#1217 Support SDF-format for Indigo-Ketcher API (#1223)

Author: even1024

api/c/indigo/src/indigo_molecule.cpp

@@ -642,7 +642,7 @@ int IndigoMoleculeComponent::getIndex()
 
 IndigoObject* IndigoMoleculeComponent::clone()
 {
-    std::unique_ptr<IndigoObject> res;
+    std::unique_ptr<IndigoBaseMolecule> res;
     BaseMolecule* newmol;
 
     if (mol.isQueryMolecule())
@@ -658,6 +658,12 @@ IndigoObject* IndigoMoleculeComponent::clone()
 
     Filter filter(mol.getDecomposition().ptr(), Filter::EQ, index);
     newmol->makeSubmolecule(mol, filter, 0, 0);
+    for (auto it = newmol->properties().begin(); it != newmol->properties().end(); ++it)
+    {
+        auto& props = newmol->properties().value(it);
+        res->getProperties().merge(props);
+    }
+
     return res.release();
 }
 

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

@@ -264,8 +264,8 @@ TEST_F(IndigoApiFormatsTest, fromGzFile)
     try
     {
         int obj = indigoLoadStructureFromFile(dataPath("molecules/basic/Compound_0000001_0000250.sdf.gz").c_str(), "query");
-        EXPECT_EQ(31, indigoCountAtoms(obj));
-        EXPECT_EQ(30, indigoCountBonds(obj));
+        EXPECT_EQ(8454, indigoCountAtoms(obj));
+        EXPECT_EQ(8478, indigoCountBonds(obj));
     }
     catch (Exception& e)
     {

api/tests/integration/ref/basic/load_structure.py.out

@@ -51,8 +51,8 @@ Atoms: 0
 Bonds: 0
 
 (** #14 **): Load from compessed binary (../../../../../data/molecules/basic/benzodiazepine.sdf.gz)
-Atoms: 33
-Bonds: 35
+Atoms: 668941
+Bonds: 707945
 
 ---- TestLoadFromFile ----
 

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

@@ -0,0 +1,2 @@
+*** KET to SDF ***
+acd2d_err3.sdf:SUCCEED

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

@@ -0,0 +1,2 @@
+*** SDF to KET ***
+acd2d_err.ket:SUCCEED

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

@@ -0,0 +1,59 @@
+import difflib
+import os
+import sys
+
+
+def find_diff(a, b):
+    return "\n".join(difflib.unified_diff(a.splitlines(), b.splitlines()))
+
+
+sys.path.append(
+    os.path.normpath(
+        os.path.join(os.path.abspath(__file__), "..", "..", "..", "common")
+    )
+)
+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 = ["acd2d_err3"]
+
+files.sort()
+for filename in files:
+    try:
+        ket = indigo.loadMoleculeFromFile(
+            os.path.join(root, filename + ".ket")
+        )
+    except:
+        try:
+            ket = indigo.loadQueryMoleculeFromFile(
+                os.path.join(root, filename + ".ket")
+            )
+        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()
+    # with open(os.path.join(ref_path, filename) + ".sdf", "w") as file:
+    #   file.write(sdf)
+
+    with open(os.path.join(ref_path, filename) + ".sdf", "r") as file:
+        sdf_ref = file.read()
+    diff = find_diff(sdf_ref, sdf)
+    if not diff:
+        print(filename + ".sdf:SUCCEED")
+    else:
+        print(filename + ".sdf:FAILED")
+        print(diff)