#2552 - "Calculate Properties" for macromolecules (#2743)

api/c/indigo/indigo.h

@@ -501,6 +501,9 @@ CEXPORT int indigoCountHydrogens(int item, int* hydro);
 // Applicable to non-query molecules and atoms.
 CEXPORT int indigoCountImplicitHydrogens(int item);
 
+// Calculate macromolecule properties. Return Json string with properties.
+CEXPORT const char* indigoMacroProperties(int object);
+
 // On success, returns always the same pointer to a 3-element array;
 // you should not free() it, but rather memcpy() it if you want to keep it.
 CEXPORT float* indigoXYZ(int atom);

api/c/indigo/src/indigo_misc.cpp

@@ -1699,6 +1699,26 @@ CEXPORT const char* indigoJson(int item)
     INDIGO_END(0);
 }
 
+CEXPORT const char* indigoMacroProperties(int object)
+{
+    INDIGO_BEGIN
+    {
+        auto& tmp = self.getThreadTmpData();
+        ArrayOutput out(tmp.string);
+
+        IndigoObject& obj = self.getObject(object);
+
+        if (IndigoBaseMolecule::is(obj) || IndigoBaseReaction::is(obj) || IndigoKetDocument::is(obj))
+        {
+            auto& doc = obj.getKetDocument();
+            doc.CalculateMacroProps(out, self.json_saving_pretty);
+        }
+        out.writeChar(0);
+        return tmp.string.ptr();
+    }
+    INDIGO_END(0);
+}
+
 CEXPORT const char* indigoGetOriginalFormat(int item)
 {
     INDIGO_BEGIN

api/dotnet/src/IndigoLib.cs

@@ -95,6 +95,9 @@ public unsafe class IndigoLib
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern int indigoClose(int item);
 
+        [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
+        public static extern byte* indigoMacroProperties(int id);
+
         [DllImport("indigo"), SuppressUnmanagedCodeSecurity]
         public static extern byte* indigoGetOriginalFormat(int id);
 

api/dotnet/src/IndigoObject.cs

@@ -138,6 +138,12 @@ public string cml()
             return dispatcher.checkResult(IndigoLib.indigoCml(self));
         }
 
+        public string macroProperties()
+        {
+            dispatcher.setSessionID();
+            return dispatcher.checkResult(IndigoLib.indigoMacroProperties(self));
+        }
+
         public string getOriginalFormat()
         {
             dispatcher.setSessionID();

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

@@ -87,6 +87,8 @@ public interface IndigoLib extends Library {
 
     int indigoRemove(int item);
 
+    Pointer indigoMacroProperties(int item);
+
     Pointer indigoGetOriginalFormat(int item);
 
     int indigoCreateMolecule();

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

@@ -102,6 +102,11 @@ public String helm(IndigoObject library) {
         return Indigo.checkResultString(this, lib.indigoHelm(self, library.self));
     }
 
+    public String macroProperties() {
+        dispatcher.setSessionID();
+        return Indigo.checkResultString(this, lib.indigoMacroProperties(self));
+    }
+
     public String getOriginalFormat() {
         dispatcher.setSessionID();
         return Indigo.checkResultString(this, lib.indigoGetOriginalFormat(self));

api/python/indigo/indigo/indigo_lib.py

@@ -286,6 +286,8 @@ def __init__(self) -> None:
         IndigoLib.lib.indigoIndex.argtypes = [c_int]
         IndigoLib.lib.indigoRemove.restype = c_int
         IndigoLib.lib.indigoRemove.argtypes = [c_int]
+        IndigoLib.lib.indigoMacroProperties.restype = c_char_p
+        IndigoLib.lib.indigoMacroProperties.argtypes = [c_int]
         IndigoLib.lib.indigoGetOriginalFormat.restype = c_char_p
         IndigoLib.lib.indigoGetOriginalFormat.argtypes = [c_int]
         IndigoLib.lib.indigoSaveMolfileToFile.restype = c_int

api/python/indigo/indigo/indigo_object.py

@@ -236,6 +236,17 @@ def remove(self):
 
         return IndigoLib.checkResult(self._lib().indigoRemove(self.id))
 
+    def macroProperties(self):
+        """Method return macro-molecules properties
+
+        Returns:
+            str: json with properties
+        """
+
+        return IndigoLib.checkResultString(
+            self._lib().indigoMacroProperties(self.id)
+        )
+
     def getOriginalFormat(self):
         """Molecule method return format molecule loaded from
 

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

@@ -0,0 +1,4 @@
+*** HELM to KET ***
+props_double_dna.json: SUCCEED
+props_peptides.json: SUCCEED
+props_peptides_micro.json: SUCCEED

api/tests/integration/tests/formats/macromol_props.py

@@ -0,0 +1,56 @@
+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,
+    IndigoException,
+    getIndigoExceptionText,
+    joinPathPy,
+)
+
+indigo = Indigo()
+indigo.setOption("json-saving-pretty", True)
+indigo.setOption("ignore-stereochemistry-errors", True)
+
+print("*** HELM to KET ***")
+
+root = joinPathPy("molecules/", __file__)
+ref = joinPathPy("ref/", __file__)
+
+macro_data = [
+    "props_double_dna",
+    "props_peptides",
+    "props_peptides_micro",
+]
+
+lib = indigo.loadMonomerLibraryFromFile(
+    os.path.join(ref, "monomer_library.ket")
+)
+
+for filename in sorted(macro_data):
+    mol = indigo.loadKetDocumentFromFile(os.path.join(root, filename + ".ket"))
+    try:
+        props = mol.macroProperties()
+    except IndigoException as e:
+        print("Test '%s' filed: %", (filename, getIndigoExceptionText(e)))
+    # with open(os.path.join(ref, filename) + ".json", "w") as file:
+    #     file.write(props)
+    with open(os.path.join(ref, filename) + ".json", "r") as file:
+        props_ref = file.read()
+    diff = find_diff(props_ref, props)
+    if not diff:
+        print(filename + ".json: SUCCEED")
+    else:
+        print(filename + ".json: FAILED")
+        print(diff)