2000(Output& output, BaseMolecule& mol, bool query)
 {
+    add_implicit_h = false;
     _handleCIP(mol);
     QueryMolecule* qmol = nullptr;
 
diff --git a/core/indigo-core/tests/common.cpp b/core/indigo-core/tests/common.cpp
index 9dafb72df0..69a38f253e 100644
--- a/core/indigo-core/tests/common.cpp
+++ b/core/indigo-core/tests/common.cpp
@@ -1,4 +1,6 @@
 #include "common.h"
+#include "reaction/reaction.h"
+#include "reaction/reaction_auto_loader.h"
 #include "reaction/reaction_cml_saver.h"
 #include "reaction/reaction_json_saver.h"
 #include "reaction/rxnfile_saver.h"
@@ -25,6 +27,13 @@ void IndigoCoreTest::loadMolecule(const char* buf, Molecule& molecule)
     loader.loadMolecule(molecule);
 }
 
+void IndigoCoreTest::loadReaction(const char* buf, Reaction& reaction)
+{
+    BufferScanner scanner(buf);
+    ReactionAutoLoader loader(scanner);
+    loader.loadReaction(reaction);
+}
+
 void IndigoCoreTest::loadQueryMolecule(const char* buf, QueryMolecule& queryMolecule)
 {
     BufferScanner scanner(buf);
diff --git a/core/indigo-core/tests/tests/molecule.cpp b/core/indigo-core/tests/tests/molecule.cpp
index 35630248fb..0401e9eb7e 100644
--- a/core/indigo-core/tests/tests/molecule.cpp
+++ b/core/indigo-core/tests/tests/molecule.cpp
@@ -15,11 +15,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  ***************************************************************************/
-
+#include <unistd.h>
 #include <gtest/gtest.h>
 
 #include <base_cpp/output.h>
 #include <base_cpp/scanner.h>
+#include <fstream>
 #include <molecule/crippen.h>
 #include <molecule/hybridization.h>
 #include <molecule/lipinski.h>
@@ -29,6 +30,11 @@
 #include <molecule/tpsa.h>
 
 #include "common.h"
+#include "molecule/elements.h"
+#include "molecule/molfile_saver.h"
+#include "reaction/reaction.h"
+#include "reaction/reaction_auto_loader.h"
+#include "reaction/reaction_automapper.h"
 
 using namespace std;
 using namespace indigo;
@@ -352,3 +358,40 @@ TEST_F(IndigoCoreMoleculeTest, dearomatize_smarts)
     // printf("%s", sm.c_str());
     EXPECT_STREQ("c1-c=c-c=c-c=1", sm.c_str());
 }
+
+TEST_F(IndigoCoreMoleculeTest, Reaction)
+{
+    Reaction reaction;
+    {
+        char dir[250];
+        getcwd(dir, 250);
+        cout << "Current directory: " << dir << "\n";
+        ifstream reactionFile("../../data/reactions/other/stereo_reaction.rxn");
+        string content;
+        string line;
+        while (getline(reactionFile, line))
+        {
+            content += line;
+            content.push_back('\n');
+        }
+        reactionFile.close();
+        //        cout << "The content is: \n" << content << "\n";
+        cout << "Loading reaction...";
+        loadReaction(content.c_str(), reaction);
+
+        reaction.aromatize(AromaticityOptions(AromaticityOptions::GENERIC));
+        ReactionAutomapper ram(reaction);
+        ram.automap(0);
+
+        for (int i = reaction.productBegin(); i < reaction.productEnd(); i = reaction.productNext(i))
+        {
+            cout << " *** Current Product Index is: " << i << " *** \n";
+            Molecule& mol = reaction.getMolecule(i);
+            string molOutStr;
+            StringOutput molOut(molOutStr);
+            MolfileSaver molSaver(molOut);
+            molSaver.saveMolecule(mol);
+            cout << molOutStr;
+        }
+    }
+}
\ No newline at end of file
diff --git a/data/reactions/other/stereo_reaction.rxn b/data/reactions/other/stereo_reaction.rxn
new file mode 100644
index 0000000000..fa2fc41435
--- /dev/null
+++ b/data/reactions/other/stereo_reaction.rxn
@@ -0,0 +1,217 @@
+$RXN
+
+      Mrv2305  052320232337
+
+  2  1
+$MOL
+
+  Mrv2305 05232323372D          
+
+ 18 19  0  0  0  0            999 V2000
+   -6.9420   -0.0902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6565   -0.5027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6565   -1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.9420   -1.7402    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2275   -1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2275   -0.5027    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.5357    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+   -4.7511   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.2661    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+   -4.7510    1.0800    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+   -5.5356    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+   -3.4411    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2031    1.3100    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.4961    1.8646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.4066    1.6399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -8.3709   -1.7403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.5130   -1.7403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8891    1.0256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  9 10  1  0  0  0  0
+ 10 11  1  0  0  0  0
+  7 11  1  0  0  0  0
+  9 12  1  1  0  0  0
+  3 16  2  0  0  0  0
+  5 17  2  0  0  0  0
+  8  9  1  0  0  0  0
+  7  8  1  0  0  0  0
+ 10 14  1  6  0  0  0
+ 12 18  1  0  0  0  0
+ 11 15  1  1  0  0  0
+ 11 13  1  6  0  0  0
+  1  6  1  0  0  0  0
+  5  6  1  0  0  0  0
+  7  6  1  1  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+M  STY  1   1 SUP
+M  SAL   1  1  15
+M  SBL   1  1  13
+M  SMT   1 Me
+M  SAP   1  1  15  11  1
+M  END
+$MOL
+
+  Mrv2305 05232323372D          
+
+ 24 26  0  0  0  0            999 V2000
+   -4.7105   -3.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382   -0.2125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+   -4.7106   -2.2750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9961   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9961   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.2816   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5671   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5671   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.2816   -2.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8527   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8527    0.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5672    0.6126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5671    1.4375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8527    1.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382    1.4376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382    0.6125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4237   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2907   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2907   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0052   -2.2750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7197   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4237   -2.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+ 10  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  2  0  0  0  0
+  4  9  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  2  0  0  0  0
+  7  8  1  0  0  0  0
+  7 10  1  0  0  0  0
+  8  9  2  0  0  0  0
+ 10 11  1  0  0  0  0
+ 10 17  1  0  0  0  0
+ 11 12  2  0  0  0  0
+ 11 16  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 14  2  0  0  0  0
+ 14 15  1  0  0  0  0
+ 15 16  2  0  0  0  0
+ 17 18  2  0  0  0  0
+ 17 24  1  0  0  0  0
+ 18 19  1  0  0  0  0
+ 19 20  2  0  0  0  0
+ 20 21  1  0  0  0  0
+ 20 23  1  0  0  0  0
+ 21 22  1  0  0  0  0
+ 23 24  2  0  0  0  0
+M  STY  1   1 SUP
+M  SAL   1 15   1   3   4   5   6   7   8   9  10  11  12  13  14  15  16
+M  SAL   1  8  17  18  19  20  21  22  23  24
+M  SBL   1  1   1
+M  SMT   1 DMTr
+M  SAP   1  1  10   2  1
+M  END
+$MOL
+
+  Mrv2305 05232323372D          
+
+ 41 45  0  0  0  0            999 V2000
+    2.9291   -0.1300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.2146   -0.5425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.2146   -1.3676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.9291   -1.7800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6436   -1.3676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6436   -0.5425    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    4.3354   -0.0398    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+    5.1200   -0.2947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.6049    0.3727    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+    5.1200    1.0402    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+    4.3354    0.7852    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+    6.4299    0.3727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6680    1.2701    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    5.3749    1.8248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    4.4645    1.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.5002   -1.7801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    4.3581   -1.7801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    6.9820    0.9858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   11.5195    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.1070    0.9858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   10.2820    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.8695    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.0445    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6320    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.0445    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.8695    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8070    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3945    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8070   -0.4432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3945   -1.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.5695   -1.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.1570   -0.4432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.5695    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3945    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.5695    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.1570    2.4147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.5695    3.1292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.1570    3.8437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.3320    3.8437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3945    3.1292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8070    2.4147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  9 10  1  0  0  0  0
+ 10 11  1  0  0  0  0
+  7 11  1  0  0  0  0
+  9 12  1  1  0  0  0
+  3 16  2  0  0  0  0
+  5 17  2  0  0  0  0
+  8  9  1  0  0  0  0
+  7  8  1  0  0  0  0
+ 10 14  1  6  0  0  0
+ 12 18  1  0  0  0  0
+ 11 15  1  1  0  0  0
+ 11 13  1  6  0  0  0
+  1  6  1  0  0  0  0
+  5  6  1  0  0  0  0
+  7  6  1  1  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+ 18 27  1  0  0  0  0
+ 19 20  1  0  0  0  0
+ 20 21  1  0  0  0  0
+ 21 22  2  0  0  0  0
+ 21 26  1  0  0  0  0
+ 22 23  1  0  0  0  0
+ 23 24  2  0  0  0  0
+ 24 25  1  0  0  0  0
+ 24 27  1  0  0  0  0
+ 25 26  2  0  0  0  0
+ 27 28  1  0  0  0  0
+ 27 34  1  0  0  0  0
+ 28 29  2  0  0  0  0
+ 28 33  1  0  0  0  0
+ 29 30  1  0  0  0  0
+ 30 31  2  0  0  0  0
+ 31 32  1  0  0  0  0
+ 32 33  2  0  0  0  0
+ 34 35  2  0  0  0  0
+ 34 41  1  0  0  0  0
+ 35 36  1  0  0  0  0
+ 36 37  2  0  0  0  0
+ 37 38  1  0  0  0  0
+ 37 40  1  0  0  0  0
+ 38 39  1  0  0  0  0
+ 40 41  2  0  0  0  0
+M  STY  2   1 SUP   2 SUP
+M  SAL   1  1  15
+M  SBL   1  1  13
+M  SMT   1 Me
+M  SAP   1  1  15  11  1
+M  SAL   2 15  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33
+M  SAL   2  8  34  35  36  37  38  39  40  41
+M  SBL   2  1  20
+M  SMT   2 DMTr
+M  SAP   2  1  27  18  1
+M  END

From 4b0267b54764435caedc268d83a2535c2b4f33fb Mon Sep 17 00:00:00 2001
From: Yechen Qiao <yqiao@sapiosciences.com>
Date: Fri, 6 Mar 2026 15:32:12 -0500
Subject: [PATCH 2/5] [Sapio] [CHEMBUGS-184] removed old hack on turning off
 implicit hydrogen counts added earlier for Issue 1 in
 https://github.com/epam/Indigo/issues/2109. Added more unit tests. Tested
 manually and confirmed original problem went away.

---
 .../molecule/src/molfile_saver.cpp            |  1 -
 core/indigo-core/tests/tests/molecule.cpp     | 67 +++++++++++++++++++
 2 files changed, 67 insertions(+), 1 deletion(-)

diff --git a/core/indigo-core/molecule/src/molfile_saver.cpp b/core/indigo-core/molecule/src/molfile_saver.cpp
index 2c753b40bb..927f34579f 100644
--- a/core/indigo-core/molecule/src/molfile_saver.cpp
+++ b/core/indigo-core/molecule/src/molfile_saver.cpp
@@ -444,7 +444,6 @@ void MolfileSaver::_writeMultiString(Output& output, const char* string, int len
 
 void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
 {
-    add_implicit_h = false;
     _handleCIP(mol);
     if (mol.tgroups.getTGroupCount())
         _handleMonomers(mol);
diff --git a/core/indigo-core/tests/tests/molecule.cpp b/core/indigo-core/tests/tests/molecule.cpp
index 0401e9eb7e..bc4fc0ced6 100644
--- a/core/indigo-core/tests/tests/molecule.cpp
+++ b/core/indigo-core/tests/tests/molecule.cpp
@@ -31,6 +31,7 @@
 
 #include "common.h"
 #include "molecule/elements.h"
+#include "molecule/molfile_loader.h"
 #include "molecule/molfile_saver.h"
 #include "reaction/reaction.h"
 #include "reaction/reaction_auto_loader.h"
@@ -359,6 +360,72 @@ TEST_F(IndigoCoreMoleculeTest, dearomatize_smarts)
     EXPECT_STREQ("c1-c=c-c=c-c=1", sm.c_str());
 }
 
+/*
+ * V3000 molfile roundtrip with add_implicit_h = true.
+ * Ensures SGROUP block is written before COLLECTION (CT file spec order) and
+ * that implicit H (e.g. MRV_IMPLICIT_H data sgroups) roundtrip correctly.
+ */
+TEST_F(IndigoCoreMoleculeTest, molfileV3000RoundtripImplicitH)
+{
+    Molecule mol;
+    loadMolecule("c1ccccc1O", mol); // phenol: aromatic carbons have implicit H
+
+    string molfileStr;
+    StringOutput out(molfileStr);
+    MolfileSaver saver(out);
+    saver.mode = MolfileSaver::MODE_3000;
+    saver.add_implicit_h = true;
+    saver.saveMolecule(mol);
+
+    // CT file order: SGROUP block must appear before COLLECTION block
+    size_t posSgroup = molfileStr.find("M  V30 BEGIN SGROUP");
+    size_t posCollection = molfileStr.find("M  V30 BEGIN COLLECTION");
+    if (posSgroup != string::npos && posCollection != string::npos)
+        EXPECT_LT(posSgroup, posCollection) << "SGROUP must be written before COLLECTION (CT file spec)";
+
+    BufferScanner scanner(molfileStr.c_str());
+    MolfileLoader loader(scanner);
+    Molecule mol2;
+    loader.loadMolecule(mol2);
+
+    EXPECT_EQ(mol.vertexCount(), mol2.vertexCount()) << "Roundtrip: atom count must match";
+    EXPECT_EQ(mol.edgeCount(), mol2.edgeCount()) << "Roundtrip: bond count must match";
+    // Same structure: roundtrip mol2 should match original as substructure and vice versa
+    EXPECT_TRUE(substructureMatch(smiles(mol2).c_str(), smiles(mol).c_str()));
+    EXPECT_TRUE(substructureMatch(smiles(mol).c_str(), smiles(mol2).c_str()));
+}
+
+/*
+ * V3000 molfile roundtrip with add_implicit_h = false (explicit H only).
+ * Ensures molecules without MRV_IMPLICIT_H sgroups roundtrip correctly.
+ */
+TEST_F(IndigoCoreMoleculeTest, molfileV3000RoundtripExplicitH)
+{
+    Molecule mol;
+    loadMolecule("CCO", mol);
+
+    string molfileStr;
+    StringOutput out(molfileStr);
+    MolfileSaver saver(out);
+    saver.mode = MolfileSaver::MODE_3000;
+    saver.add_implicit_h = false;
+    saver.saveMolecule(mol);
+
+    size_t posSgroup = molfileStr.find("M  V30 BEGIN SGROUP");
+    size_t posCollection = molfileStr.find("M  V30 BEGIN COLLECTION");
+    if (posSgroup != string::npos && posCollection != string::npos)
+        EXPECT_LT(posSgroup, posCollection) << "SGROUP must be written before COLLECTION (CT file spec)";
+
+    BufferScanner scanner(molfileStr.c_str());
+    MolfileLoader loader(scanner);
+    Molecule mol2;
+    loader.loadMolecule(mol2);
+
+    EXPECT_EQ(mol.vertexCount(), mol2.vertexCount()) << "Roundtrip: atom count must match";
+    EXPECT_EQ(mol.edgeCount(), mol2.edgeCount()) << "Roundtrip: bond count must match";
+    EXPECT_STREQ(smiles(mol).c_str(), smiles(mol2).c_str()) << "Roundtrip: SMILES must match";
+}
+
 TEST_F(IndigoCoreMoleculeTest, Reaction)
 {
     Reaction reaction;

From e4ce543220e55d73dff939a0d111fc61ad40cd3c Mon Sep 17 00:00:00 2001
From: Yechen Qiao <yqiao@sapiosciences.com>
Date: Thu, 12 Mar 2026 08:42:52 -0400
Subject: [PATCH 3/5] clang format and windows env fix.

---
 core/indigo-core/tests/tests/molecule.cpp | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/core/indigo-core/tests/tests/molecule.cpp b/core/indigo-core/tests/tests/molecule.cpp
index bc4fc0ced6..65fdef5f62 100644
--- a/core/indigo-core/tests/tests/molecule.cpp
+++ b/core/indigo-core/tests/tests/molecule.cpp
@@ -15,7 +15,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  ***************************************************************************/
+
+#ifdef _WIN32
+#include <direct.h>
+#define getcwd _getcwd
+#else
 #include <unistd.h>
+#endif
 #include <gtest/gtest.h>
 
 #include <base_cpp/output.h>

From 4efd18b4d77291f0a6d6bb8a28f070a213c1d8a5 Mon Sep 17 00:00:00 2001
From: Yechen Qiao <yqiao@sapiosciences.com>
Date: Thu, 12 Mar 2026 11:03:26 -0400
Subject: [PATCH 4/5] CHEMBUGS-184 Merge Up Fixes. 1. Use the old ordering
 unless S-Group block is actively being used. 2. Changed unit test on
 molecule.cpp so that it is no longer testing reaction but individual
 problematic molecules in reaction.

---
 .../molecule/src/molfile_saver.cpp            | 196 ++++++-----
 core/indigo-core/tests/tests/molecule.cpp     | 333 ++++++++++++------
 data/reactions/other/stereo_reaction.rxn      | 217 ------------
 3 files changed, 340 insertions(+), 406 deletions(-)
 delete mode 100644 data/reactions/other/stereo_reaction.rxn

diff --git a/core/indigo-core/molecule/src/molfile_saver.cpp b/core/indigo-core/molecule/src/molfile_saver.cpp
index 927f34579f..6d638c69c1 100644
--- a/core/indigo-core/molecule/src/molfile_saver.cpp
+++ b/core/indigo-core/molecule/src/molfile_saver.cpp
@@ -21,6 +21,7 @@
 #include <ctime>
 #include <map>
 #include <sstream>
+#include <string>
 
 #include "base_cpp/locale_guard.h"
 #include "base_cpp/output.h"
@@ -790,7 +791,110 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
     QS_DEF(Array<int>, sgs_sorted);
     _checkSGroupIndices(mol, sgs_sorted);
 
-    if (mol.countSGroups() > 0)
+    //[Sapio] [CHEMBUGS-184] S-GROUP needs to be before COLLECTION when S GROUP is used.
+    const bool has_sgroups = (mol.countSGroups() > 0);
+    MoleculeStereocenters& stereocenters = mol.stereocenters;
+    const bool has_collection = (stereocenters.begin() != stereocenters.end() || mol.hasHighlighting() || mol.custom_collections.size() > 0);
+    const bool sgroup_collection_order_reversed = (has_sgroups && has_collection);
+
+    // Default order: COLLECTION before SGROUP.
+    // When sgroup_collection_order_reversed, write SGROUP then COLLECTION (CT spec) page 22.
+    std::string collection_str;
+    StringOutput collection_buf(collection_str);
+    Output* collection_dest_ptr;
+    if (sgroup_collection_order_reversed)
+        collection_dest_ptr = static_cast<Output*>(&collection_buf);
+    else
+        collection_dest_ptr = &output;
+    Output& collection_dest = *collection_dest_ptr;
+
+    if (has_collection)
+    {
+        collection_dest.writeStringCR("M  V30 BEGIN COLLECTION");
+
+        QS_DEF(Array<int>, processed);
+
+        processed.clear_resize(mol.vertexEnd());
+        processed.zerofill();
+
+        for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
+        {
+            if (processed[i])
+                continue;
+
+            ArrayOutput out(buf);
+            int j, type = stereocenters.getType(i);
+
+            if (type == MoleculeStereocenters::ATOM_ABS)
+                out.writeString("MDLV30/STEABS ATOMS=(");
+            else if (type == MoleculeStereocenters::ATOM_OR)
+                out.printf("MDLV30/STEREL%d ATOMS=(", stereocenters.getGroup(i));
+            else if (type == MoleculeStereocenters::ATOM_AND)
+                out.printf("MDLV30/STERAC%d ATOMS=(", stereocenters.getGroup(i));
+            else
+                continue;
+
+            QS_DEF(Array<int>, list);
+
+            list.clear();
+            list.push(i);
+
+            for (j = mol.vertexNext(i); j < mol.vertexEnd(); j = mol.vertexNext(j))
+                if (stereocenters.sameGroup(i, j))
+                {
+                    list.push(j);
+                    processed[j] = 1;
+                }
+
+            out.printf("%d", list.size());
+            for (j = 0; j < list.size(); j++)
+                out.printf(" %d", _atom_mapping[list[j]]);
+            out.writeChar(')');
+
+            _writeMultiString(collection_dest, buf.ptr(), buf.size());
+        }
+
+        if (mol.hasHighlighting())
+        {
+            if (mol.countHighlightedBonds() > 0)
+            {
+                ArrayOutput out(buf);
+
+                out.printf("MDLV30/HILITE BONDS=(%d", mol.countHighlightedBonds());
+
+                for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
+                    if (mol.isBondHighlighted(i))
+                        out.printf(" %d", _bond_mapping[i]);
+                out.writeChar(')');
+
+                _writeMultiString(collection_dest, buf.ptr(), buf.size());
+            }
+            if (mol.countHighlightedAtoms() > 0)
+            {
+                ArrayOutput out(buf);
+                out.printf("MDLV30/HILITE ATOMS=(%d", mol.countHighlightedAtoms());
+                for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
+                    if (mol.isAtomHighlighted(i))
+                        out.printf(" %d", _atom_mapping[i]);
+                out.writeChar(')');
+
+                _writeMultiString(collection_dest, buf.ptr(), buf.size());
+            }
+        }
+        if (mol.custom_collections.size() > 0)
+        {
+            for (i = mol.custom_collections.begin(); i != mol.custom_collections.end(); i = mol.custom_collections.next(i))
+            {
+                ArrayOutput out(buf);
+                out.printf("%s", mol.custom_collections.at(i));
+                _writeMultiString(collection_dest, buf.ptr(), buf.size());
+            }
+        }
+
+        collection_dest.writeStringCR("M  V30 END COLLECTION");
+    }
+
+    if (has_sgroups)
     {
         MoleculeSGroups* sgroups = &mol.sgroups;
         int idx = 1;
@@ -986,93 +1090,8 @@ void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
         _removeImplicitSGroups(mol, implicit_sgroups_indexes);
     }
 
-    MoleculeStereocenters& stereocenters = mol.stereocenters;
-
-    if (stereocenters.begin() != stereocenters.end() || mol.hasHighlighting())
-    {
-        output.writeStringCR("M  V30 BEGIN COLLECTION");
-
-        QS_DEF(Array<int>, processed);
-
-        processed.clear_resize(mol.vertexEnd());
-        processed.zerofill();
-
-        for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
-        {
-            if (processed[i])
-                continue;
-
-            ArrayOutput out(buf);
-            int j, type = stereocenters.getType(i);
-
-            if (type == MoleculeStereocenters::ATOM_ABS)
-                out.writeString("MDLV30/STEABS ATOMS=(");
-            else if (type == MoleculeStereocenters::ATOM_OR)
-                out.printf("MDLV30/STEREL%d ATOMS=(", stereocenters.getGroup(i));
-            else if (type == MoleculeStereocenters::ATOM_AND)
-                out.printf("MDLV30/STERAC%d ATOMS=(", stereocenters.getGroup(i));
-            else
-                continue;
-
-            QS_DEF(Array<int>, list);
-
-            list.clear();
-            list.push(i);
-
-            for (j = mol.vertexNext(i); j < mol.vertexEnd(); j = mol.vertexNext(j))
-                if (stereocenters.sameGroup(i, j))
-                {
-                    list.push(j);
-                    processed[j] = 1;
-                }
-
-            out.printf("%d", list.size());
-            for (j = 0; j < list.size(); j++)
-                out.printf(" %d", _atom_mapping[list[j]]);
-            out.writeChar(')');
-
-            _writeMultiString(output, buf.ptr(), buf.size());
-        }
-
-        if (mol.hasHighlighting())
-        {
-            if (mol.countHighlightedBonds() > 0)
-            {
-                ArrayOutput out(buf);
-
-                out.printf("MDLV30/HILITE BONDS=(%d", mol.countHighlightedBonds());
-
-                for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
-                    if (mol.isBondHighlighted(i))
-                        out.printf(" %d", _bond_mapping[i]);
-                out.writeChar(')');
-
-                _writeMultiString(output, buf.ptr(), buf.size());
-            }
-            if (mol.countHighlightedAtoms() > 0)
-            {
-                ArrayOutput out(buf);
-                out.printf("MDLV30/HILITE ATOMS=(%d", mol.countHighlightedAtoms());
-                for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
-                    if (mol.isAtomHighlighted(i))
-                        out.printf(" %d", _atom_mapping[i]);
-                out.writeChar(')');
-
-                _writeMultiString(output, buf.ptr(), buf.size());
-            }
-        }
-        if (mol.custom_collections.size() > 0)
-        {
-            for (i = mol.custom_collections.begin(); i != mol.custom_collections.end(); i = mol.custom_collections.next(i))
-            {
-                ArrayOutput out(buf);
-                out.printf("%s", mol.custom_collections.at(i));
-                _writeMultiString(output, buf.ptr(), buf.size());
-            }
-        }
-
-        output.writeStringCR("M  V30 END COLLECTION");
-    }
+    if (sgroup_collection_order_reversed)
+        output.write(collection_str.data(), static_cast<int>(collection_str.size()));
 
     output.writeStringCR("M  V30 END CTAB");
 
@@ -1212,7 +1231,6 @@ void MolfileSaver::_writeTGroup(Output& output, BaseMolecule& mol, int tg_idx)
 
 void MolfileSaver::_writeCtab2000(Output& output, BaseMolecule& mol, bool query)
 {
-    add_implicit_h = false;
     _handleCIP(mol);
     QueryMolecule* qmol = nullptr;
 
diff --git a/core/indigo-core/tests/tests/molecule.cpp b/core/indigo-core/tests/tests/molecule.cpp
index 65fdef5f62..3d569d1ca2 100644
--- a/core/indigo-core/tests/tests/molecule.cpp
+++ b/core/indigo-core/tests/tests/molecule.cpp
@@ -16,32 +16,21 @@
  * limitations under the License.
  ***************************************************************************/
 
-#ifdef _WIN32
-#include <direct.h>
-#define getcwd _getcwd
-#else
-#include <unistd.h>
-#endif
 #include <gtest/gtest.h>
 
 #include <base_cpp/output.h>
 #include <base_cpp/scanner.h>
-#include <fstream>
 #include <molecule/crippen.h>
 #include <molecule/hybridization.h>
 #include <molecule/lipinski.h>
 #include <molecule/molecule_mass.h>
+#include <molecule/molfile_loader.h>
 #include <molecule/smiles_loader.h>
 #include <molecule/smiles_saver.h>
 #include <molecule/tpsa.h>
 
 #include "common.h"
 #include "molecule/elements.h"
-#include "molecule/molfile_loader.h"
-#include "molecule/molfile_saver.h"
-#include "reaction/reaction.h"
-#include "reaction/reaction_auto_loader.h"
-#include "reaction/reaction_automapper.h"
 
 using namespace std;
 using namespace indigo;
@@ -366,105 +355,249 @@ TEST_F(IndigoCoreMoleculeTest, dearomatize_smarts)
     EXPECT_STREQ("c1-c=c-c=c-c=1", sm.c_str());
 }
 
-/*
- * V3000 molfile roundtrip with add_implicit_h = true.
- * Ensures SGROUP block is written before COLLECTION (CT file spec order) and
- * that implicit H (e.g. MRV_IMPLICIT_H data sgroups) roundtrip correctly.
- */
-TEST_F(IndigoCoreMoleculeTest, molfileV3000RoundtripImplicitH)
+// [Sapio] [CHEMBUGS-184] Stereo reaction molecules (from former stereo_reaction.rxn): load as mol blocks to verify parsing.
+namespace
 {
-    Molecule mol;
-    loadMolecule("c1ccccc1O", mol); // phenol: aromatic carbons have implicit H
-
-    string molfileStr;
-    StringOutput out(molfileStr);
-    MolfileSaver saver(out);
-    saver.mode = MolfileSaver::MODE_3000;
-    saver.add_implicit_h = true;
-    saver.saveMolecule(mol);
+    const char* const stereoReactionReactant1 = R"(
+  Mrv2305 05232323372D
 
-    // CT file order: SGROUP block must appear before COLLECTION block
-    size_t posSgroup = molfileStr.find("M  V30 BEGIN SGROUP");
-    size_t posCollection = molfileStr.find("M  V30 BEGIN COLLECTION");
-    if (posSgroup != string::npos && posCollection != string::npos)
-        EXPECT_LT(posSgroup, posCollection) << "SGROUP must be written before COLLECTION (CT file spec)";
+ 18 19  0  0  0  0            999 V2000
+   -6.9420   -0.0902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6565   -0.5027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -7.6565   -1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.9420   -1.7402    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2275   -1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2275   -0.5027    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.5357    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+   -4.7511   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.2661    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+   -4.7510    1.0800    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+   -5.5356    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+   -3.4411    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -6.2031    1.3100    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.4961    1.8646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.4066    1.6399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -8.3709   -1.7403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -5.5130   -1.7403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.8891    1.0256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  9 10  1  0  0  0  0
+ 10 11  1  0  0  0  0
+  7 11  1  0  0  0  0
+  9 12  1  1  0  0  0
+  3 16  2  0  0  0  0
+  5 17  2  0  0  0  0
+  8  9  1  0  0  0  0
+  7  8  1  0  0  0  0
+ 10 14  1  6  0  0  0
+ 12 18  1  0  0  0  0
+ 11 15  1  1  0  0  0
+ 11 13  1  6  0  0  0
+  1  6  1  0  0  0  0
+  5  6  1  0  0  0  0
+  7  6  1  1  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+M  STY  1   1 SUP
+M  SAL   1  1  15
+M  SBL   1  1  13
+M  SMT   1 Me
+M  SAP   1  1  15  11  1
+M  END
+)";
+    const char* const stereoReactionReactant2 = R"(
+  Mrv2305 05232323372D
 
-    BufferScanner scanner(molfileStr.c_str());
-    MolfileLoader loader(scanner);
-    Molecule mol2;
-    loader.loadMolecule(mol2);
+ 24 26  0  0  0  0            999 V2000
+   -4.7105   -3.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382   -0.2125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+   -4.7106   -2.2750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9961   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.9961   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.2816   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5671   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5671   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.2816   -2.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8527   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8527    0.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5672    0.6126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.5671    1.4375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.8527    1.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382    1.4376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382    0.6125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4237   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2907   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2907   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.0052   -2.2750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7197   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.4237   -2.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1382   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+ 10  2  1  0  0  0  0
+  1  3  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  2  0  0  0  0
+  4  9  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  2  0  0  0  0
+  7  8  1  0  0  0  0
+  7 10  1  0  0  0  0
+  8  9  2  0  0  0  0
+ 10 11  1  0  0  0  0
+ 10 17  1  0  0  0  0
+ 11 12  2  0  0  0  0
+ 11 16  1  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 14  2  0  0  0  0
+ 14 15  1  0  0  0  0
+ 15 16  2  0  0  0  0
+ 17 18  2  0  0  0  0
+ 17 24  1  0  0  0  0
+ 18 19  1  0  0  0  0
+ 19 20  2  0  0  0  0
+ 20 21  1  0  0  0  0
+ 20 23  1  0  0  0  0
+ 21 22  1  0  0  0  0
+ 23 24  2  0  0  0  0
+M  STY  1   1 SUP
+M  SAL   1 15   1   3   4   5   6   7   8   9  10  11  12  13  14  15  16
+M  SAL   1  8  17  18  19  20  21  22  23  24
+M  SBL   1  1   1
+M  SMT   1 DMTr
+M  SAP   1  1  10   2  1
+M  END
+)";
+    const char* const stereoReactionProduct = R"(
+  Mrv2305 05232323372D
 
-    EXPECT_EQ(mol.vertexCount(), mol2.vertexCount()) << "Roundtrip: atom count must match";
-    EXPECT_EQ(mol.edgeCount(), mol2.edgeCount()) << "Roundtrip: bond count must match";
-    // Same structure: roundtrip mol2 should match original as substructure and vice versa
-    EXPECT_TRUE(substructureMatch(smiles(mol2).c_str(), smiles(mol).c_str()));
-    EXPECT_TRUE(substructureMatch(smiles(mol).c_str(), smiles(mol2).c_str()));
+ 41 45  0  0  0  0            999 V2000
+    2.9291   -0.1300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.2146   -0.5425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.2146   -1.3676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.9291   -1.7800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6436   -1.3676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6436   -0.5425    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    4.3354   -0.0398    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+    5.1200   -0.2947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.6049    0.3727    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+    5.1200    1.0402    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
+    4.3354    0.7852    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
+    6.4299    0.3727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.6680    1.2701    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
+    5.3749    1.8248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    4.4645    1.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.5002   -1.7801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    4.3581   -1.7801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    6.9820    0.9858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   11.5195    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   11.1070    0.9858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+   10.2820    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.8695    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.0445    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6320    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.0445    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.8695    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8070    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3945    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8070   -0.4432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3945   -1.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.5695   -1.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.1570   -0.4432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.5695    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3945    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.5695    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.1570    2.4147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.5695    3.1292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    6.1570    3.8437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    5.3320    3.8437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3945    3.1292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.8070    2.4147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  9 10  1  0  0  0  0
+ 10 11  1  0  0  0  0
+  7 11  1  0  0  0  0
+  9 12  1  1  0  0  0
+  3 16  2  0  0  0  0
+  5 17  2  0  0  0  0
+  8  9  1  0  0  0  0
+  7  8  1  0  0  0  0
+ 10 14  1  6  0  0  0
+ 12 18  1  0  0  0  0
+ 11 15  1  1  0  0  0
+ 11 13  1  6  0  0  0
+  1  6  1  0  0  0  0
+  5  6  1  0  0  0  0
+  7  6  1  1  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+ 18 27  1  0  0  0  0
+ 19 20  1  0  0  0  0
+ 20 21  1  0  0  0  0
+ 21 22  2  0  0  0  0
+ 21 26  1  0  0  0  0
+ 22 23  1  0  0  0  0
+ 23 24  2  0  0  0  0
+ 24 25  1  0  0  0  0
+ 24 27  1  0  0  0  0
+ 25 26  2  0  0  0  0
+ 27 28  1  0  0  0  0
+ 27 34  1  0  0  0  0
+ 28 29  2  0  0  0  0
+ 28 33  1  0  0  0  0
+ 29 30  1  0  0  0  0
+ 30 31  2  0  0  0  0
+ 31 32  1  0  0  0  0
+ 32 33  2  0  0  0  0
+ 34 35  2  0  0  0  0
+ 34 41  1  0  0  0  0
+ 35 36  1  0  0  0  0
+ 36 37  2  0  0  0  0
+ 37 38  1  0  0  0  0
+ 37 40  1  0  0  0  0
+ 38 39  1  0  0  0  0
+ 40 41  2  0  0  0  0
+M  STY  2   1 SUP   2 SUP
+M  SAL   1  1  15
+M  SBL   1  1  13
+M  SMT   1 Me
+M  SAP   1  1  15  11  1
+M  SAL   2 15  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33
+M  SAL   2  8  34  35  36  37  38  39  40  41
+M  SBL   2  1  20
+M  SMT   2 DMTr
+M  SAP   2  1  27  18  1
+M  END
+)";
 }
 
-/*
- * V3000 molfile roundtrip with add_implicit_h = false (explicit H only).
- * Ensures molecules without MRV_IMPLICIT_H sgroups roundtrip correctly.
- */
-TEST_F(IndigoCoreMoleculeTest, molfileV3000RoundtripExplicitH)
+TEST_F(IndigoCoreMoleculeTest, stereoReactionReactant1)
 {
     Molecule mol;
-    loadMolecule("CCO", mol);
-
-    string molfileStr;
-    StringOutput out(molfileStr);
-    MolfileSaver saver(out);
-    saver.mode = MolfileSaver::MODE_3000;
-    saver.add_implicit_h = false;
-    saver.saveMolecule(mol);
-
-    size_t posSgroup = molfileStr.find("M  V30 BEGIN SGROUP");
-    size_t posCollection = molfileStr.find("M  V30 BEGIN COLLECTION");
-    if (posSgroup != string::npos && posCollection != string::npos)
-        EXPECT_LT(posSgroup, posCollection) << "SGROUP must be written before COLLECTION (CT file spec)";
-
-    BufferScanner scanner(molfileStr.c_str());
+    BufferScanner scanner(stereoReactionReactant1);
     MolfileLoader loader(scanner);
-    Molecule mol2;
-    loader.loadMolecule(mol2);
-
-    EXPECT_EQ(mol.vertexCount(), mol2.vertexCount()) << "Roundtrip: atom count must match";
-    EXPECT_EQ(mol.edgeCount(), mol2.edgeCount()) << "Roundtrip: bond count must match";
-    EXPECT_STREQ(smiles(mol).c_str(), smiles(mol2).c_str()) << "Roundtrip: SMILES must match";
+    loader.loadMolecule(mol);
+    EXPECT_EQ(18, mol.vertexCount());
+    EXPECT_EQ(19, mol.edgeCount());
 }
 
-TEST_F(IndigoCoreMoleculeTest, Reaction)
+TEST_F(IndigoCoreMoleculeTest, stereoReactionReactant2)
 {
-    Reaction reaction;
-    {
-        char dir[250];
-        getcwd(dir, 250);
-        cout << "Current directory: " << dir << "\n";
-        ifstream reactionFile("../../data/reactions/other/stereo_reaction.rxn");
-        string content;
-        string line;
-        while (getline(reactionFile, line))
-        {
-            content += line;
-            content.push_back('\n');
-        }
-        reactionFile.close();
-        //        cout << "The content is: \n" << content << "\n";
-        cout << "Loading reaction...";
-        loadReaction(content.c_str(), reaction);
-
-        reaction.aromatize(AromaticityOptions(AromaticityOptions::GENERIC));
-        ReactionAutomapper ram(reaction);
-        ram.automap(0);
+    Molecule mol;
+    BufferScanner scanner(stereoReactionReactant2);
+    MolfileLoader loader(scanner);
+    loader.loadMolecule(mol);
+    EXPECT_EQ(24, mol.vertexCount());
+    EXPECT_EQ(26, mol.edgeCount());
+}
 
-        for (int i = reaction.productBegin(); i < reaction.productEnd(); i = reaction.productNext(i))
-        {
-            cout << " *** Current Product Index is: " << i << " *** \n";
-            Molecule& mol = reaction.getMolecule(i);
-            string molOutStr;
-            StringOutput molOut(molOutStr);
-            MolfileSaver molSaver(molOut);
-            molSaver.saveMolecule(mol);
-            cout << molOutStr;
-        }
-    }
+TEST_F(IndigoCoreMoleculeTest, stereoReactionProduct)
+{
+    Molecule mol;
+    BufferScanner scanner(stereoReactionProduct);
+    MolfileLoader loader(scanner);
+    loader.loadMolecule(mol);
+    EXPECT_EQ(41, mol.vertexCount());
+    EXPECT_EQ(45, mol.edgeCount());
 }
\ No newline at end of file
diff --git a/data/reactions/other/stereo_reaction.rxn b/data/reactions/other/stereo_reaction.rxn
deleted file mode 100644
index fa2fc41435..0000000000
--- a/data/reactions/other/stereo_reaction.rxn
+++ /dev/null
@@ -1,217 +0,0 @@
-$RXN
-
-      Mrv2305  052320232337
-
-  2  1
-$MOL
-
-  Mrv2305 05232323372D          
-
- 18 19  0  0  0  0            999 V2000
-   -6.9420   -0.0902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -7.6565   -0.5027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -7.6565   -1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -6.9420   -1.7402    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -6.2275   -1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -6.2275   -0.5027    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-   -5.5357    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
-   -4.7511   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -4.2661    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
-   -4.7510    1.0800    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
-   -5.5356    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
-   -3.4411    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -6.2031    1.3100    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-   -4.4961    1.8646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -5.4066    1.6399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -8.3709   -1.7403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -5.5130   -1.7403    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.8891    1.0256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-  1  2  2  0  0  0  0
-  2  3  1  0  0  0  0
-  9 10  1  0  0  0  0
- 10 11  1  0  0  0  0
-  7 11  1  0  0  0  0
-  9 12  1  1  0  0  0
-  3 16  2  0  0  0  0
-  5 17  2  0  0  0  0
-  8  9  1  0  0  0  0
-  7  8  1  0  0  0  0
- 10 14  1  6  0  0  0
- 12 18  1  0  0  0  0
- 11 15  1  1  0  0  0
- 11 13  1  6  0  0  0
-  1  6  1  0  0  0  0
-  5  6  1  0  0  0  0
-  7  6  1  1  0  0  0
-  3  4  1  0  0  0  0
-  4  5  1  0  0  0  0
-M  STY  1   1 SUP
-M  SAL   1  1  15
-M  SBL   1  1  13
-M  SMT   1 Me
-M  SAP   1  1  15  11  1
-M  END
-$MOL
-
-  Mrv2305 05232323372D          
-
- 24 26  0  0  0  0            999 V2000
-   -4.7105   -3.1000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.1382   -0.2125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
-   -4.7106   -2.2750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.9961   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.9961   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.2816   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.5671   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.5671   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -3.2816   -2.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.8527   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.8527    0.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.5672    0.6126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -2.5671    1.4375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.8527    1.8500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.1382    1.4376    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.1382    0.6125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.1382   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.4237   -0.6250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.2907   -1.0375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    0.2907   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    1.0052   -2.2750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    1.7197   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -0.4237   -2.2750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   -1.1382   -1.8625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
- 10  2  1  0  0  0  0
-  1  3  1  0  0  0  0
-  3  4  1  0  0  0  0
-  4  5  2  0  0  0  0
-  4  9  1  0  0  0  0
-  5  6  1  0  0  0  0
-  6  7  2  0  0  0  0
-  7  8  1  0  0  0  0
-  7 10  1  0  0  0  0
-  8  9  2  0  0  0  0
- 10 11  1  0  0  0  0
- 10 17  1  0  0  0  0
- 11 12  2  0  0  0  0
- 11 16  1  0  0  0  0
- 12 13  1  0  0  0  0
- 13 14  2  0  0  0  0
- 14 15  1  0  0  0  0
- 15 16  2  0  0  0  0
- 17 18  2  0  0  0  0
- 17 24  1  0  0  0  0
- 18 19  1  0  0  0  0
- 19 20  2  0  0  0  0
- 20 21  1  0  0  0  0
- 20 23  1  0  0  0  0
- 21 22  1  0  0  0  0
- 23 24  2  0  0  0  0
-M  STY  1   1 SUP
-M  SAL   1 15   1   3   4   5   6   7   8   9  10  11  12  13  14  15  16
-M  SAL   1  8  17  18  19  20  21  22  23  24
-M  SBL   1  1   1
-M  SMT   1 DMTr
-M  SAP   1  1  10   2  1
-M  END
-$MOL
-
-  Mrv2305 05232323372D          
-
- 41 45  0  0  0  0            999 V2000
-    2.9291   -0.1300    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.2146   -0.5425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.2146   -1.3676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    2.9291   -1.7800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-    3.6436   -1.3676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.6436   -0.5425    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
-    4.3354   -0.0398    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
-    5.1200   -0.2947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    5.6049    0.3727    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
-    5.1200    1.0402    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
-    4.3354    0.7852    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
-    6.4299    0.3727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    3.6680    1.2701    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
-    5.3749    1.8248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    4.4645    1.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    1.5002   -1.7801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    4.3581   -1.7801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    6.9820    0.9858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   11.5195    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-   11.1070    0.9858    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-   10.2820    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    9.8695    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    9.0445    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    8.6320    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    9.0445    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    9.8695    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.8070    0.9858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.3945    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.8070   -0.4432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.3945   -1.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.5695   -1.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.1570   -0.4432    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.5695    0.2713    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.3945    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.5695    1.7003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.1570    2.4147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.5695    3.1292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    6.1570    3.8437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
-    5.3320    3.8437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.3945    3.1292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-    7.8070    2.4147    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
-  1  2  2  0  0  0  0
-  2  3  1  0  0  0  0
-  9 10  1  0  0  0  0
- 10 11  1  0  0  0  0
-  7 11  1  0  0  0  0
-  9 12  1  1  0  0  0
-  3 16  2  0  0  0  0
-  5 17  2  0  0  0  0
-  8  9  1  0  0  0  0
-  7  8  1  0  0  0  0
- 10 14  1  6  0  0  0
- 12 18  1  0  0  0  0
- 11 15  1  1  0  0  0
- 11 13  1  6  0  0  0
-  1  6  1  0  0  0  0
-  5  6  1  0  0  0  0
-  7  6  1  1  0  0  0
-  3  4  1  0  0  0  0
-  4  5  1  0  0  0  0
- 18 27  1  0  0  0  0
- 19 20  1  0  0  0  0
- 20 21  1  0  0  0  0
- 21 22  2  0  0  0  0
- 21 26  1  0  0  0  0
- 22 23  1  0  0  0  0
- 23 24  2  0  0  0  0
- 24 25  1  0  0  0  0
- 24 27  1  0  0  0  0
- 25 26  2  0  0  0  0
- 27 28  1  0  0  0  0
- 27 34  1  0  0  0  0
- 28 29  2  0  0  0  0
- 28 33  1  0  0  0  0
- 29 30  1  0  0  0  0
- 30 31  2  0  0  0  0
- 31 32  1  0  0  0  0
- 32 33  2  0  0  0  0
- 34 35  2  0  0  0  0
- 34 41  1  0  0  0  0
- 35 36  1  0  0  0  0
- 36 37  2  0  0  0  0
- 37 38  1  0  0  0  0
- 37 40  1  0  0  0  0
- 38 39  1  0  0  0  0
- 40 41  2  0  0  0  0
-M  STY  2   1 SUP   2 SUP
-M  SAL   1  1  15
-M  SBL   1  1  13
-M  SMT   1 Me
-M  SAP   1  1  15  11  1
-M  SAL   2 15  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33
-M  SAL   2  8  34  35  36  37  38  39  40  41
-M  SBL   2  1  20
-M  SMT   2 DMTr
-M  SAP   2  1  27  18  1
-M  END

From 6addc5610f9e6bd0115d7faf45499ae20c4b3dd8 Mon Sep 17 00:00:00 2001
From: Yechen Qiao <yqiao@sapiosciences.com>
Date: Thu, 12 Mar 2026 11:30:26 -0400
Subject: [PATCH 5/5] CHEMBUGS-184 Fixed merge up on commons.cpp my changes.

---
 core/indigo-core/tests/common.cpp | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/core/indigo-core/tests/common.cpp b/core/indigo-core/tests/common.cpp
index 69a38f253e..4a442bce02 100644
--- a/core/indigo-core/tests/common.cpp
+++ b/core/indigo-core/tests/common.cpp
@@ -27,13 +27,6 @@ void IndigoCoreTest::loadMolecule(const char* buf, Molecule& molecule)
     loader.loadMolecule(molecule);
 }
 
-void IndigoCoreTest::loadReaction(const char* buf, Reaction& reaction)
-{
-    BufferScanner scanner(buf);
-    ReactionAutoLoader loader(scanner);
-    loader.loadReaction(reaction);
-}
-
 void IndigoCoreTest::loadQueryMolecule(const char* buf, QueryMolecule& queryMolecule)
 {
     BufferScanner scanner(buf);