#1440 Add support for query features in MOL, SDF and RXN formats (Ma…

…rvin extension) (#1464)
epam · Jan 3, 2024 · 9c181a5 · 9c181a5
1 parent faa03d1
commit 9c181a5
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Showing 16 changed files with 279 additions and 82 deletions.
diff --git a/api/c/indigo/src/indigo.cpp b/api/c/indigo/src/indigo.cpp
@@ -128,6 +128,7 @@ void Indigo::init()
     json_saving_pretty = false;
 
     molfile_saving_add_implicit_h = true;
+    molfile_saving_add_mrv_sma = true;
 
     smiles_saving_write_name = false;
     smiles_saving_smarts_mode = false;
@@ -189,6 +190,7 @@ void Indigo::initMolfileSaver(MolfileSaver& saver)
     saver.no_chiral = molfile_saving_no_chiral;
     saver.add_stereo_desc = molfile_saving_add_stereo_desc;
     saver.add_implicit_h = molfile_saving_add_implicit_h;
+    saver.add_mrv_sma = molfile_saving_add_mrv_sma;
     saver.chiral_flag = molfile_saving_chiral_flag;
 }
 
@@ -210,6 +212,7 @@ void Indigo::initRxnfileSaver(RxnfileSaver& saver)
     saver.skip_date = molfile_saving_skip_date;
     saver.add_stereo_desc = molfile_saving_add_stereo_desc;
     saver.add_implicit_h = molfile_saving_add_implicit_h;
+    saver.add_mrv_sma = molfile_saving_add_mrv_sma;
 }
 
 Indigo::~Indigo()

diff --git a/api/c/indigo/src/indigo_internal.h b/api/c/indigo/src/indigo_internal.h
@@ -319,6 +319,7 @@ class DLLEXPORT Indigo
     bool molfile_saving_skip_date;
     bool molfile_saving_add_stereo_desc;
     bool molfile_saving_add_implicit_h;
+    bool molfile_saving_add_mrv_sma;
     bool json_saving_add_stereo_desc;
     bool json_saving_pretty;
     bool smiles_saving_write_name;

diff --git a/api/c/indigo/src/indigo_options.cpp b/api/c/indigo/src/indigo_options.cpp
@@ -290,6 +290,7 @@ void IndigoOptionHandlerSetter::setBasicOptionHandlers(const qword id)
     mgr->setOptionHandlerBool("json-saving-add-stereo-desc", SETTER_GETTER_BOOL_OPTION(indigo.json_saving_add_stereo_desc));
     mgr->setOptionHandlerBool("json-saving-pretty", SETTER_GETTER_BOOL_OPTION(indigo.json_saving_pretty));
     mgr->setOptionHandlerBool("molfile-saving-add-implicit-h", SETTER_GETTER_BOOL_OPTION(indigo.molfile_saving_add_implicit_h));
+    mgr->setOptionHandlerBool("molfile-saving-add-mrv-sma", SETTER_GETTER_BOOL_OPTION(indigo.molfile_saving_add_mrv_sma));
     mgr->setOptionHandlerBool("smiles-saving-write-name", SETTER_GETTER_BOOL_OPTION(indigo.smiles_saving_write_name));
     mgr->setOptionHandlerString("filename-encoding", indigoSetFilenameEncoding, indigoGetFilenameEncoding);
     mgr->setOptionHandlerInt("fp-ord-qwords", SETTER_GETTER_INT_OPTION(indigo.fp_params.ord_qwords));

diff --git a/api/tests/integration/ref/basic/check_query.py.out b/api/tests/integration/ref/basic/check_query.py.out
@@ -402,6 +402,7 @@ M  UNS  1   4   1
 M  RBC  1  33  -2
 A   59
 CYC
+M  MRV SMA  16 [#6;H2]
 M  STY  2   1 DAT   2 DAT
 M  SPL  1   2   1
 M  SLB  2   1   1   2   2
@@ -636,3 +637,27 @@ Check query for bond 18 returns 0
 Check query for bond 19 returns 0
 Check query for bond 20 returns 0
 Check query for bond 21 returns 0
+[#6]1[#6][#6,#7,F;a;r6;R1;h1;H][!Cl;!Br;!I;a;R1;h1;H][#6][c;r6;R1;X3;v3;h1;H]1
+
+  -INDIGO-01000000002D
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  2  0  3  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 L   0  0  0  2  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 L   0  0  0  2  0  0  0  0  0  0  0  0
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  6  0  0  0  0
+  2  3  6  0  0  0  0
+  3  4  6  0  0  0  0
+  4  5  6  0  0  0  0
+  5  6  6  0  0  0  0
+  6  1  6  0  0  0  0
+M  ALS   4  3 T Cl  Br  I   
+M  ALS   5  3 F C   N   F   
+M  MRV SMA   2 [#6;Hh1X3R1r6a]
+M  MRV SMA   4 [!#17;!#35;!#53;Hh1R1a]
+M  MRV SMA   5 [#6,#7,#9;Hh1R1r6a]
+M  END
+
diff --git a/api/tests/integration/ref/deco/deco_recursive_smarts.py.out b/api/tests/integration/ref/deco/deco_recursive_smarts.py.out
@@ -13,6 +13,9 @@ full scaffold:
   3  4  2  0  0  0  0
   5  2  1  0  0  0  0
   6  4  1  0  0  0  0
+M  MRV SMA   2 [#7;A]
+M  MRV SMA   3 [#6;A]
+M  MRV SMA   4 [#8;A]
 M  RGP  2   5   1   6   2
 M  END
 

diff --git a/api/tests/integration/ref/formats/mol_features.py.out b/api/tests/integration/ref/formats/mol_features.py.out
@@ -7928,7 +7928,7 @@ M  V30 11 C 5.9062 -4.5267 0.0 0
 M  V30 12 C 6.6195 -4.1121 0.0 0
 M  V30 13 O 4.4773 -4.531 0.0 0 CHG=-1
 M  V30 14 Fe 5.1995 -9.0694 0.0 0 VAL=-1
-M  V30 15 A 3.7701 -8.2434 0.0 0
+M  V30 15 [Gln,Lys] 3.7701 -8.2434 0.0 0
 M  V30 16 C 3.7715 -6.5918 0.0 0
 M  V30 17 C 6.6313 -8.2424 0.0 0
 M  V30 END ATOM
@@ -7976,7 +7976,7 @@ M  END
     6.6195   -4.1121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
     4.4773   -4.5310    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
     5.1995   -9.0694    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
-    3.7701   -8.2434    0.0000 A   0  0  0  0  0  0  0  0  0  0  0  0
+    3.7701   -8.2434    0.0000 L   0  0  0  0  0  0  0  0  0  0  0  0
     3.7715   -6.5918    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
     6.6313   -8.2424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   7  8  1  0  0  0  0
@@ -7998,8 +7998,10 @@ M  END
   4 17  1  0  0  0  0
 M  CHG  1  13  -1
 M  ALS  10  2 F N   P   
+M  ALS  15  2 F Gln Lys 
 A   16
 Fred
+M  MRV SMA   5 [#6;H0]
 M  END
 
  molfile-saving-mode: 3000
@@ -8024,7 +8026,7 @@ M  V30 11 C 5.9062 -4.5267 0.0 0
 M  V30 12 C 6.6195 -4.1121 0.0 0
 M  V30 13 O 4.4773 -4.531 0.0 0 CHG=-1
 M  V30 14 Fe 5.1995 -9.0694 0.0 0 VAL=-1
-M  V30 15 A 3.7701 -8.2434 0.0 0
+M  V30 15 [Gln,Lys] 3.7701 -8.2434 0.0 0
 M  V30 16 C 3.7715 -6.5918 0.0 0
 M  V30 17 C 6.6313 -8.2424 0.0 0
 M  V30 END ATOM
@@ -8845,6 +8847,8 @@ ind-928-asdrawn.mol:
 M  UNS  2   3   1  11   1
 M  SUB  2   4  -2   5   4
 M  RBC  2   4   3   7  -2
+M  MRV SMA  10 [#6;H2]
+M  MRV SMA  13 [#6;H]
 M  END
 
  molfile-saving-mode: 2000
@@ -8884,6 +8888,8 @@ M  END
 M  UNS  2   3   1  11   1
 M  SUB  2   4  -2   5   4
 M  RBC  2   4   3   7  -2
+M  MRV SMA  10 [#6;H2]
+M  MRV SMA  13 [#6;H]
 M  END
 
  molfile-saving-mode: 3000

diff --git a/api/tests/integration/ref/formats/mol_to_cml.py.out b/api/tests/integration/ref/formats/mol_to_cml.py.out
@@ -753,6 +753,7 @@ M  SUB  1   9  -2
 M  RBC  1   5  -2
 M  ALS  14  3 F B   Si  As  
 M  ALS  15  3 T N   P   As  
+M  MRV SMA   7 [#6;H3]
 M  RGP  1   1   1
 M  LOG  1   1   0   0     
 M  END
@@ -886,6 +887,7 @@ M  SUB  1   9  -2
 M  RBC  1   5  -2
 M  ALS  14  3 F B   Si  As  
 M  ALS  15  3 T N   P   As  
+M  MRV SMA   7 [#6;H3]
 M  RGP  1   1   1
 M  LOG  1   1   0   0     
 M  END

diff --git a/api/tests/integration/tests/basic/check_query.py b/api/tests/integration/tests/basic/check_query.py
@@ -69,3 +69,10 @@
         "Check query for bond %d returns %d"
         % (bond.index(), bond.checkQuery())
     )
+
+mol = indigo.loadSmarts(
+    "[#6]1[#6;a;H1h1v3X3R1r6][#6][!#17!#35!#53;a;H1h1R1][#6,#7,#9;a;H1h1R1r6][#6]1"
+)
+
+print(mol.smarts())
+print(mol.molfile())
diff --git a/core/indigo-core/molecule/molfile_saver.h b/core/indigo-core/molecule/molfile_saver.h
@@ -59,6 +59,7 @@ namespace indigo
         bool add_implicit_h;  // If true then MRV_IMPLICIT_H Data S-groups will be added for saving
                               // the number of implicit H for aromatic atoms
                               // (if it is required for correct de-aromatization) (default value is true)
+        bool add_mrv_sma;     // If true then "MRV SMA" extension will be added for query molecules (default value is true)
         static int parseFormatMode(const char* mode);
         static void saveFormatMode(int mode, Array<char>& output);
 

diff --git a/core/indigo-core/molecule/query_molecule.h b/core/indigo-core/molecule/query_molecule.h
@@ -348,6 +348,7 @@ 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, int original_format);
+        static std::string getMolMrvSmaExtension(QueryMolecule& qm, int aid);
         static void writeSmartsAtom(Output& output, Atom* atom, int aam, int chirality, int depth, bool has_or_parent, bool has_not_parent,
                                     int original_format);
 
@@ -397,6 +398,8 @@ namespace indigo
         Atom* releaseAtom(int idx);
         void resetAtom(int idx, Atom* atom);
 
+        static bool isAtomProperty(OpType type);
+
         Bond& getBond(int idx);
         Bond* releaseBond(int idx);
         void resetBond(int idx, Bond* bond);
@@ -428,7 +431,7 @@ namespace indigo
 
         bool standardize(const StandardizeOptions& options);
 
-        static int parseQueryAtomSmarts(QueryMolecule& qm, int aid, std::vector<int>& list, std::map<int, std::unique_ptr<Atom>>& properties);
+        static int parseQueryAtomSmarts(QueryMolecule& qm, int aid, std::vector<std::unique_ptr<Atom>>& list, std::map<int, std::unique_ptr<Atom>>& properties);
 
     protected:
         void _getAtomDescription(Atom* atom, Output& out, int depth);
@@ -444,10 +447,10 @@ namespace indigo
         void _removeBonds(const Array<int>& indices) override;
 
         using AtomList = std::pair<bool, std::set<int>>;
-        static bool _isAtomListOr(Atom* pqa, std::vector<int>& list);
-        static bool _isAtomOrListAndProps(Atom* pqa, std::vector<int>& list, bool& neg, std::map<int, std::unique_ptr<Atom>>& properties);
+        static bool _isAtomListOr(Atom* pqa, std::vector<std::unique_ptr<Atom>>& list);
+        static bool _isAtomOrListAndProps(Atom* pqa, std::vector<std::unique_ptr<Atom>>& list, bool& neg, std::map<int, std::unique_ptr<Atom>>& properties);
         static bool _isAtomList(Atom* qa, AtomList list);
-        static bool _tryToConvertToList(Atom* p_query_atom, std::vector<int>& atoms, std::map<int, std::unique_ptr<Atom>>& properties);
+        static bool _tryToConvertToList(Atom* p_query_atom, std::vector<std::unique_ptr<Atom>>& atoms, std::map<int, std::unique_ptr<Atom>>& properties);
 
         Array<int> _min_h;
 

diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp
@@ -706,7 +706,7 @@ void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
         else
         {
             bool is_qatom_list = false;
-            std::vector<int> atoms;
+            std::vector<std::unique_ptr<QueryMolecule::Atom>> atoms;
             if (_pqmol)
                 query_atom_type = QueryMolecule::parseQueryAtomSmarts(*_pqmol, i, atoms, query_atom_properties);
             if (mol.isPseudoAtom(i))
@@ -751,13 +751,18 @@ void MoleculeJsonSaver::saveAtoms(BaseMolecule& mol, JsonWriter& writer)
                         }
                         writer.Key("elements");
                         writer.StartArray();
-                        for (auto atom : atoms)
-                            writer.String(Element::toString(atom));
+                        for (auto& atom : atoms)
+                            if (atom->type == QueryMolecule::ATOM_NUMBER)
+                                writer.String(Element::toString(atom->value_max));
+                            else if (atom->type == QueryMolecule::ATOM_PSEUDO)
+                                writer.String(atom->alias.ptr());
+                            else
+                                throw Error("Wrong atom type %d", atom->type);
                         writer.EndArray();
                     }
                     else if (query_atom_type == QueryMolecule::QUERY_ATOM_SINGLE)
                     {
-                        anum = *atoms.begin();
+                        anum = (*atoms.begin()).get()->value_max;
                         buf.readString(Element::toString(anum), true);
                         if (anum == ELEM_H && query_atom_properties.count(QueryMolecule::ATOM_ISOTOPE) > 0)
                         {