#1619 Import/export of variant monomers from IDT (#2198)

Co-authored-by: Aliakasndr Dziarkach <Aliakasndr.Dziarkach@gmail.com>

api/c/indigo/indigo.h

@@ -198,6 +198,12 @@ CEXPORT int indigoLoadSmartsFromBuffer(const char* buffer, int size);
 CEXPORT int indigoLoadMonomerLibrary(int source);
 CEXPORT int indigoLoadMonomerLibraryFromString(const char* string);
 CEXPORT int indigoLoadMonomerLibraryFromFile(const char* filename);
+CEXPORT int indigoLoadMonomerLibraryFromBuffer(const char* buffer, int size);
+
+CEXPORT int indigoLoadKetDocument(int source);
+CEXPORT int indigoLoadKetDocumentFromString(const char* string);
+CEXPORT int indigoLoadKetDocumentFromFile(const char* filename);
+CEXPORT int indigoLoadKetDocumentFromBuffer(const char* buffer, int size);
 
 CEXPORT int indigoLoadSequence(int source, const char* seq_type, int library);
 CEXPORT int indigoLoadSequenceFromString(const char* string, const char* seq_type, int library);

api/c/indigo/src/indigo_macros.c

@@ -84,6 +84,14 @@ WRAPPER_LOAD_FROM_STRING(indigoLoadReactionSmarts)
 WRAPPER_LOAD_FROM_FILE(indigoLoadReactionSmarts)
 WRAPPER_LOAD_FROM_BUFFER(indigoLoadReactionSmarts)
 
+WRAPPER_LOAD_FROM_STRING(indigoLoadMonomerLibrary)
+WRAPPER_LOAD_FROM_FILE(indigoLoadMonomerLibrary)
+WRAPPER_LOAD_FROM_BUFFER(indigoLoadMonomerLibrary)
+
+WRAPPER_LOAD_FROM_STRING(indigoLoadKetDocument)
+WRAPPER_LOAD_FROM_FILE(indigoLoadKetDocument)
+WRAPPER_LOAD_FROM_BUFFER(indigoLoadKetDocument)
+
 CEXPORT int indigoSaveMolfileToFile(int molecule, const char* filename)
 {
     int f = indigoWriteFile(filename);

api/c/indigo/src/indigo_molecule.cpp

@@ -28,6 +28,7 @@
 #include "molecule/canonical_smiles_saver.h"
 #include "molecule/elements.h"
 #include "molecule/hybridization.h"
+#include "molecule/ket_document_json_loader.h"
 #include "molecule/molecule_auto_loader.h"
 #include "molecule/molecule_automorphism_search.h"
 #include "molecule/molecule_fingerprint.h"
@@ -543,36 +544,18 @@ CEXPORT int indigoLoadMonomerLibrary(int source)
     INDIGO_END(-1);
 }
 
-CEXPORT int indigoLoadMonomerLibraryFromString(const char* string)
+CEXPORT int indigoLoadKetDocument(int source)
 {
     INDIGO_BEGIN
     {
-        int source = indigoReadString(string);
-        int result;
-
-        if (source <= 0)
-            return -1;
-
-        result = indigoLoadMonomerLibrary(source);
-        indigoFree(source);
-        return result;
-    }
-    INDIGO_END(-1);
-}
-
-CEXPORT int indigoLoadMonomerLibraryFromFile(const char* filename)
-{
-    INDIGO_BEGIN
-    {
-        int source = indigoReadFile(filename);
-        int result;
-
-        if (source < 0)
-            return -1;
-
-        result = indigoLoadMonomerLibrary(source);
-        indigoFree(source);
-        return result;
+        IndigoObject& obj = self.getObject(source);
+        auto& scanner = IndigoScanner::get(obj);
+        std::string json_str;
+        scanner.readAll(json_str);
+        std::unique_ptr<IndigoKetDocument> docptr = std::make_unique<IndigoKetDocument>();
+        KetDocumentJsonLoader loader{};
+        loader.parseJson(json_str, docptr->get());
+        return self.addObject(docptr.release());
     }
     INDIGO_END(-1);
 }

api/c/indigo/src/indigo_savers.cpp

@@ -24,6 +24,7 @@
 #include "base_cpp/scanner.h"
 #include "molecule/canonical_smiles_saver.h"
 #include "molecule/cml_saver.h"
+#include "molecule/ket_document_json_saver.h"
 #include "molecule/molecule_cdxml_saver.h"
 #include "molecule/molecule_json_saver.h"
 #include "molecule/molfile_loader.h"
@@ -639,6 +640,14 @@ CEXPORT int indigoSaveIdt(int item, int output, int library)
             out.flush();
             return 1;
         }
+        else if (IndigoKetDocument::is(obj))
+        {
+            IndigoObject& lib_obj = self.getObject(library);
+            SequenceSaver saver(out, IndigoMonomerLibrary::get(lib_obj));
+            saver.saveKetDocument(static_cast<IndigoKetDocument&>(obj).get(), SequenceSaver::SeqFormat::IDT);
+            out.flush();
+            return 1;
+        }
         throw IndigoError("indigoSaveIdt(): expected molecule, got %s", obj.debugInfo());
     }
     INDIGO_END(-1);
@@ -688,6 +697,14 @@ CEXPORT int indigoSaveJson(int item, int output)
             out.flush();
             return 1;
         }
+        else if (IndigoKetDocument::is(obj))
+        {
+            KetDocumentJsonSaver js(out);
+            js.pretty_json = self.json_saving_pretty;
+            js.saveKetDocument(static_cast<IndigoKetDocument&>(obj).get());
+            out.flush();
+            return 1;
+        }
         throw IndigoError("indigoSaveJson(): expected molecule or reaction, got %s", obj.debugInfo());
     }
     INDIGO_END(-1);

api/c/tests/unit/tests/formats.cpp

@@ -24,6 +24,9 @@
 
 #include "common.h"
 
+#include <algorithm>
+#include <fstream>
+
 using namespace std;
 using namespace indigo;
 
@@ -282,3 +285,30 @@ TEST_F(IndigoApiFormatsTest, noFile)
         },
         Exception);
 }
+
+TEST_F(IndigoApiFormatsTest, idt_to_ket)
+{
+    int obj = -1;
+    int library = indigoLoadMonomerLibraryFromFile(dataPath("molecules/basic/monomer_library.ket").c_str());
+    obj = indigoLoadIdtFromString("ARAS", library);
+    indigoSetOptionBool("json-saving-pretty", true);
+    const char* res = indigoJson(obj);
+    // printf("res=%s", res);
+    std::ifstream is(dataPath("molecules/basic/idt_mixed_std.ket"), std::ios::binary | std::ios::ate);
+    auto size = is.tellg();
+    std::string str(size, '\0'); // construct string to stream size
+    is.seekg(0);
+    is.read(&str[0], size);
+    str.erase(std::remove(str.begin(), str.end(), '\r'), str.end());
+    ASSERT_STREQ(res, str.c_str());
+}
+
+TEST_F(IndigoApiFormatsTest, ket_to_idt)
+{
+    int obj = -1;
+    int library = indigoLoadMonomerLibraryFromFile(dataPath("molecules/basic/monomer_library.ket").c_str());
+    obj = indigoLoadKetDocumentFromFile(dataPath("molecules/basic/idt_mixed_std.ket").c_str());
+    const char* res = indigoIdt(obj, library);
+    // printf("res=%s", res);
+    ASSERT_STREQ("ARAS", res);
+}

api/dotnet/src/Indigo.cs

@@ -448,6 +448,12 @@ public IndigoObject loadMonomerLibrary(string str)
             return new IndigoObject(this, checkResult(IndigoLib.indigoLoadMonomerLibraryFromString(str)));
         }
 
+        public IndigoObject loadKetDocument(string str)
+        {
+            setSessionID();
+            return new IndigoObject(this, checkResult(IndigoLib.indigoLoadKetDocumentFromString(str)));
+        }
+
         public IndigoObject loadSequence(string str, string seq_type, IndigoObject library)
         {
             setSessionID();
@@ -490,6 +496,12 @@ public IndigoObject loadMonomerLibraryFromFile(string path)
             return new IndigoObject(this, checkResult(IndigoLib.indigoLoadMonomerLibraryFromFile(path)));
         }
 
+        public IndigoObject loadKetDocumentFromFile(string path)
+        {
+            setSessionID();
+            return new IndigoObject(this, checkResult(IndigoLib.indigoLoadKetDocumentFromFile(path)));
+        }
+
         public IndigoObject loadSequenceFromFile(string path, string seq_type, IndigoObject library)
         {
             setSessionID();

api/dotnet/src/IndigoLib.cs

@@ -131,6 +131,9 @@ public unsafe class IndigoLib
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern int indigoLoadMonomerLibraryFromString(string str);
 
+        [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
+        public static extern int indigoLoadKetDocumentFromString(string str);
+
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern int indigoLoadSequenceFromString(string str, string seq_type, int library);
 
@@ -146,6 +149,9 @@ public unsafe class IndigoLib
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern int indigoLoadMonomerLibraryFromFile(string filename);
 
+        [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
+        public static extern int indigoLoadKetDocumentFromFile(string filename);
+
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern int indigoLoadSequenceFromFile(string filename, string seq_type, int library);
 

api/java/indigo/src/main/java/com/epam/indigo/Indigo.java

@@ -370,6 +370,16 @@ public IndigoObject loadMonomerLibraryFromFile(String path) {
         return new IndigoObject(this, checkResult(this, lib.indigoLoadMonomerLibraryFromFile(path)));
     }
 
+    public IndigoObject loadKetDocument(String str) {
+        setSessionID();
+        return new IndigoObject(this, checkResult(this, lib.indigoLoadKetDocumentFromString(str)));
+    }
+
+    public IndigoObject loadKetDocumentFromFile(String path) {
+        setSessionID();
+        return new IndigoObject(this, checkResult(this, lib.indigoLoadKetDocumentFromFile(path)));
+    }
+
     public IndigoObject loadSequence(String str, String seq_type, IndigoObject library) {
         setSessionID();
         return new IndigoObject(this, checkResult(this, lib.indigoLoadSequenceFromString(str, seq_type, library.self)));

api/java/indigo/src/main/java/com/epam/indigo/IndigoLib.java

@@ -123,6 +123,12 @@ public interface IndigoLib extends Library {
 
     int indigoLoadMonomerLibraryFromFile(String filename);
 
+    int indigoLoadKetDocument(int source);
+
+    int indigoLoadKetDocumentFromString(String str);
+
+    int indigoLoadKetDocumentFromFile(String filename);
+
     int indigoLoadSequence(int source, String seq_type, int library);
 
     int indigoLoadSequenceFromString(String str, String seq_type, int library);

api/python/indigo/indigo/indigo.py

@@ -548,6 +548,46 @@ def loadMonomerLibraryFromFile(self, filename):
             ),
         )
 
+    def loadKetDocument(self, string):
+        """Loads ket document from ket string
+
+        Args:
+            string (str): ket
+
+        Returns:
+            IndigoObject: loaded ket document
+
+        Raises:
+            IndigoException: Exception if structure format is incorrect
+        """
+
+        return IndigoObject(
+            self,
+            IndigoLib.checkResult(
+                self._lib().indigoLoadKetDocumentFromString(string.encode())
+            ),
+        )
+
+    def loadKetDocumentFromFile(self, filename):
+        """Loads ket document from from file in ket format
+
+        Args:
+            string (str): full path to the file with ket
+
+        Returns:
+            IndigoObject: loaded ket document
+
+        Raises:
+            IndigoException: Exception if structure format is incorrect
+        """
+
+        return IndigoObject(
+            self,
+            IndigoLib.checkResult(
+                self._lib().indigoLoadKetDocumentFromFile(filename.encode())
+            ),
+        )
+
     def loadSequence(self, string, seq_type, library):
         """Loads molecule from DNA/RNA/PEPTIDE sequence string
 

api/python/indigo/indigo/indigo_lib.py

@@ -136,6 +136,10 @@ def __init__(self) -> None:
         IndigoLib.lib.indigoLoadMonomerLibraryFromString.argtypes = [c_char_p]
         IndigoLib.lib.indigoLoadMonomerLibraryFromFile.restype = c_int
         IndigoLib.lib.indigoLoadMonomerLibraryFromFile.argtypes = [c_char_p]
+        IndigoLib.lib.indigoLoadKetDocumentFromString.restype = c_int
+        IndigoLib.lib.indigoLoadKetDocumentFromString.argtypes = [c_char_p]
+        IndigoLib.lib.indigoLoadKetDocumentFromFile.restype = c_int
+        IndigoLib.lib.indigoLoadKetDocumentFromFile.argtypes = [c_char_p]
         IndigoLib.lib.indigoLoadSequenceFromString.restype = c_int
         IndigoLib.lib.indigoLoadSequenceFromString.argtypes = [
             c_char_p,

api/tests/integration/ref/formats/idt_to_ket.py.out

@@ -17,6 +17,7 @@ idt_i2moera_sp_32moera.ket:SUCCEED
 idt_i2moera_t.ket:SUCCEED
 idt_many_molecules.ket:SUCCEED
 idt_mixed.ket:SUCCEED
+idt_mixed_custom.ket:SUCCEED
 idt_mixed_std.ket:SUCCEED
 idt_mod_phosphates.ket:SUCCEED
 idt_modifications.ket:SUCCEED

api/tests/integration/ref/formats/ket_to_idt.py.out

@@ -17,6 +17,8 @@ idt_i2moera_sp_32moera.ket:SUCCEED
 idt_i2moera_t.ket:SUCCEED
 idt_many_molecules.ket:SUCCEED
 idt_mixed.ket:SUCCEED
+idt_mixed_custom.ket:SUCCEED
+idt_mixed_std.ket:SUCCEED
 idt_mod_phosphates.ket:SUCCEED
 idt_modifications.ket:SUCCEED
 idt_more_than_80_chars.ket:SUCCEED

api/tests/integration/tests/formats/idt_to_ket.py

@@ -57,6 +57,7 @@ def find_diff(a, b):
     "idt_unresolved_many": "/unr0/A/unr1/C/unr2/ACTG/unr3/G/unr4/",
     "idt_unsplit": "/5UNSPLIT/A",
     "idt_mixed_std": "ARAS",
+    "idt_mixed_custom": "(N1:10203050)(N1)N",
 }
 
 lib = indigo.loadMonomerLibraryFromFile(

api/tests/integration/tests/formats/ket_to_idt.py

@@ -61,10 +61,12 @@ def find_diff(a, b):
     "idt_52moera_sp_i2moera_sp": "/52MOErA/*/i2MOErA/*",
     "idt_unsplit": "/5UNSPLIT/A",
     "idt_more_than_80_chars": "/52MOErA//i2MOErA//i2MOErA//i2MOErA//i2MOErA//i2MOErA//i2MOErA//i2MOErA//i2MOErA//i2MOErA//i2MOErA//i2MOErA//3Phos/",
+    "idt_mixed_std": "ARAS",
+    "idt_mixed_custom": "(N1:10203050)(N1)N",
 }
 
 for filename in sorted(idt_data.keys()):
-    mol = indigo.loadMoleculeFromFile(os.path.join(ref, filename + ".ket"))
+    mol = indigo.loadKetDocumentFromFile(os.path.join(ref, filename + ".ket"))
     idt = mol.idt(lib)
     idt_ref = idt_data[filename]
     if idt_ref == idt:

api/tests/integration/tests/formats/ref/idt_3phos.ket

@@ -5,7 +5,6 @@
                 "$ref": "monomer0"
             }
         ],
-        "connections": [],
         "templates": [
             {
                 "$ref": "monomerTemplate-P___Phosphate"

api/tests/integration/tests/formats/ref/idt_5phos.ket

@@ -5,7 +5,6 @@
                 "$ref": "monomer0"
             }
         ],
-        "connections": [],
         "templates": [
             {
                 "$ref": "monomerTemplate-P___Phosphate"