#1256 - Inability to save a structure with R-Group in the SDF file format

api/c/indigo/indigo.h

@@ -1002,6 +1002,12 @@ CEXPORT long long indigoTell64(int handle);
 
 // Saves the molecule to an SDF output stream
 CEXPORT int indigoSdfAppend(int output, int item);
+
+// Splits the item into fragments (connected components for a molecule,
+// constituent molecules for a reaction) and returns the whole multi-record
+// SDF as a string. Single entry point for SDF-by-fragments serialization.
+CEXPORT const char* indigoFragmentedSdf(int item);
+
 // Saves the molecule to a multiline SMILES output stream
 CEXPORT int indigoSmilesAppend(int output, int item);
 

api/c/indigo/src/indigo_savers.cpp

@@ -19,6 +19,11 @@
 #include "indigo_savers.h"
 
 #include <ctime>
+#include <memory>
+#include <unordered_set>
+
+#include "indigo_molecule.h"
+#include "indigo_reaction.h"
 
 #include "base_cpp/output.h"
 #include "base_cpp/scanner.h"
@@ -353,6 +358,87 @@ void IndigoSdfSaver::saveMonomerLibrary(const MonomerTemplateLibrary& monomers_l
     _output.flush();
 }
 
+// A component clone unconditionally carries every R-group in `mol` (see
+// BaseMolecule::mergeWithSubmolecule), so callers must trim it with
+// copyUsedRGroupsFrom() or R-group content gets duplicated across records.
+//
+// Builds a record holding only R-group `keep_idx` from `mol`, with zero
+// main-graph atoms.
+static IndigoObject* makeSingleRGroupObject(BaseMolecule& mol, int keep_idx)
+{
+    std::unique_ptr<IndigoBaseMolecule> res;
+    BaseMolecule* newmol;
+    if (mol.isQueryMolecule())
+    {
+        res = std::make_unique<IndigoQueryMolecule>();
+        newmol = &(((IndigoQueryMolecule*)res.get())->qmol);
+    }
+    else
+    {
+        res = std::make_unique<IndigoMolecule>();
+        newmol = &(((IndigoMolecule*)res.get())->mol);
+    }
+
+    QS_DEF(Array<int>, no_vertices);
+    no_vertices.clear();
+    newmol->makeSubmolecule(mol, no_vertices, 0, 0);
+
+    for (int i = 1; i <= newmol->rgroups.getRGroupCount(); i++)
+    {
+        if (i != keep_idx)
+        {
+            newmol->rgroups.getRGroup(i).fragments.clear();
+            newmol->rgroups.getRGroup(i).clear();
+        }
+    }
+
+    return res.release();
+}
+
+void IndigoSdfSaver::appendFragments(Output& output, IndigoObject& object)
+{
+    if (IndigoBaseReaction::is(object))
+    {
+        // A reaction is split into its constituent molecules.
+        IndigoReactionIter fragments(object.getBaseReaction(), IndigoReactionIter::MOLECULES);
+        while (fragments.hasNext())
+        {
+            std::unique_ptr<IndigoObject> fragment(fragments.next());
+            std::unique_ptr<IndigoObject> clone(fragment->clone());
+            IndigoSdfSaver::append(output, *clone);
+        }
+        return;
+    }
+
+    // A molecule is split into the connected components of its main graph.
+    BaseMolecule& mol = object.getBaseMolecule();
+    std::unordered_set<int> written_rgroups;
+    IndigoComponentsIter fragments(mol);
+    while (fragments.hasNext())
+    {
+        std::unique_ptr<IndigoObject> fragment(fragments.next());
+        std::unique_ptr<IndigoObject> clone(fragment->clone());
+        BaseMolecule& clone_mol = clone->getBaseMolecule();
+        clone_mol.rgroups.clear();
+        clone_mol.copyUsedRGroupsFrom(mol);
+        for (int i = 1; i <= clone_mol.rgroups.getRGroupCount(); i++)
+            if (clone_mol.rgroups.getRGroup(i).fragments.size() > 0)
+                written_rgroups.insert(i);
+        IndigoSdfSaver::append(output, *clone);
+    }
+
+    // Any R-group no component claimed (e.g. a free R-group with no r-site
+    // reference) does not belong to another structure, so each one is emitted
+    // independently as its own atom-less record. (#1256)
+    for (int i = 1; i <= mol.rgroups.getRGroupCount(); i++)
+    {
+        if (mol.rgroups.getRGroup(i).fragments.size() == 0 || written_rgroups.count(i))
+            continue;
+        std::unique_ptr<IndigoObject> leftover(makeSingleRGroupObject(mol, i));
+        IndigoSdfSaver::append(output, *leftover);
+    }
+}
+
 CEXPORT int indigoSdfAppend(int output, int molecule)
 {
     INDIGO_BEGIN
@@ -365,6 +451,20 @@ CEXPORT int indigoSdfAppend(int output, int molecule)
     INDIGO_END(-1);
 }
 
+CEXPORT const char* indigoFragmentedSdf(int item)
+{
+    INDIGO_BEGIN
+    {
+        IndigoObject& obj = self.getObject(item);
+        auto& tmp = self.getThreadTmpData();
+        ArrayOutput out(tmp.string);
+        IndigoSdfSaver::appendFragments(out, obj);
+        tmp.string.push(0);
+        return tmp.string.ptr();
+    }
+    INDIGO_END(0);
+}
+
 //
 // IndigoSmilesSaver
 //

api/c/indigo/src/indigo_savers.h

@@ -82,6 +82,10 @@ class IndigoSdfSaver : public IndigoSaver
     const char* debugInfo() const override;
     static void append(Output& output, IndigoObject& object);
     static void appendMolfile(Output& output, IndigoObject& object);
+    // Splits the object into fragments (connected components for a molecule,
+    // constituent molecules for a reaction) and writes each one as a separate
+    // SDF record. Single entry point shared by all SDF-by-fragments consumers.
+    static void appendFragments(Output& output, IndigoObject& object);
     void saveMonomerLibrary(const MonomerTemplateLibrary& monomers_library);
 
 protected:

api/dotnet/src/IndigoLib.cs

@@ -260,6 +260,9 @@ public unsafe class IndigoLib
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern byte* indigoMonomerLibrary(int lib);
 
+        [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
+        public static extern byte* indigoFragmentedSdf(int item);
+
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern int indigoSaveCdxml(int molecule, int output);
 

api/dotnet/src/IndigoObject.cs

@@ -174,6 +174,12 @@ public string monomerLibrary()
             return dispatcher.checkResult(IndigoLib.indigoMonomerLibrary(self));
         }
 
+        public string fragmentedSdf()
+        {
+            dispatcher.setSessionID();
+            return dispatcher.checkResult(IndigoLib.indigoFragmentedSdf(self));
+        }
+
         public void saveCml(string filename)
         {
             dispatcher.setSessionID();

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

@@ -223,6 +223,8 @@ public interface IndigoLib extends Library {
 
     Pointer indigoJson(int object);
 
+    Pointer indigoFragmentedSdf(int item);
+
     Pointer indigoMonomerLibrary(int object);
 
     @SuppressWarnings("checkstyle:Indentation")

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

@@ -158,6 +158,11 @@ public String monomerLibrary() {
         return Indigo.checkResultString(this, lib.indigoMonomerLibrary(self));
     }
 
+    public String fragmentedSdf() {
+        dispatcher.setSessionID();
+        return Indigo.checkResultString(this, lib.indigoFragmentedSdf(self));
+    }
+
     public void saveCml(String filename) {
         dispatcher.setSessionID();
         Indigo.checkResult(this, lib.indigoSaveCmlToFile(self, filename));

api/python/indigo/indigo/indigo_lib.py

@@ -1112,6 +1112,8 @@ def __init__(self) -> None:
         IndigoLib.lib.indigoTell.argtypes = [c_int]
         IndigoLib.lib.indigoSdfAppend.restype = c_int
         IndigoLib.lib.indigoSdfAppend.argtypes = [c_int, c_int]
+        IndigoLib.lib.indigoFragmentedSdf.restype = c_char_p
+        IndigoLib.lib.indigoFragmentedSdf.argtypes = [c_int]
         IndigoLib.lib.indigoSmilesAppend.restype = c_int
         IndigoLib.lib.indigoSmilesAppend.argtypes = [c_int, c_int]
         IndigoLib.lib.indigoRdfHeader.restype = c_int

api/python/indigo/indigo/indigo_object.py

@@ -304,6 +304,17 @@ def cml(self):
 
         return IndigoLib.checkResultString(self._lib().indigoCml(self.id))
 
+    def fragmentedSdf(self):
+        """Structure method returns the structure as a string in SDF format,
+        splitting it into fragments.
+
+        Returns:
+            str: SDF string
+        """
+        return IndigoLib.checkResultString(
+            self._lib().indigoFragmentedSdf(self.id)
+        )
+
     def saveCdxml(self, filename):
         """Molecule method saves the structure into a CDXML file
 

api/tests/integration/ref/formats/ket_to_sdf_1256.py.out

@@ -0,0 +1,7 @@
+*** KET to SDF ***
+1256-ketR20-from2815.sdf:SUCCEED
+1256-salt-attached-rgroup.sdf:SUCCEED
+1256-standard-plus-two-independent.sdf:SUCCEED
+1256-two-independent-rgroups.sdf:SUCCEED
+1256-reaction-one-independent-rgroup.sdf:SUCCEED
+1256-reaction-two-independent-rgroups.sdf:SUCCEED

api/tests/integration/tests/formats/ket_to_sdf.py

@@ -53,12 +53,7 @@ def expect_monomer_library_load_error(root, filename, expected_error):
         except IndigoException as e:
             print("  %s" % (getIndigoExceptionText(e)))
 
-    buffer = indigo.writeBuffer()
-    sdfSaver = indigo.createSaver(buffer, "sdf")
-    for frag in ket.iterateComponents():
-        sdfSaver.append(frag.clone())
-    sdfSaver.close()
-    sdf = buffer.toString()
+    sdf = ket.fragmentedSdf()
     compare_diff(ref_path, filename + ".sdf", sdf)
 
 root = joinPathPy("reactions/", __file__)
@@ -80,12 +75,7 @@ def expect_monomer_library_load_error(root, filename, expected_error):
         except IndigoException as e:
             print("  %s" % (getIndigoExceptionText(e)))
 
-    buffer = indigo.writeBuffer()
-    sdfSaver = indigo.createSaver(buffer, "sdf")
-    for mol in ket.iterateMolecules():
-        sdfSaver.append(mol.clone())
-    sdfSaver.close()
-    sdf = buffer.toString()
+    sdf = ket.fragmentedSdf()
     compare_diff(ref_path, filename + ".sdf", sdf)
 
 print("*** KET-monomer library to SDF ***")

api/tests/integration/tests/formats/ket_to_sdf_1256.py

@@ -0,0 +1,63 @@
+import os
+import sys
+
+sys.path.append(
+    os.path.normpath(
+        os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
+    )
+)
+from common.util import compare_diff
+from env_indigo import *  # noqa
+
+indigo = Indigo()
+indigo.setOption("json-saving-pretty", True)
+indigo.setOption("molfile-saving-skip-date", True)
+indigo.setOption("ignore-stereochemistry-errors", True)
+
+print("*** KET to SDF ***")
+
+root = joinPathPy("molecules/", __file__)
+ref_path = joinPathPy("ref/", __file__)
+
+files = [
+    "1256-ketR20-from2815",
+    "1256-salt-attached-rgroup",
+    "1256-two-independent-rgroups",
+    "1256-standard-plus-two-independent",
+]
+
+files.sort()
+for filename in files:
+    try:
+        ket = indigo.loadMoleculeFromFile(
+            os.path.join(root, filename + ".ket")
+        )
+    except IndigoException:
+        ket = indigo.loadQueryMoleculeFromFile(
+            os.path.join(root, filename + ".ket")
+        )
+
+    sdf = ket.fragmentedSdf()
+    compare_diff(ref_path, filename + ".sdf", sdf)
+
+root = joinPathPy("reactions/", __file__)
+ref_path = joinPathPy("ref/", __file__)
+
+files = [
+    "1256-reaction-one-independent-rgroup",
+    "1256-reaction-two-independent-rgroups",
+]
+
+files.sort()
+for filename in files:
+    try:
+        ket = indigo.loadReactionFromFile(
+            os.path.join(root, filename + ".ket")
+        )
+    except IndigoException:
+        ket = indigo.loadQueryReactionFromFile(
+            os.path.join(root, filename + ".ket")
+        )
+
+    sdf = ket.fragmentedSdf()
+    compare_diff(ref_path, filename + ".sdf", sdf)