#1371 Chirality symbol is added to the SMARTS when 'single up/down' …

…or 'double cis/trans' bond type is set up (#1382)
epam · Oct 26, 2023 · 4f550a7 · 4f550a7
1 parent 86722e0
commit 4f550a7
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Showing 7 changed files with 143 additions and 14 deletions.
diff --git a/api/tests/integration/ref/formats/custom_query.py.out b/api/tests/integration/ref/formats/custom_query.py.out
@@ -4,3 +4,5 @@
 ket_with_rb_as_drawn.ket OK. Smarts equals expected string '[#6](-[#6])(-[#6;x0])-[#6]'
 **** #1337 wrong smarts for ring bond count as drawn ****
 ket_with_custom_query_with_list.ket OK. Smarts equals expected string '[#6]1-[#6]=[Cl,Br,I,Na,O]-[#6]=[#6]-[#6]=1'
+**** #1371Chirality symbol is added to the SMARTS when 'single up/down' or 'double cis/trans' bond type is set up wrong smarts for ring bond count as drawn ****
+ket_with_bond_stereo_ether.ket OK. Smarts equals expected string '[#6]1-[#6]=[#6]-[#6]=[#6]\[#6]=1'
diff --git a/api/tests/integration/tests/formats/custom_query.py b/api/tests/integration/tests/formats/custom_query.py
@@ -50,3 +50,12 @@ def test_ket_to_smarts(filename, expected_str):
 fname = "ket_with_custom_query_with_list.ket"
 expected = "[#6]1-[#6]=[Cl,Br,I,Na,O]-[#6]=[#6]-[#6]=1"
 test_ket_to_smarts(fname, expected)
+
+print(
+    "**** #1371Chirality symbol is added to the SMARTS when "
+    "'single up/down' or 'double cis/trans' bond type is set up"
+    " wrong smarts for ring bond count as drawn ****"
+)
+fname = "ket_with_bond_stereo_ether.ket"
+expected = "[#6]1-[#6]=[#6]-[#6]=[#6]\[#6]=1"
+test_ket_to_smarts(fname, expected)
diff --git a/api/tests/integration/tests/formats/ref/ket_with_bond_stereo_ether.ket b/api/tests/integration/tests/formats/ref/ket_with_bond_stereo_ether.ket
@@ -0,0 +1,108 @@
+{
+    "root": {
+        "nodes": [
+            {
+                "$ref": "mol0"
+            }
+        ]
+    },
+    "mol0": {
+        "type": "molecule",
+        "atoms": [
+            {
+                "label": "C",
+                "location": [
+                    2.9673491521285666,
+                    -16.35007441717461,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    4.697650847871435,
+                    -16.349589229177205,
+                    0
+                ],
+                "stereoLabel": "abs"
+            },
+            {
+                "label": "C",
+                "location": [
+                    3.8341375094912395,
+                    -15.849966888850188,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    4.697650847871435,
+                    -17.35053206782215,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    2.9673491521285666,
+                    -17.35502005679814,
+                    0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    3.836320855479559,
+                    -17.850033111149813,
+                    0
+                ]
+            }
+        ],
+        "bonds": [
+            {
+                "type": 2,
+                "atoms": [
+                    2,
+                    0
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    0,
+                    4
+                ]
+            },
+            {
+                "type": 2,
+                "atoms": [
+                    4,
+                    5
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    5,
+                    3
+                ]
+            },
+            {
+                "type": 2,
+                "atoms": [
+                    3,
+                    1
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    1,
+                    2
+                ],
+                "stereo": 6
+            }
+        ]
+    }
+}
diff --git a/core/indigo-core/molecule/query_molecule.h b/core/indigo-core/molecule/query_molecule.h
@@ -334,8 +334,9 @@ namespace indigo
 
         static std::string getSmartsBondStr(QueryMolecule::Bond* bond);
         static void writeSmartsBond(Output& output, QueryMolecule::Bond* bond, bool has_or_parent);
-        static std::string getSmartsAtomStr(QueryMolecule::Atom* atom);
-        static void writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent);
+        static std::string getSmartsAtomStr(QueryMolecule::Atom* atom, int original_format);
+        static void writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent,
+                                    int original_format);
 
         enum QUERY_ATOM
         {

diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp
@@ -830,7 +830,7 @@ void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
                 if (needCustomQuery)
                 {
                     QueryMolecule::Atom& atom = _pqmol->getAtom(i);
-                    std::string customQuery = QueryMolecule::getSmartsAtomStr(&atom);
+                    std::string customQuery = QueryMolecule::getSmartsAtomStr(&atom, _pqmol->original_format);
                     writer.Key("customQuery");
                     writer.String(customQuery.c_str());
                 }

diff --git a/core/indigo-core/molecule/src/query_molecule.cpp b/core/indigo-core/molecule/src/query_molecule.cpp
@@ -404,11 +404,11 @@ void QueryMolecule::writeSmartsBond(Output& output, Bond* bond, bool has_or_pare
     }
 }
 
-std::string QueryMolecule::getSmartsAtomStr(QueryMolecule::Atom* atom)
+std::string QueryMolecule::getSmartsAtomStr(QueryMolecule::Atom* atom, int original_format)
 {
     Array<char> out;
     ArrayOutput output(out);
-    writeSmartsAtom(output, atom, -1, -1, 1, false, false);
+    writeSmartsAtom(output, atom, -1, -1, 1, false, false, original_format);
     std::string result{out.ptr(), static_cast<std::size_t>(out.size())};
     return result;
 }
@@ -438,7 +438,7 @@ static void writeAnd(Output& _output, QueryMolecule::Node* node, bool has_or_par
         _output.writeChar(';');
 }
 
-void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent)
+void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent, int original_format)
 {
     int i;
 
@@ -454,7 +454,7 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi
             break;
         }
         output.writeChar('!');
-        writeSmartsAtom(output, atom->child(0), aam, chirality, depth + 1, has_or_parent, true);
+        writeSmartsAtom(output, atom->child(0), aam, chirality, depth + 1, has_or_parent, true, original_format);
         break;
     }
     case OP_AND: {
@@ -498,7 +498,7 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi
                 output.writeChar(has_or_parent ? '&' : ';');
                 cur_pos = output.tell();
             }
-            writeSmartsAtom(output, atom->child(i), aam, chirality, depth + 1, has_or_parent, has_not_parent);
+            writeSmartsAtom(output, atom->child(i), aam, chirality, depth + 1, has_or_parent, has_not_parent, original_format);
         }
         break;
     }
@@ -512,7 +512,7 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi
 
             if (i > 0)
                 output.printf(has_not_parent ? "!" : ",");
-            writeSmartsAtom(output, atom->child(i), aam, chirality, depth + 1, true, has_not_parent);
+            writeSmartsAtom(output, atom->child(i), aam, chirality, depth + 1, true, has_not_parent, original_format);
         }
         break;
     }
@@ -521,10 +521,19 @@ void QueryMolecule::writeSmartsAtom(Output& output, Atom* atom, int aam, int chi
         break;
     case ATOM_NUMBER: {
         output.printf("#%d", atom->value_max);
-        if (chirality == 1)
-            output.printf("@");
-        else if (chirality == 2)
-            output.printf("@@");
+        switch (original_format)
+        {
+        case SMARTS:
+        case KET:
+            // SMARTS and ket save chirality in ATOM_CHIRALITY for query molecule
+            break;
+        default:
+            if (chirality == CHIRALITY_ANTICLOCKWISE)
+                output.printf("@");
+            else if (chirality == CHIRALITY_CLOCKWISE)
+                output.printf("@@");
+            break;
+        }
 
         if (aam > 0)
             output.printf(":%d", aam);

diff --git a/core/indigo-core/molecule/src/smiles_saver.cpp b/core/indigo-core/molecule/src/smiles_saver.cpp
@@ -601,7 +601,7 @@ void SmilesSaver::_saveMolecule()
             else if (_qmol != 0)
             {
                 int aam = _bmol->reaction_atom_mapping[v_idx];
-                QueryMolecule::writeSmartsAtom(_output, &_qmol->getAtom(v_idx), aam, _atoms[v_idx].chirality, 0, false, false);
+                QueryMolecule::writeSmartsAtom(_output, &_qmol->getAtom(v_idx), aam, _atoms[v_idx].chirality, 0, false, false, _qmol->original_format);
             }
             else
                 throw Error("SMARTS format available for query only!");